Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-26 23:55 -0400 (Sat, 26 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4832
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4574
merida1macOS 12.7.5 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 9/30HostnameOS / ArchCHECK
biodbNci 1.12.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-26 09:55 -0400 (Sat, 26 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_21
git_last_commit: a398ae4
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

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

raw results


Summary

Package: biodbNci
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz
StartedAt: 2025-04-26 16:01:22 -0400 (Sat, 26 Apr 2025)
EndedAt: 2025-04-26 16:34:39 -0400 (Sat, 26 Apr 2025)
EllapsedTime: 1996.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-04-26 16:02:40.624][biodb::testContext]
biodb.INFO [2025-04-26 16:02:40.628][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:02:40.629][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-26 16:02:40.630][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:02:40.631][biodb::testContext]
biodb.INFO [2025-04-26 16:02:40.638][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:02:40.640][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:02:40.648][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:02:40.649][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:02:40.651][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:02:40.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.655][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:02:40.680][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:02:40.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.685][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:02:40.686][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:02:40.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.691][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:02:40.692][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:02:40.693][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:02:40.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.698][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:02:40.699][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:02:40.700][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:02:40.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.705][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:02:40.706][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:02:40.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.710][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:02:40.712][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:02:40.713][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:02:40.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.717][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:02:40.719][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:02:40.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.723][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:02:40.724][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:02:40.726][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:02:40.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.730][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:02:40.731][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:02:40.733][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:02:40.734][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:02:40.735][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:02:40.736][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:02:40.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.740][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[2025-04-26 16:02:40.741][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:02:40.742][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:02:40.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.747][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:02:40.748][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:02:40.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.753][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:02:40.754][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:02:40.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.759][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:02:40.760][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:02:40.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.764][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:02:40.766][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:02:40.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.770][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:02:40.772][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:02:40.783][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:02:40.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.788][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:02:40.789][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:02:40.790][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:02:40.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:40.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:40.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:40.797][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:02:40.842][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.870][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-26 16:02:40.871][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.873][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:40.874][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.875][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.876][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.877][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.879][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:02:40.880][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:40.881][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.882][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:02:40.884][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:40.885][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.886][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.887][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:02:40.887][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:02:40.887][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:02:40.887][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:02:40.887][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:02:40.889][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:40.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.892][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:40.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.894][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.895][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.897][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.898][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:40.899][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:40.900][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.901][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.903][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:02:40.905][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.907][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:02:40.908][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.909][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:40.910][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.911][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.913][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.914][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.915][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:02:40.916][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:40.918][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.919][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:02:40.920][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:40.921][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.922][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.924][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:02:40.924][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:02:40.924][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:02:40.924][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:02:40.924][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:02:40.925][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:40.926][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.927][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.928][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:40.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.932][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.933][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.934][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:40.935][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:40.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.937][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.939][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:02:40.941][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.942][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-26 16:02:40.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:40.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.951][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:02:40.952][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:40.953][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.954][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:02:40.956][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:40.957][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.958][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.959][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.960][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:40.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:40.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.968][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:40.971][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:40.972][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.973][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.975][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:02:40.977][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.978][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:02:40.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:40.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.983][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.984][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.985][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:40.986][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:02:40.988][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:40.989][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:40.990][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:02:40.991][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:40.992][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.994][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:40.995][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:40.996][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:40.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:40.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:40.999][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:41.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:41.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:41.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:41.004][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:41.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:41.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:41.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:41.009][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:41.013][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:02:41.014][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.111][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:02:41.116][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:02:41.118][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:02:41.119][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:02:41.121][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:02:41.123][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:02:41.124][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:02:41.126][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:02:41.128][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:02:41.129][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:02:41.131][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:02:41.133][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:02:41.134][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:02:41.136][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:02:41.138][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:02:41.139][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:02:41.141][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:02:41.142][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:02:41.144][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:02:41.146][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:02:41.147][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:02:41.149][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:02:41.151][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:02:41.152][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:02:41.154][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:02:41.156][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:02:41.158][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:02:41.160][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:02:41.161][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:02:41.163][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:02:41.165][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:02:41.166][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:02:41.168][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:02:41.170][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:02:41.171][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:02:41.173][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:02:41.175][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:02:41.176][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:02:41.178][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:02:41.180][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:02:41.182][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:02:41.183][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:02:41.185][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:02:41.187][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:02:41.188][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:02:41.190][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:02:41.192][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:02:41.193][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:02:41.195][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:02:41.197][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:02:41.198][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:02:41.200][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:02:41.202][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:02:41.203][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:02:41.205][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:02:41.207][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:02:41.208][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:02:41.210][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:02:41.212][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:02:41.213][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:02:41.215][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:02:41.217][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:02:41.218][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:02:41.220][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:02:41.222][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:02:41.223][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:02:41.225][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:02:41.227][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:02:41.229][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:02:41.230][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:02:41.232][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:02:41.234][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:02:41.235][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:02:41.237][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:02:41.239][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:02:41.240][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:02:41.242][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:02:41.244][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:02:41.245][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:02:41.247][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:02:41.249][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:02:41.250][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:02:41.252][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:02:41.259][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:02:41.261][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:02:41.264][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:02:41.265][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.268][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.301][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[2025-04-26 16:02:41.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:41.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:41.418][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-26 16:02:41.432][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-26 16:02:41.435][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:41.436][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-26 16:02:41.437][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:41.438][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:41.440][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:41.441][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-26 16:02:41.442][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:41.443][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:41.445][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-26 16:02:41.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:41.447][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:41.448][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-26 16:02:41.449][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-26 16:02:41.451][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-26 16:02:41.452][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:41.453][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:41.455][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:02:41.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:41.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:41.458][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:41.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:41.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:41.461][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:41.463][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:02:41.463][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:02:41.463][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-26 16:02:41.463][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-26 16:02:41.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:41.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:41.466][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:41.467][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:41.475][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-26 16:02:41.497][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-26 16:02:41.499][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-26 16:02:41.503][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-26 16:02:41.507][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-26 16:02:41.512][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:02:41.513][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:02:41.515][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:02:41.516][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:02:41.518][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:02:41.519][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-26 16:02:41.560][biodb::testThat]
biodb.INFO [2025-04-26 16:02:41.561][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:02:41.562][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:02:41.564][biodb::testThat]
biodb.TRACE[2025-04-26 16:02:41.568][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-04-26 16:02:41.570][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:02:41.573][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:02:41.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:02:41.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:41.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:41.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:41.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:41.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:41.602][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:02:41.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:41.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:41.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:41.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:41.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:41.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:41.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:41.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:41.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:41.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:41.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:41.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:41.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:41.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:41.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.733][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.738][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.748][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:02:41.835][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-04-26 16:02:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:41.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:41.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:41.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:41.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.848][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:41.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:41.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.853][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:41.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:41.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.896][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.938][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.942][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.947][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:41.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.980][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.981][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.983][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:41.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:41.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:41.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:41.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.000][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.005][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.010][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.015][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.016][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.049][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.050][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.052][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.083][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.084][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.086][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.117][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.118][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.121][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.137][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.138][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.145][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.151][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.152][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.155][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.161][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.162][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.170][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.172][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.173][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.174][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.180][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.182][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.183][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.184][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.207][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-04-26 16:02:42.255][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:02:42.256][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:02:42.258][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:02:42.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:42.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:42.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:42.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:42.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:42.271][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.TRACE[2025-04-26 16:02:42.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.325][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.330][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.357][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.418][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.423][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.433][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:02:42.469][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-04-26 16:02:42.497][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:42.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:42.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:42.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:42.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.511][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:42.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:42.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.516][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:42.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:42.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.532][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.574][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.579][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.584][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:42.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.626][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.627][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.629][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.656][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.661][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.662][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.665][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.666][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.700][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.701][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.703][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.729][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.734][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.735][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.737][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.759][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.769][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.770][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.772][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.803][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.805][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.807][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.808][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.823][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.838][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.840][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.841][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.842][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.843][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.858][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:42.860][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:42.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.862][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.869][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.870][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:42.871][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.873][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.884][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:42.885][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:42.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.887][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.894][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:42.895][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:42.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.897][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.904][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.905][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:42.906][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.908][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.914][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.916][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:42.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.918][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:42.924][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:42.926][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:42.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:42.928][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:02:42.939][biodb::testThat]
biodb.INFO [2025-04-26 16:02:42.940][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:02:42.941][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:02:42.942][biodb::testThat]
biodb.DEBUG[2025-04-26 16:02:42.945][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-04-26 16:02:42.952][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-04-26 16:02:42.957][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-04-26 16:02:42.958][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-04-26 16:02:42.959][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-04-26 16:02:42.961][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2025-04-26 16:02:45.626][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactusc9e31f0d061dgz".
biodb.TRACE[2025-04-26 16:02:45.628][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:02:45.629][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:02:45.631][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:02:45.632][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-04-26 16:02:45.635][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerc9e3100c69d8marker".
biodb.TRACE[2025-04-26 16:02:45.636][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-04-26 16:02:45.638][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:02:45.639][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-04-26 16:02:45.641][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-04-26 16:02:45.642][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-04-26 16:02:45.644][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:04:01.320][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-04-26 16:04:01.323][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-04-26 16:32:00.528][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-04-26 16:32:00.953][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-04-26 16:34:32.338][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:34:32.342][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-04-26 16:34:36.433][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerc9e31ef8ec23marker".
biodb.TRACE[2025-04-26 16:34:36.434][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-04-26 16:34:36.436][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-04-26 16:34:36.438][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-04-26 16:34:36.439][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-26 16:34:36.443][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-04-26 16:34:36.444][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:34:36.446][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-04-26 16:34:36.447][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:34:36.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:34:36.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:36.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:36.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:36.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:36.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:36.463][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:34:36.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:34:36.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:34:36.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:34:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:34:36.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:34:36.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:34:36.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:34:36.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:34:36.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.628][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.635][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:34:36.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:34:36.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:36.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:36.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:36.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:36.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:36.686][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:34:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.725][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:34:36.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:34:36.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.737][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:34:36.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:34:36.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:34:36.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:34:36.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:34:36.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:34:36.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:34:36.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:34:36.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:34:36.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:34:36.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:34:36.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:34:36.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:34:36.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:34:36.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.880][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.890][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:34:36.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:34:36.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:34:36.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:34:36.947][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-04-26 16:34:36.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:34:36.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:34:36.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:34:36.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:34:36.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:34:36.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:34:36.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:34:36.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:34:36.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:34:36.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:34:36.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:36.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:34:36.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:34:36.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:36.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:34:36.994][biodb::testThat]
biodb.INFO [2025-04-26 16:34:36.995][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:34:36.996][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:36.998][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.006][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.007][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:34:37.009][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:37.010][biodb::testThat]
biodb.WARN [2025-04-26 16:34:37.037][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-26 16:34:37.064][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-26 16:34:37.075][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.077][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:34:37.078][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:37.079][biodb::testThat]
biodb.TRACE[2025-04-26 16:34:37.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.123][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.128][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:34:37.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:34:37.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.133][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:34:37.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:34:37.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.192][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.198][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:34:37.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:34:37.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:34:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:34:37.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:34:37.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:34:37.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:34:37.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:34:37.223][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.224][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:34:37.226][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:37.227][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.240][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.242][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:34:37.243][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:37.245][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.257][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.259][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:34:37.261][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:37.262][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.273][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.275][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:34:37.276][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:34:37.278][biodb::testThat]
biodb.INFO [2025-04-26 16:34:37.288][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:34:37.290][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-26 16:34:37.292][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-26 16:34:37.293][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:34:37.295][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.298][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.301][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-26 16:34:37.319][biodb::testContext]
biodb.INFO [2025-04-26 16:34:37.320][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:34:37.322][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-04-26 16:34:37.323][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:34:37.325][biodb::testContext]
biodb.INFO [2025-04-26 16:34:37.339][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:34:37.350][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:34:37.357][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:34:37.359][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:34:37.360][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:34:37.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.366][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:34:37.367][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:34:37.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.373][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:34:37.375][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:34:37.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.380][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:34:37.381][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:34:37.383][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:34:37.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.388][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:34:37.389][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:34:37.391][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:34:37.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.396][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:34:37.397][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:34:37.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.402][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:34:37.404][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:34:37.405][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:34:37.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.411][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:34:37.412][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:34:37.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.417][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:34:37.419][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:34:37.420][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:34:37.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.425][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:34:37.426][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:34:37.427][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:34:37.429][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:34:37.430][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:34:37.431][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:34:37.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.436][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:34:37.437][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:34:37.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.442][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:34:37.443][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:34:37.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.448][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:34:37.449][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:34:37.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.454][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:34:37.455][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:34:37.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.461][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:34:37.462][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:34:37.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.467][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:34:37.468][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:34:37.507][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:34:37.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.512][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:34:37.514][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:34:37.515][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:34:37.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.518][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[2025-04-26 16:34:37.520][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:34:37.522][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.523][self$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[2025-04-26 16:34:37.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:34:37.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.530][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.532][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:34:37.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:34:37.535][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.536][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:34:37.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:34:37.539][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.540][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.541][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:34:37.541][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:34:37.541][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:34:37.541][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:34:37.541][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:34:37.543][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:34:37.544][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:34:37.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.550][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.551][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.552][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:34:37.553][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:34:37.555][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.556][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.557][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:34:37.560][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.561][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:34:37.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.564][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:34:37.565][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.566][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.568][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.569][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.570][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:34:37.571][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:34:37.573][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.574][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:34:37.575][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:34:37.577][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.581][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:34:37.581][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:34:37.581][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:34:37.581][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:34:37.581][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:34:37.583][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:34:37.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.587][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:34:37.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.591][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.592][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.593][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:34:37.594][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:34:37.595][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.597][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.598][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:34:37.601][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.602][self$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[2025-04-26 16:34:37.603][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:34:37.606][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.607][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.609][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.610][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.611][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:34:37.613][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:34:37.614][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.616][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:34:37.617][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:34:37.618][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.620][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.621][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.622][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:34:37.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.626][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:34:37.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.629][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.631][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:34:37.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:34:37.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.635][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.637][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:34:37.639][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.640][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:34:37.642][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.643][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:34:37.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.645][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.647][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.649][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:34:37.650][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:34:37.652][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.653][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:34:37.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:34:37.655][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.657][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:37.658][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.659][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:34:37.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.663][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:34:37.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:37.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:37.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:34:37.668][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:34:37.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:34:37.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:37.673][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:37.674][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:34:37.675][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.768][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[2025-04-26 16:34:37.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.785][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:34:37.787][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:34:37.789][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:34:37.791][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:34:37.792][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:34:37.794][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:34:37.796][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:34:37.798][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:34:37.799][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:34:37.801][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:34:37.803][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:34:37.805][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:34:37.806][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:34:37.808][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:34:37.810][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:34:37.812][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:34:37.813][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:34:37.815][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:34:37.817][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:34:37.818][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:34:37.820][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:34:37.822][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:34:37.824][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:34:37.826][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:34:37.827][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:34:37.829][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:34:37.831][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:34:37.833][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:34:37.834][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:34:37.836][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:34:37.838][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:34:37.840][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:34:37.841][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:34:37.843][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:34:37.845][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:34:37.846][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:34:37.848][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:34:37.850][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:34:37.852][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:34:37.853][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:34:37.855][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:34:37.857][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:34:37.859][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:34:37.860][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:34:37.862][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:34:37.864][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:34:37.866][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:34:37.867][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:34:37.869][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:34:37.871][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:34:37.873][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:34:37.874][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:34:37.876][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:34:37.878][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:34:37.880][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:34:37.881][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:34:37.883][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:34:37.885][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:34:37.887][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:34:37.888][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:34:37.890][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:34:37.892][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:34:37.894][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:34:37.895][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:34:37.897][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:34:37.899][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:34:37.901][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:34:37.902][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:34:37.904][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:34:37.906][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:34:37.907][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:34:37.909][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:34:37.911][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:34:37.913][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:34:37.914][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:34:37.916][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:34:37.918][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:34:37.920][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:34:37.921][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:34:37.923][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:34:37.925][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:34:37.927][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:34:37.928][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:34:37.930][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:34:37.932][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-26 16:34:37.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:34:37.935][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.937][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.969][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[2025-04-26 16:34:37.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:37.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:37.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:37.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:37.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:37.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:37.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:37.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:34:38.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:34:38.077][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-26 16:34:38.079][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-26 16:34:38.082][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:38.083][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-26 16:34:38.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:38.085][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:34:38.087][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:38.088][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-26 16:34:38.089][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:38.090][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:34:38.092][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-26 16:34:38.093][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:34:38.094][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:38.096][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-26 16:34:38.097][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-26 16:34:38.098][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-26 16:34:38.100][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:34:38.101][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:38.102][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:34:38.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:38.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:38.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:34:38.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:34:38.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:34:38.110][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:34:38.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:34:38.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:34:38.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-26 16:34:38.112][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-26 16:34:38.113][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:34:38.114][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:34:38.115][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:34:38.117][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:34:38.119][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-26 16:34:38.123][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-26 16:34:38.124][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-26 16:34:38.126][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-26 16:34:38.128][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-26 16:34:38.130][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:34:38.131][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:34:38.133][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:34:38.134][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:34:38.136][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:34:38.137][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-26 16:34:38.139][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:34:38.140][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-26 16:34:38.142][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-26 16:34:38.143][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:34:38.144][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:34:38.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:34:38.146][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:34:38.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:34:38.149][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:34:38.150][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
    user   system  elapsed 
1226.224  259.712 1919.799

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

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

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.12.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)