Back to Long Tests report for BioC 3.22

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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4722
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4494
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4523
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 1.13.0  (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: devel
git_last_commit: 536802f
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo2

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: 1.13.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.0.tar.gz
StartedAt: 2025-04-26 16:04:36 -0400 (Sat, 26 Apr 2025)
EndedAt: 2025-04-26 16:15:42 -0400 (Sat, 26 Apr 2025)
EllapsedTime: 666.3 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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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 16:05:33.358][biodb::testContext]
biodb.INFO [2025-04-26 16:05:33.360][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:05:33.361][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-26 16:05:33.362][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:05:33.363][biodb::testContext]
biodb.INFO [2025-04-26 16:05:33.368][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:05:33.370][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:05:33.377][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:05:33.378][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:05:33.379][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:05:33.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.382][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:05:33.399][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:05:33.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.401][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 16:05:33.402][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:05:33.403][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:05:33.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.406][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:05:33.407][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:05:33.408][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:05:33.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.412][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:05:33.413][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:05:33.414][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:05:33.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.417][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:05:33.418][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:05:33.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.421][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:05:33.422][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:05:33.423][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:05:33.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.426][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:05:33.427][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:05:33.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.431][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:05:33.431][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:05:33.432][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:05:33.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.436][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:05:33.437][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:05:33.438][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:05:33.439][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:05:33.439][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:05:33.440][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:05:33.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.444][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:05:33.445][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:05:33.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.448][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:05:33.449][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:05:33.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.452][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:05:33.453][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:05:33.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.457][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:05:33.458][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:05:33.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.461][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:05:33.462][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:05:33.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.465][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:05:33.466][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:05:33.469][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:05:33.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.473][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:05:33.474][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:05:33.474][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:05:33.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.480][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:05:33.511][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.531][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-26 16:05:33.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.533][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:05:33.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.534][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.535][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.536][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.537][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:05:33.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:05:33.539][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.540][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:05:33.541][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:05:33.542][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.543][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.544][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:05:33.544][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:05:33.544][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:05:33.544][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:05:33.544][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:05:33.544][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:05:33.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.547][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:05:33.548][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.550][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.551][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.551][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:05:33.552][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:05:33.553][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.554][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.555][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:05:33.557][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.558][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:05:33.559][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.560][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:05:33.560][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.561][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.562][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.563][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.564][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:05:33.565][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:05:33.566][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.567][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:05:33.568][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:05:33.569][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.570][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.570][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:05:33.570][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:05:33.570][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:05:33.570][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:05:33.570][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:05:33.571][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:05:33.572][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.574][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:05:33.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.577][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.578][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:05:33.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:05:33.580][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.581][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.582][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:05:33.584][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.585][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-26 16:05:33.586][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:05:33.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.591][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:05:33.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:05:33.593][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.594][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:05:33.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:05:33.596][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.597][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.598][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.599][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:05:33.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:05:33.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.605][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:05:33.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:05:33.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.609][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.610][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:05:33.611][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.612][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:05:33.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:05:33.615][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.616][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.617][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.619][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:05:33.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:05:33.621][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.621][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:05:33.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:05:33.623][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.625][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.626][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:05:33.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.629][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:05:33.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:33.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:33.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.632][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.633][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:05:33.634][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:05:33.635][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.635][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:33.639][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:05:33.640][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.643][FUN] 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 16:05:33.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.647][FUN] 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 16:05:33.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.651][FUN] 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 16:05:33.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.655][FUN] 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 16:05:33.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.660][FUN] 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 16:05:33.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.664][FUN] 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 16:05:33.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.668][FUN] 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 16:05:33.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.680][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 16:05:33.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.684][FUN] 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 16:05:33.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.686][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.DEBUG[2025-04-26 16:05:33.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.692][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 16:05:33.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.700][FUN] 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 16:05:33.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.704][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 16:05:33.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.708][FUN] 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 16:05:33.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.709][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 16:05:33.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.712][FUN] 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 16:05:33.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.714][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:05:33.719][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:05:33.720][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:05:33.721][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:05:33.723][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:05:33.724][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:05:33.725][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:05:33.726][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:05:33.728][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:05:33.729][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:05:33.730][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:05:33.732][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:05:33.733][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:05:33.734][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:05:33.735][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:05:33.737][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:05:33.738][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:05:33.739][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:05:33.741][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:05:33.742][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:05:33.743][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:05:33.744][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:05:33.746][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:05:33.747][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:05:33.748][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:05:33.750][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:05:33.751][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:05:33.752][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:05:33.753][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:05:33.762][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:05:33.764][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:05:33.765][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:05:33.767][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:05:33.768][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:05:33.770][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:05:33.771][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:05:33.773][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:05:33.774][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:05:33.776][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:05:33.777][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:05:33.779][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:05:33.780][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:05:33.782][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:05:33.783][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:05:33.784][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:05:33.786][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:05:33.787][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:05:33.789][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:05:33.790][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:05:33.792][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:05:33.793][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:05:33.795][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:05:33.796][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:05:33.798][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:05:33.799][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:05:33.800][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:05:33.802][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:05:33.803][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:05:33.805][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:05:33.806][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:05:33.808][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:05:33.809][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:05:33.811][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:05:33.812][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:05:33.814][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:05:33.815][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:05:33.817][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:05:33.818][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:05:33.820][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:05:33.821][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:05:33.822][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:05:33.824][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:05:33.825][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:05:33.827][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:05:33.828][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:05:33.830][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:05:33.831][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:05:33.832][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:05:33.834][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:05:33.835][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:05:33.837][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:05:33.838][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:05:33.840][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:05:33.847][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:05:33.849][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:05:33.852][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:05:33.853][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.854][FUN] 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 16:05:33.855][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.865][FUN] 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 16:05:33.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.871][FUN] 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 16:05:33.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.897][FUN] 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 16:05:33.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.903][FUN] 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 16:05:33.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.909][FUN] 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 16:05:33.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.922][FUN] 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 16:05:33.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.953][FUN] 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 16:05:33.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.954][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 16:05:33.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.959][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 16:05:33.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:05:33.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:05:33.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.970][FUN] 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 16:05:33.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:33.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:05:33.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:33.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:33.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:33.976][FUN] 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 16:05:33.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:33.977][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 16:05:33.979][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-26 16:05:33.988][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-26 16:05:33.990][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.991][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-26 16:05:33.992][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.993][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:05:33.994][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:33.995][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-26 16:05:33.995][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:33.996][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:05:33.997][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-26 16:05:33.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:05:33.999][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:34.000][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-26 16:05:34.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-26 16:05:34.002][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-26 16:05:34.003][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:05:34.004][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:34.005][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:05:34.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:34.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:34.007][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:05:34.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:05:34.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:05:34.010][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:05:34.011][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:05:34.011][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:05:34.011][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-26 16:05:34.011][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-26 16:05:34.012][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:05:34.013][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:05:34.013][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:05:34.014][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:05:34.020][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-26 16:05:34.041][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-26 16:05:34.042][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-26 16:05:34.046][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-26 16:05:34.050][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-26 16:05:34.053][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:05:34.054][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:05:34.055][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:05:34.057][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:05:34.058][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:05:34.059][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-26 16:05:34.067][biodb::testThat]
biodb.INFO [2025-04-26 16:05:34.068][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:05:34.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:05:34.099][biodb::testThat]
biodb.TRACE[2025-04-26 16:05:34.102][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-04-26 16:05:34.103][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:05:34.106][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:05:34.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:05:34.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:34.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:34.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:34.126][FUN] 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 16:05:34.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:34.128][FUN] Functions in observer BiodbConfig: [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 16:05:34.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.163][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.222][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.229][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:05:34.291][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-04-26 16:05:34.293][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.300][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:05:34.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:05:34.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.304][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:05:34.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:05:34.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.336][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.366][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.370][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.374][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.398][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.401][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.412][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.419][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.423][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.424][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.426][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.427][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.437][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.448][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.449][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.451][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.473][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.474][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.476][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.497][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.498][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.500][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.511][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.512][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.514][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.518][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.519][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.519][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.520][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.528][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.529][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.530][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.534][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.535][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.537][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.540][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.542][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.543][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.559][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-04-26 16:05:34.592][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:05:34.593][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:05:34.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:05:34.595][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:05:34.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:05:34.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:05:34.601][FUN] 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 16:05:34.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:05:34.602][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 16:05:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.635][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.638][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.646][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.704][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.707][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.715][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:05:34.740][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-04-26 16:05:34.760][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.763][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:05:34.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.767][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:05:34.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:05:34.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.771][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:05:34.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:05:34.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.816][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.823][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:05:34.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.852][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.853][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.855][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:34.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:34.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.866][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.869][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.873][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.877][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.878][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.878][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.879][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.880][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:34.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.901][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.902][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.904][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:34.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:34.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.922][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.929][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.932][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:34.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:34.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.953][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.954][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.956][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:34.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.978][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.979][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.980][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:34.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:34.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:34.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.005][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.015][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:05:35.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:05:35.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.018][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.022][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:05:35.023][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:05:35.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.024][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.028][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:05:35.029][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:05:35.030][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.031][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.034][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:05:35.035][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:05:35.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.037][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.041][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.042][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:05:35.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.047][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.051][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:35.052][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:05:35.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.054][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:05:35.057][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:05:35.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:05:35.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:05:35.060][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:05:35.066][biodb::testThat]
biodb.INFO [2025-04-26 16:05:35.067][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:05:35.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:05:35.069][biodb::testThat]
biodb.DEBUG[2025-04-26 16:05:35.070][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-04-26 16:05:35.077][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2025-04-26 16:05:35.080][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2025-04-26 16:05:35.082][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-04-26 16:05:35.083][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-04-26 16:05:35.083][private$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 16:05:35.085][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 16:06:06.922][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/nci.cactus4d2c825a6b679gz".
biodb.TRACE[2025-04-26 16:06:06.926][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:06:06.929][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:06:06.933][self$getDownloadPath] Download path of nci.cactus is "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:06:06.935][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-04-26 16:06:06.940][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker4d2c8566de946marker".
biodb.TRACE[2025-04-26 16:06:06.942][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-04-26 16:06:06.945][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:06:06.948][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-04-26 16:06:06.952][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-04-26 16:06:06.954][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-04-26 16:06:06.957][self$getDownloadPath] Download path of nci.cactus is "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:07:08.678][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-04-26 16:07:08.680][private$doExtractDownload] Extract single entries from downloaded file "/home/biocbuild/.cache/R/biodb/tmp/cactus_rdfs", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2025-04-26 16:15:32.923][self$addFilesToCache] Moving files to cache [265242]: "/home/biocbuild/.cache/R/biodb/tmp/entry_1.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_2.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_3.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_4.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_5.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_6.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_7.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_8.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_9.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-04-26 16:15:33.298][private$doAddFilesToCache] Destination files are [265242]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-04-26 16:15:40.407][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:15:40.409][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-04-26 16:15:40.614][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker4d2c8358f8469marker".
biodb.TRACE[2025-04-26 16:15:40.616][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-04-26 16:15:40.617][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-04-26 16:15:40.618][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-04-26 16:15:40.620][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-26 16:15:40.621][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-04-26 16:15:40.622][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:15:40.624][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-04-26 16:15:40.625][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:15:40.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:15:40.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:40.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:40.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:40.636][FUN] 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 16:15:40.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:40.638][FUN] Functions in observer BiodbConfig: [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 16:15:40.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:15:40.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:15:40.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.661][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:15:40.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:15:40.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:15:40.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:15:40.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:15:40.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:15:40.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.683][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.691][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.695][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.703][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:15:40.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:15:40.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:40.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:40.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:40.727][FUN] 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 16:15:40.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:40.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:15:40.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.747][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:15:40.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:15:40.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.751][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:15:40.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:15:40.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:15:40.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:15:40.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:15:40.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:15:40.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:15:40.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.784][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:15:40.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:15:40.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:15:40.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:15:40.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.805][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:15:40.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:15:40.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:15:40.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.819][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.823][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.831][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:15:40.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:15:40.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:15:40.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:15:40.871][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-04-26 16:15:40.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:15:40.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:15:40.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:15:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:15:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:15:40.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:15:40.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:15:40.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:15:40.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:15:40.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:15:40.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:40.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:15:40.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:15:40.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:15:40.907][biodb::testThat]
biodb.INFO [2025-04-26 16:15:40.908][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:15:40.909][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:40.910][biodb::testThat]
biodb.INFO [2025-04-26 16:15:40.916][biodb::testThat]
biodb.INFO [2025-04-26 16:15:40.917][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:15:40.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:40.919][biodb::testThat]
biodb.WARN [2025-04-26 16:15:40.940][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-26 16:15:40.960][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-26 16:15:40.969][biodb::testThat]
biodb.INFO [2025-04-26 16:15:40.970][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:15:40.971][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:40.972][biodb::testThat]
biodb.TRACE[2025-04-26 16:15:40.996][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:15:40.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:15:40.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:40.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.000][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:15:41.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:15:41.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.004][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:15:41.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:15:41.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:15:41.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:15:41.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:15:41.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:15:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:15:41.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:15:41.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:15:41.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:15:41.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:15:41.059][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:15:41.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:15:41.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:15:41.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:15:41.068][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.069][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:15:41.070][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:41.071][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.078][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.079][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:15:41.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:41.081][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.088][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.089][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:15:41.090][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:41.091][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.096][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.097][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:15:41.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:15:41.099][biodb::testThat]
biodb.INFO [2025-04-26 16:15:41.105][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:15:41.106][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-26 16:15:41.107][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-26 16:15:41.108][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:15:41.109][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.111][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:15:41.113][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-26 16:15:41.124][biodb::testContext]
biodb.INFO [2025-04-26 16:15:41.125][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:15:41.126][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-04-26 16:15:41.127][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:15:41.127][biodb::testContext]
biodb.INFO [2025-04-26 16:15:41.130][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:15:41.131][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:15:41.135][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:15:41.136][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:15:41.138][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:15:41.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.141][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:15:41.142][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:15:41.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.146][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:15:41.147][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:15:41.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.151][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:15:41.152][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:15:41.153][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:15:41.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.157][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:15:41.158][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:15:41.159][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:15:41.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.162][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:15:41.163][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:15:41.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.167][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:15:41.168][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:15:41.169][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:15:41.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.173][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:15:41.174][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:15:41.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.178][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:15:41.179][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:15:41.180][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:15:41.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.183][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:15:41.184][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:15:41.185][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:15:41.186][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:15:41.187][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:15:41.188][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:15:41.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.192][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:15:41.193][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:15:41.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.197][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:15:41.198][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:15:41.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.202][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:15:41.203][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:15:41.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.206][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:15:41.207][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:15:41.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.211][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:15:41.212][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:15:41.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.216][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:15:41.217][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:15:41.221][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:15:41.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.224][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:15:41.225][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:15:41.226][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:15:41.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.230][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:15:41.232][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.233][self$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 16:15:41.234][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.235][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:15:41.237][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.238][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.238][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.240][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.240][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:15:41.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:15:41.243][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.244][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:15:41.245][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:15:41.246][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.247][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.248][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:15:41.248][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:15:41.248][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:15:41.248][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:15:41.248][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:15:41.249][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:15:41.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.251][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:15:41.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.255][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:15:41.257][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:15:41.258][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.259][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.260][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:15:41.262][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.263][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:15:41.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:15:41.266][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.267][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.268][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.269][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.270][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:15:41.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:15:41.272][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.273][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:15:41.274][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:15:41.275][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.276][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.277][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:15:41.277][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:15:41.277][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:15:41.277][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:15:41.277][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:15:41.278][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:15:41.279][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.280][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.281][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:15:41.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.284][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.285][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.286][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:15:41.287][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:15:41.288][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.289][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.290][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:15:41.292][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.293][self$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 16:15:41.294][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.295][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:15:41.296][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.297][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.298][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.299][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.300][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:15:41.301][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:15:41.302][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.303][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:15:41.304][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:15:41.305][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.306][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.307][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.308][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:15:41.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.310][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:15:41.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.314][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.315][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:15:41.316][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:15:41.317][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.318][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.319][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:15:41.321][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.322][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:15:41.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:15:41.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.327][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.328][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.329][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:15:41.330][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:15:41.331][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.332][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:15:41.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:15:41.334][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.336][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.337][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:15:41.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:15:41.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.342][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.344][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.345][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:15:41.345][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:15:41.346][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.347][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.349][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:15:41.350][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.353][FUN] 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 16:15:41.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.358][FUN] 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 16:15:41.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.362][FUN] 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 16:15:41.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.364][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 16:15:41.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.367][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 16:15:41.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.371][FUN] 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 16:15:41.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.376][FUN] 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 16:15:41.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.378][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 16:15:41.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.380][FUN] 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 16:15:41.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.385][FUN] 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 16:15:41.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.389][FUN] 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 16:15:41.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.394][FUN] 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 16:15:41.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.398][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 16:15:41.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.400][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 16:15:41.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.402][FUN] 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 16:15:41.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.407][FUN] 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 16:15:41.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.409][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 16:15:41.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.411][FUN] 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 16:15:41.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.413][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 16:15:41.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.416][FUN] 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 16:15:41.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.420][FUN] 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 16:15:41.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.425][FUN] 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 16:15:41.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.428][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:15:41.429][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:15:41.431][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:15:41.432][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:15:41.433][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:15:41.435][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:15:41.436][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:15:41.438][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:15:41.439][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:15:41.440][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:15:41.442][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:15:41.443][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:15:41.445][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:15:41.446][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:15:41.447][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:15:41.449][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:15:41.450][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:15:41.452][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:15:41.453][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:15:41.455][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:15:41.456][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:15:41.457][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:15:41.459][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:15:41.460][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:15:41.462][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:15:41.463][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:15:41.464][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:15:41.466][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:15:41.467][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:15:41.469][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:15:41.470][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:15:41.471][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:15:41.473][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:15:41.474][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:15:41.476][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:15:41.477][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:15:41.478][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:15:41.480][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:15:41.481][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:15:41.483][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:15:41.484][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:15:41.485][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:15:41.487][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:15:41.488][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:15:41.490][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:15:41.491][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:15:41.492][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:15:41.494][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:15:41.495][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:15:41.497][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:15:41.498][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:15:41.499][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:15:41.501][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:15:41.502][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:15:41.504][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:15:41.505][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:15:41.506][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:15:41.508][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:15:41.509][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:15:41.511][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:15:41.512][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:15:41.513][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:15:41.515][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:15:41.516][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:15:41.518][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:15:41.519][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:15:41.520][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:15:41.522][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:15:41.523][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:15:41.525][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:15:41.526][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:15:41.527][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:15:41.529][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:15:41.530][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:15:41.532][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:15:41.533][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:15:41.534][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:15:41.536][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:15:41.537][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:15:41.539][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:15:41.540][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:15:41.541][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:15:41.543][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:15:41.544][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:15:41.546][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:15:41.547][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:15:41.548][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.549][FUN] 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 16:15:41.549][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.555][FUN] 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 16:15:41.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:15:41.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.567][FUN] 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 16:15:41.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:15:41.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.580][FUN] 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 16:15:41.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:15:41.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.592][FUN] 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 16:15:41.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.598][FUN] 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 16:15:41.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.604][FUN] 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 16:15:41.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:15:41.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.617][FUN] 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 16:15:41.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:15:41.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.630][FUN] 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 16:15:41.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.636][FUN] 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 16:15:41.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.642][FUN] 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 16:15:41.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.648][FUN] 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 16:15:41.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:15:41.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:15:41.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.654][FUN] 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 16:15:41.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:15:41.658][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-26 16:15:41.659][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-26 16:15:41.661][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.662][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-26 16:15:41.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:15:41.665][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.666][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-26 16:15:41.667][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.668][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.669][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-26 16:15:41.670][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:15:41.671][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.672][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-26 16:15:41.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-26 16:15:41.674][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-26 16:15:41.675][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:15:41.676][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.677][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:15:41.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:15:41.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:15:41.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:15:41.683][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:15:41.684][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:15:41.684][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:15:41.684][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-26 16:15:41.684][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-26 16:15:41.685][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:15:41.686][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:15:41.687][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:15:41.688][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:15:41.689][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-26 16:15:41.692][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-26 16:15:41.693][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-26 16:15:41.695][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-26 16:15:41.696][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-26 16:15:41.697][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:15:41.698][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:15:41.700][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:15:41.701][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:15:41.702][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:15:41.703][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-26 16:15:41.704][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:15:41.705][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-26 16:15:41.707][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-26 16:15:41.707][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:15:41.708][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:15:41.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:15:41.710][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:15:41.711][FUN] 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 16:15:41.712][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:15:41.713][FUN] Functions in observer 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 
550.403  28.242 609.987

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* 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 ‘1.13.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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 loading without being on the library search path ... 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
  ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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)