Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-05 23:55 -0400 (Sat, 05 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4807
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4576
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4605
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: 2025-04-05 09:55 -0400 (Sat, 05 Apr 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 -0400 (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 palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --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: 2025-04-05 16:04:43 -0400 (Sat, 05 Apr 2025)
EndedAt: 2025-04-05 16:06:03 -0400 (Sat, 05 Apr 2025)
EllapsedTime: 79.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 [2025-04-05 16:05:58.554][biodb::testContext]
biodb.INFO [2025-04-05 16:05:58.557][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:05:58.558][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-05 16:05:58.559][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:05:58.560][biodb::testContext]
biodb.INFO [2025-04-05 16:05:58.566][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:05:58.568][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-05 16:05:58.576][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:05:58.577][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-05 16:05:58.578][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-05 16:05:58.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.583][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-05 16:05:58.600][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-05 16:05:58.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.605][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-05 16:05:58.606][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-05 16:05:58.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.610][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-05 16:05:58.611][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-05 16:05:58.612][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-05 16:05:58.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.617][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-05 16:05:58.618][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-05 16:05:58.619][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-05 16:05:58.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.623][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-05 16:05:58.624][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-05 16:05:58.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.629][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-05 16:05:58.630][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-05 16:05:58.631][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-05 16:05:58.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.635][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-05 16:05:58.636][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-05 16:05:58.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.640][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-05 16:05:58.642][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-05 16:05:58.643][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-05 16:05:58.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.647][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:05:58.648][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-05 16:05:58.649][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-05 16:05:58.650][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-05 16:05:58.651][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-05 16:05:58.653][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-05 16:05:58.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.657][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-05 16:05:58.658][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-05 16:05:58.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.662][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-05 16:05:58.663][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-05 16:05:58.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.666][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[2025-04-05 16:05:58.668][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-05 16:05:58.669][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-05 16:05:58.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.673][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-05 16:05:58.674][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-05 16:05:58.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.677][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[2025-04-05 16:05:58.678][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-05 16:05:58.679][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-05 16:05:58.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.684][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:05:58.685][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-05 16:05:58.688][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-05 16:05:58.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.692][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-05 16:05:58.693][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-05 16:05:58.694][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-05 16:05:58.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.700][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-05 16:05:58.727][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.747][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-05 16:05:58.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.750][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:05:58.751][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.752][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.753][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.754][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.755][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:05:58.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:05:58.758][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.759][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-05 16:05:58.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:05:58.761][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.763][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:05:58.763][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:05:58.763][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:05:58.763][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:05:58.763][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:05:58.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:05:58.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:05:58.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.771][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.772][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.773][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:05:58.774][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:05:58.775][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.777][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.778][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-05 16:05:58.780][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.781][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:05:58.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:05:58.784][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.785][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.787][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.788][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.789][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:05:58.790][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:05:58.791][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.792][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-05 16:05:58.793][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:05:58.795][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.796][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.797][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:05:58.797][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:05:58.797][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:05:58.797][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:05:58.797][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:05:58.798][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:05:58.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.801][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:05:58.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.806][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:05:58.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:05:58.809][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.810][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.811][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-05 16:05:58.813][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.814][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-05 16:05:58.816][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:05:58.818][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.820][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.822][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:05:58.823][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:05:58.825][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.826][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-05 16:05:58.827][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:05:58.828][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.829][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.830][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.831][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:05:58.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:05:58.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.838][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.839][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.840][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:05:58.841][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:05:58.842][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.843][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.845][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-05 16:05:58.846][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.848][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:05:58.849][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.850][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:05:58.851][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.852][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.853][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.854][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.856][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:05:58.857][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:05:58.858][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.859][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-05 16:05:58.860][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:05:58.861][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.862][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:58.864][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.865][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:05:58.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.868][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:05:58.869][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:58.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:58.871][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:05:58.872][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.873][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:05:58.874][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:05:58.876][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:58.877][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:58.880][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:05:58.881][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.903][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[2025-04-05 16:05:58.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.913][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[2025-04-05 16:05:58.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.929][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[2025-04-05 16:05:58.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.944][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[2025-04-05 16:05:58.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.959][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[2025-04-05 16:05:58.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.969][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[2025-04-05 16:05:58.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:58.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:58.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:58.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:58.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:58.975][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-05 16:05:58.979][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-05 16:05:58.981][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-05 16:05:58.982][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-05 16:05:58.984][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-05 16:05:58.985][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-05 16:05:58.987][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-05 16:05:58.988][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-05 16:05:58.990][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-05 16:05:58.991][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-05 16:05:58.993][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-05 16:05:58.994][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-05 16:05:58.996][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-05 16:05:58.997][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-05 16:05:58.999][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-05 16:05:59.000][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-05 16:05:59.002][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-05 16:05:59.003][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-05 16:05:59.005][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-05 16:05:59.006][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-05 16:05:59.008][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-05 16:05:59.009][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-05 16:05:59.011][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-05 16:05:59.012][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-05 16:05:59.014][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-05 16:05:59.015][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-05 16:05:59.017][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-05 16:05:59.018][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-05 16:05:59.020][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-05 16:05:59.021][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-05 16:05:59.023][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-05 16:05:59.024][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-05 16:05:59.026][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-05 16:05:59.027][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-05 16:05:59.029][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-05 16:05:59.030][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-05 16:05:59.032][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-05 16:05:59.033][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-05 16:05:59.035][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-05 16:05:59.036][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-05 16:05:59.038][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-05 16:05:59.039][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-05 16:05:59.041][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-05 16:05:59.042][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-05 16:05:59.044][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-05 16:05:59.045][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-05 16:05:59.047][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-05 16:05:59.048][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-05 16:05:59.050][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-05 16:05:59.051][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-05 16:05:59.053][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-05 16:05:59.054][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-05 16:05:59.056][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-05 16:05:59.057][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-05 16:05:59.059][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-05 16:05:59.060][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-05 16:05:59.062][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-05 16:05:59.063][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-05 16:05:59.065][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-05 16:05:59.066][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-05 16:05:59.068][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-05 16:05:59.069][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-05 16:05:59.071][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-05 16:05:59.072][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-05 16:05:59.074][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-05 16:05:59.075][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-05 16:05:59.077][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-05 16:05:59.078][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-05 16:05:59.080][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-05 16:05:59.081][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-05 16:05:59.083][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-05 16:05:59.084][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-05 16:05:59.086][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-05 16:05:59.087][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-05 16:05:59.089][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-05 16:05:59.090][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-05 16:05:59.092][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-05 16:05:59.093][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-05 16:05:59.095][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-05 16:05:59.096][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-05 16:05:59.098][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-05 16:05:59.099][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-05 16:05:59.101][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-05 16:05:59.123][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-05 16:05:59.125][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:05:59.128][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:05:59.129][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:05:59.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:05:59.289][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-05 16:05:59.298][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-05 16:05:59.300][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:59.301][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-05 16:05:59.302][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:59.303][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:05:59.305][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:59.306][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-05 16:05:59.307][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:59.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:05:59.309][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-05 16:05:59.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:05:59.312][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:59.313][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-05 16:05:59.314][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-05 16:05:59.315][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-05 16:05:59.316][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-05 16:05:59.317][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:59.318][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-05 16:05:59.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:59.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:59.322][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:05:59.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:05:59.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:05:59.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:05:59.326][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-05 16:05:59.326][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-05 16:05:59.326][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-05 16:05:59.326][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-05 16:05:59.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:05:59.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:05:59.329][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-05 16:05:59.331][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:05:59.336][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-05 16:05:59.356][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-05 16:05:59.358][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-05 16:05:59.361][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-05 16:05:59.365][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-05 16:05:59.369][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:05:59.370][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:05:59.371][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-05 16:05:59.373][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-05 16:05:59.374][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-05 16:05:59.375][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-05 16:05:59.385][biodb::testThat]
biodb.INFO [2025-04-05 16:05:59.386][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-05 16:05:59.387][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:05:59.388][biodb::testThat]
biodb.TRACE[2025-04-05 16:05:59.393][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-04-05 16:05:59.395][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-05 16:05:59.406][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-05 16:05:59.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:05:59.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:05:59.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:05:59.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:05:59.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:05:59.434][FUN] Functions in observer BiodbConfig: [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[2025-04-05 16:05:59.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.472][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.531][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.536][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:05:59.612][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-04-05 16:05:59.615][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:05:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:05:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:05:59.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:05:59.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:05:59.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:05:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:05:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:05:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.670][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.709][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.714][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.719][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:05:59.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.751][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.752][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.754][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.778][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.783][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.784][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.785][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.786][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.815][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.817][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.818][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.819][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.838][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.848][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.849][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.851][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.880][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.881][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.883][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.898][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:05:59.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:05:59.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.902][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.908][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:05:59.914][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:05:59.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.916][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.922][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:05:59.924][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:05:59.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.926][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.932][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.933][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:05:59.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.936][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.942][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.943][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:05:59.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:05:59.945][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:05:59.963][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-04-05 16:05:59.991][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-05 16:05:59.993][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-05 16:05:59.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:05:59.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:05:59.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:00.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:00.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:00.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:00.006][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.TRACE[2025-04-05 16:06:00.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.039][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.126][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.131][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.140][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:06:00.172][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-04-05 16:06:00.190][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:06:00.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:06:00.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.195][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:06:00.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:06:00.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:06:00.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:06:00.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:06:00.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:06:00.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.224][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.264][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.269][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.273][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.308][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.312][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.327][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.332][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.336][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.341][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.342][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.344][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.345][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.378][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.379][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.381][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.396][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.401][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.410][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.412][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.414][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.415][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.443][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.444][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.446][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.475][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.476][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.478][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.503][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.507][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.509][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.511][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.526][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.527][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.529][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.535][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.537][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.538][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.539][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.545][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.546][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.547][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.548][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.559][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.561][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.562][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.568][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.570][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.572][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.578][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.579][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.580][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.581][ef$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.587][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.589][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.591][ef$get] fields variable is a list.
biodb.INFO [2025-04-05 16:06:00.602][biodb::testThat]
biodb.INFO [2025-04-05 16:06:00.604][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-05 16:06:00.605][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:00.606][biodb::testThat]
biodb.DEBUG[2025-04-05 16:06:00.608][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-04-05 16:06:00.614][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-04-05 16:06:00.621][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-04-05 16:06:00.622][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-04-05 16:06:00.625][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-04-05 16:06:00.626][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-05 16:06:00.655][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-04-05 16:06:00.657][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-05 16:06:00.659][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-04-05 16:06:00.661][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-04-05 16:06:00.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:06:00.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:00.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:00.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:00.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:00.674][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:00.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-05 16:06:00.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.697][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.726][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.736][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.740][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.750][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:06:00.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-05 16:06:00.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:00.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:00.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:00.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:00.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:00.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-05 16:06:00.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.805][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.810][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-05 16:06:00.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-05 16:06:00.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-05 16:06:00.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-05 16:06:00.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.844][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.862][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-05 16:06:00.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-05 16:06:00.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-05 16:06:00.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-05 16:06:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-05 16:06:00.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.887][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.892][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.901][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-05 16:06:00.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-05 16:06:00.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-05 16:06:00.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-05 16:06:00.951][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-04-05 16:06:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-05 16:06:00.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-05 16:06:00.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:06:00.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:06:00.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:06:00.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:06:00.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-05 16:06:00.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-05 16:06:00.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:06:00.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-05 16:06:00.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:00.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:06:00.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-05 16:06:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:00.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-05 16:06:00.997][biodb::testThat]
biodb.INFO [2025-04-05 16:06:00.998][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-05 16:06:00.999][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.000][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.008][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.009][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-05 16:06:01.010][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.012][biodb::testThat]
biodb.WARN [2025-04-05 16:06:01.028][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-05 16:06:01.045][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-05 16:06:01.056][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.058][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-05 16:06:01.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.060][biodb::testThat]
biodb.TRACE[2025-04-05 16:06:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.094][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:06:01.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:06:01.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.103][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:06:01.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:06:01.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.134][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.139][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-05 16:06:01.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.144][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-05 16:06:01.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-05 16:06:01.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-05 16:06:01.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-05 16:06:01.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-05 16:06:01.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-05 16:06:01.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-05 16:06:01.160][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.161][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-05 16:06:01.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.163][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.173][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.174][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-05 16:06:01.176][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.177][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.186][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.187][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-05 16:06:01.188][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.190][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.198][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.199][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-05 16:06:01.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-05 16:06:01.201][biodb::testThat]
biodb.INFO [2025-04-05 16:06:01.209][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-05 16:06:01.211][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-05 16:06:01.212][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-05 16:06:01.213][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-05 16:06:01.214][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.216][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.218][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.219][FUN] Functions in observer BiodbConfig: [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 [2025-04-05 16:06:01.229][biodb::testContext]
biodb.INFO [2025-04-05 16:06:01.231][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:06:01.236][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-04-05 16:06:01.237][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-05 16:06:01.239][biodb::testContext]
biodb.INFO [2025-04-05 16:06:01.241][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:06:01.243][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-05 16:06:01.248][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:06:01.249][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-05 16:06:01.251][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-05 16:06:01.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.255][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-05 16:06:01.256][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-05 16:06:01.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.260][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-05 16:06:01.261][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-05 16:06:01.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.266][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-05 16:06:01.267][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-05 16:06:01.268][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-05 16:06:01.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.272][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-05 16:06:01.273][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-05 16:06:01.275][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-05 16:06:01.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.279][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-05 16:06:01.280][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-05 16:06:01.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.284][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-05 16:06:01.285][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-05 16:06:01.286][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-05 16:06:01.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.291][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-05 16:06:01.292][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-05 16:06:01.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.296][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-05 16:06:01.297][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-05 16:06:01.298][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-05 16:06:01.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.303][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:06:01.304][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-05 16:06:01.305][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-05 16:06:01.306][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-05 16:06:01.307][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-05 16:06:01.308][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-05 16:06:01.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.312][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-05 16:06:01.314][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-05 16:06:01.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.318][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-05 16:06:01.319][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-05 16:06:01.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.323][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-05 16:06:01.324][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-05 16:06:01.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.329][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-05 16:06:01.330][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-05 16:06:01.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.334][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-05 16:06:01.335][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-05 16:06:01.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.339][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-05 16:06:01.341][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-05 16:06:01.344][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-05 16:06:01.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.348][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-05 16:06:01.349][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-05 16:06:01.350][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-05 16:06:01.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.355][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-05 16:06:01.356][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.358][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-05 16:06:01.359][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.360][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:06:01.361][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.362][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.363][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.366][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:06:01.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:06:01.368][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.369][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-05 16:06:01.370][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:06:01.372][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.373][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.374][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:06:01.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:06:01.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:06:01.374][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:06:01.374][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:06:01.375][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:06:01.376][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.377][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.378][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:06:01.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.382][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.383][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:06:01.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:06:01.386][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.387][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.389][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-05 16:06:01.391][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.392][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:06:01.393][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:06:01.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.401][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.404][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:06:01.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:06:01.407][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.408][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-05 16:06:01.409][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:06:01.410][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.411][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.413][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-05 16:06:01.413][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-05 16:06:01.413][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-05 16:06:01.413][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-05 16:06:01.413][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-05 16:06:01.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:06:01.415][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.417][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:06:01.418][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.420][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.422][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:06:01.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:06:01.425][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.426][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.427][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-05 16:06:01.429][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.430][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-05 16:06:01.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:06:01.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.435][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.436][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.437][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.438][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-05 16:06:01.440][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:06:01.441][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.442][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-05 16:06:01.443][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:06:01.444][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.445][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.446][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.448][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:06:01.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.451][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:06:01.452][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.454][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.455][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.457][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:06:01.458][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:06:01.459][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.460][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.461][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-05 16:06:01.463][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.464][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-05 16:06:01.465][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.466][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:06:01.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.470][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.471][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.472][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-05 16:06:01.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:06:01.475][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.476][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-05 16:06:01.477][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:06:01.478][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.479][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.480][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.481][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-05 16:06:01.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:06:01.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.489][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.490][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:06:01.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:06:01.493][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.494][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.495][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:06:01.496][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.592][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-05 16:06:01.595][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-05 16:06:01.597][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-05 16:06:01.598][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-05 16:06:01.600][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-05 16:06:01.601][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-05 16:06:01.603][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-05 16:06:01.604][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-05 16:06:01.606][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-05 16:06:01.607][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-05 16:06:01.609][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-05 16:06:01.610][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-05 16:06:01.612][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-05 16:06:01.613][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-05 16:06:01.615][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-05 16:06:01.616][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-05 16:06:01.618][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-05 16:06:01.619][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-05 16:06:01.621][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-05 16:06:01.623][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-05 16:06:01.624][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-05 16:06:01.626][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-05 16:06:01.627][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-05 16:06:01.629][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-05 16:06:01.630][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-05 16:06:01.632][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-05 16:06:01.633][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-05 16:06:01.635][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-05 16:06:01.636][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-05 16:06:01.638][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-05 16:06:01.639][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-05 16:06:01.641][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-05 16:06:01.642][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-05 16:06:01.644][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-05 16:06:01.645][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-05 16:06:01.647][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-05 16:06:01.648][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-05 16:06:01.650][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-05 16:06:01.651][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-05 16:06:01.653][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-05 16:06:01.654][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-05 16:06:01.656][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-05 16:06:01.658][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-05 16:06:01.659][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-05 16:06:01.661][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-05 16:06:01.662][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-05 16:06:01.664][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-05 16:06:01.665][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-05 16:06:01.667][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-05 16:06:01.668][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-05 16:06:01.670][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-05 16:06:01.671][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-05 16:06:01.673][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-05 16:06:01.674][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-05 16:06:01.676][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-05 16:06:01.677][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-05 16:06:01.679][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-05 16:06:01.680][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-05 16:06:01.682][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-05 16:06:01.683][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-05 16:06:01.685][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-05 16:06:01.686][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-05 16:06:01.688][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-05 16:06:01.689][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-05 16:06:01.691][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-05 16:06:01.692][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-05 16:06:01.694][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-05 16:06:01.695][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-05 16:06:01.697][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-05 16:06:01.698][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-05 16:06:01.700][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-05 16:06:01.702][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-05 16:06:01.708][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-05 16:06:01.710][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-05 16:06:01.711][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-05 16:06:01.713][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-05 16:06:01.714][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-05 16:06:01.716][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-05 16:06:01.717][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-05 16:06:01.719][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-05 16:06:01.720][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-05 16:06:01.722][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-05 16:06:01.723][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-05 16:06:01.725][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-05 16:06:01.727][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-04-05 16:06:01.728][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-05 16:06:01.729][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.732][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.790][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[2025-04-05 16:06:01.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.804][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[2025-04-05 16:06:01.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-05 16:06:01.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-05 16:06:01.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.854][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[2025-04-05 16:06:01.857][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-05 16:06:01.863][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-05 16:06:01.865][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.866][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-05 16:06:01.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-05 16:06:01.870][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.871][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-05 16:06:01.872][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.874][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-05 16:06:01.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-05 16:06:01.877][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.878][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-05 16:06:01.879][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-05 16:06:01.880][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-05 16:06:01.881][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-05 16:06:01.882][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.884][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-05 16:06:01.885][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.886][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.887][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-05 16:06:01.888][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-05 16:06:01.889][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-05 16:06:01.890][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-05 16:06:01.891][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-05 16:06:01.891][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-05 16:06:01.891][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-05 16:06:01.891][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-05 16:06:01.893][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-05 16:06:01.894][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-05 16:06:01.895][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-05 16:06:01.896][self$setPropertyValue]
biodb.DEBUG[2025-04-05 16:06:01.897][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-05 16:06:01.900][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-05 16:06:01.902][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-05 16:06:01.903][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-05 16:06:01.905][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-05 16:06:01.906][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:06:01.907][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-05 16:06:01.909][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-05 16:06:01.910][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-05 16:06:01.912][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-05 16:06:01.913][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-05 16:06:01.914][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-05 16:06:01.915][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-05 16:06:01.916][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-05 16:06:01.917][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-05 16:06:01.918][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-05 16:06:01.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-05 16:06:01.920][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-05 16:06:01.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-05 16:06:01.922][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-05 16:06:01.923][FUN] Functions in observer 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 
   4.75    0.37    5.10

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --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 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'biodbNci' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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
  'E:/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: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbNci.dll tmp.def RcppExports.o extractEntries.o test-100-example.o test-runner.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)