Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-29 23:55 -0400 (Sat, 29 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
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 7/32HostnameOS / ArchCHECK
biodbExpasy 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-29 09:55 -0400 (Sat, 29 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_20
git_last_commit: 4403c2f
git_last_commit_date: 2024-10-29 11:09:35 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on merida1

To the developers/maintainers of the biodbExpasy 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: biodbExpasy
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
StartedAt: 2025-03-29 16:01:17 -0400 (Sat, 29 Mar 2025)
EndedAt: 2025-03-29 16:02:19 -0400 (Sat, 29 Mar 2025)
EllapsedTime: 62.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2025-03-29 16:02:10.490][biodb::testContext]
biodb.INFO [2025-03-29 16:02:10.494][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:02:10.496][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-29 16:02:10.497][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:02:10.498][biodb::testContext]
biodb.INFO [2025-03-29 16:02:10.506][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:02:10.509][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:02:10.517][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:10.519][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:02:10.520][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:02:10.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.526][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:02:10.564][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:02:10.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.568][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:02:10.570][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:02:10.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.574][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:02:10.575][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:02:10.577][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:02:10.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.581][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:02:10.582][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:02:10.584][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:02:10.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.588][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:02:10.589][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:02:10.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.594][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:02:10.595][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:02:10.596][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:02:10.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.601][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:02:10.602][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:02:10.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.607][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:02:10.608][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:02:10.609][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:02:10.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.614][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:02:10.615][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:02:10.616][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:02:10.617][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:02:10.618][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:02:10.620][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:02:10.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.624][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:02:10.626][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:02:10.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.630][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:02:10.631][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:02:10.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.636][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:02:10.637][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:02:10.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.642][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:02:10.643][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:02:10.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.647][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:02:10.649][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:02:10.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.653][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:02:10.654][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:02:10.664][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:02:10.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.669][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:02:10.670][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:02:10.672][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:02:10.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.678][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:02:10.722][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.745][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-29 16:02:10.746][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:10.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.752][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.753][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.754][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:02:10.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:10.757][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.758][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:02:10.759][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:10.761][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:10.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:02:10.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:02:10.764][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:02:10.764][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:02:10.770][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:10.771][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.774][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:10.775][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.777][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.778][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.780][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:10.781][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:10.782][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.783][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.785][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:02:10.787][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.788][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:02:10.789][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.791][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:10.792][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.793][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.794][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.796][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.797][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:02:10.798][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:10.799][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.801][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:02:10.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:10.803][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.804][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.806][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:10.806][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:02:10.806][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:02:10.806][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:02:10.806][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:02:10.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:10.808][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.809][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.811][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:10.812][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.815][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.817][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:10.818][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:10.819][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.820][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.822][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:02:10.824][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.825][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-29 16:02:10.826][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.828][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:10.829][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.834][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:02:10.835][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:10.837][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.838][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:02:10.839][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:10.840][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.842][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.843][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.844][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:10.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:10.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.851][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.853][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:10.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:10.856][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.857][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.859][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:02:10.861][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.862][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:02:10.864][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.865][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:10.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.868][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.871][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:02:10.873][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:10.874][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.875][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:02:10.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:10.878][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:10.880][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.882][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:10.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.885][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:10.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:10.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:10.889][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:10.890][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.891][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:10.892][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:10.894][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:10.895][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:10.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:10.900][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:10.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:10.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:10.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:10.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:10.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.002][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:02:11.006][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:02:11.008][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:02:11.010][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:02:11.011][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:02:11.013][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:02:11.015][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:02:11.016][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:02:11.018][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:02:11.020][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:02:11.021][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:02:11.023][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:02:11.025][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:02:11.027][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:02:11.029][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:02:11.030][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:02:11.032][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:02:11.034][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:02:11.036][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:02:11.037][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:02:11.039][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:02:11.041][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:02:11.043][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:02:11.045][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:02:11.046][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:02:11.048][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:02:11.050][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:02:11.052][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:02:11.053][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:02:11.055][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:02:11.057][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:02:11.059][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:02:11.060][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:02:11.062][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:02:11.064][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:02:11.065][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:02:11.067][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:02:11.069][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:02:11.070][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:02:11.072][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:02:11.074][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:02:11.076][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:02:11.077][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:02:11.079][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:02:11.081][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:02:11.083][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:02:11.084][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:02:11.086][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:02:11.088][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:02:11.089][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:02:11.091][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:02:11.093][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:02:11.095][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:02:11.096][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:02:11.098][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:02:11.100][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:02:11.101][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:02:11.103][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:02:11.105][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:02:11.106][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:02:11.108][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:02:11.110][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:02:11.111][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:02:11.113][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:02:11.115][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:02:11.117][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:02:11.118][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:02:11.120][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:02:11.122][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:02:11.123][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:02:11.125][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:02:11.127][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:02:11.128][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:02:11.130][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:02:11.132][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:02:11.133][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:02:11.135][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:02:11.137][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:02:11.138][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:02:11.140][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:02:11.142][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:02:11.144][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:02:11.145][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:02:11.153][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:02:11.155][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:02:11.158][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:11.159][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.161][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.191][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[2025-03-29 16:02:11.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:11.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:11.306][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-29 16:02:11.319][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:02:11.322][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:11.323][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-29 16:02:11.324][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:11.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:11.327][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:11.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:11.329][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:11.331][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:11.332][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-29 16:02:11.333][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:11.334][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:11.336][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-29 16:02:11.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:11.338][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-29 16:02:11.338][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:02:11.338][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:02:11.338][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:02:11.339][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:11.341][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:11.342][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:02:11.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:11.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:11.345][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:11.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:11.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:11.349][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:11.350][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-29 16:02:11.351][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:11.353][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:11.354][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:11.355][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:11.363][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:02:11.386][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:02:11.388][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-29 16:02:11.392][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:02:11.397][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-29 16:02:11.402][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:02:11.403][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:02:11.404][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-29 16:02:11.415][biodb::testThat]
biodb.INFO [2025-03-29 16:02:11.416][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-29 16:02:11.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:11.419][biodb::testThat]
biodb.TRACE[2025-03-29 16:02:11.423][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2025-03-29 16:02:11.425][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:02:11.436][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-29 16:02:11.444][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:11.445][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:11.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:11.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:11.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:11.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:11.465][FUN] Functions in observer BiodbConfig: [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[2025-03-29 16:02:11.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.517][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:11.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.538][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.549][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:02:11.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.554][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.559][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.564][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.569][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:02:11.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.597][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.709][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.714][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.725][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:11.761][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-03-29 16:02:11.764][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:11.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:11.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:11.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:11.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.774][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:11.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:11.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.779][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:11.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:11.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.823][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.870][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.875][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.880][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:11.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.909][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.910][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.913][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:11.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:11.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.929][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.944][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.946][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.964][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.970][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.975][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.980][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.981][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.983][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:11.985][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:11.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:11.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.000][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.005][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.010][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.015][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.020][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.023][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.024][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.039][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.040][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.043][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.049][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.050][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.059][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-29 16:02:12.061][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:12.062][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.069][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.070][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.096][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2025-03-29 16:02:12.145][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-29 16:02:12.146][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-29 16:02:12.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:12.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:12.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:12.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:12.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:12.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:12.160][FUN] Functions in observer BiodbConfig: [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[2025-03-29 16:02:12.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.168][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.178][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:02:12.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:12.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.184][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.193][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.203][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:12.241][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-03-29 16:02:12.270][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:12.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:12.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.275][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:12.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:12.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.280][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:12.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:12.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.285][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:12.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:12.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.301][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.343][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.348][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.353][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:12.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.398][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.399][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.433][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.453][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.458][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.463][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.468][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.469][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.473][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.488][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:12.489][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:12.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.491][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.498][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.499][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:12.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:12.507][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:12.509][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:12.510][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:12.511][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:02:12.521][biodb::testThat]
biodb.INFO [2025-03-29 16:02:12.523][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-29 16:02:12.524][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:12.525][biodb::testThat]
biodb.DEBUG[2025-03-29 16:02:12.528][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-03-29 16:02:12.534][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-29 16:02:12.540][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-03-29 16:02:12.542][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-03-29 16:02:12.543][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-29 16:02:12.545][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-29 16:02:12.546][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-03-29 16:02:12.552][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-29 16:02:12.554][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-29 16:02:12.555][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-29 16:02:12.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:12.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:12.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:12.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:12.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:12.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:12.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:12.573][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-03-29 16:02:12.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-29 16:02:12.603][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-29 16:02:12.604][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-03-29 16:02:13.270][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-03-29 16:02:13.729][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-29 16:02:13.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-03-29 16:02:13.751][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-03-29 16:02:13.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:13.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:13.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:13.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:13.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:13.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:13.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:13.795][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-03-29 16:02:13.816][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-29 16:02:13.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-29 16:02:13.846][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-03-29 16:02:14.294][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-03-29 16:02:14.743][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-29 16:02:14.746][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-03-29 16:02:14.750][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-03-29 16:02:14.753][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2025-03-29 16:02:14.756][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-29 16:02:14.757][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-03-29 16:02:14.758][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-29 16:02:14.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:14.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:14.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:14.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:14.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:14.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:14.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:02:14.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.780][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:14.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:14.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.791][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:02:14.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:14.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.821][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:14.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-29 16:02:14.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:14.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:14.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:14.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:14.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:14.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-29 16:02:14.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-29 16:02:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:14.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:14.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.893][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-29 16:02:14.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-29 16:02:14.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-29 16:02:14.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-29 16:02:14.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-29 16:02:14.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:14.963][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-03-29 16:02:14.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:02:14.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:02:14.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:02:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:02:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:02:14.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:02:14.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-29 16:02:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-29 16:02:14.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:02:14.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-29 16:02:14.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:14.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:14.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:02:15.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-29 16:02:15.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:15.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:02:15.013][biodb::testThat]
biodb.INFO [2025-03-29 16:02:15.014][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-29 16:02:15.016][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:15.017][biodb::testThat]
biodb.TRACE[2025-03-29 16:02:15.021][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:15.022][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:15.023][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:15.025][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:15.026][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-03-29 16:02:15.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:15.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:15.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:15.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:15.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:15.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:15.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:15.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:15.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:15.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:15.078][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-03-29 16:02:15.081][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-29 16:02:15.084][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-29 16:02:15.086][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-29 16:02:15.087][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-03-29 16:02:15.564][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-03-29 16:02:16.040][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-29 16:02:16.043][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-03-29 16:02:16.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-03-29 16:02:16.054][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-03-29 16:02:16.081][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.082][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-29 16:02:16.084][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:16.085][biodb::testThat]
biodb.TRACE[2025-03-29 16:02:16.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:16.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:16.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.122][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:16.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:16.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:16.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:16.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-29 16:02:16.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-29 16:02:16.170][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-29 16:02:16.191][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-03-29 16:02:16.193][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-29 16:02:16.194][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-03-29 16:02:16.221][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.222][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-29 16:02:16.224][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:16.225][biodb::testThat]
biodb.TRACE[2025-03-29 16:02:16.237][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.247][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:16.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:16.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-29 16:02:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:16.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-29 16:02:16.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:16.317][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-29 16:02:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:16.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-29 16:02:16.332][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.333][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-29 16:02:16.335][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:16.336][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.347][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.348][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-29 16:02:16.350][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:16.351][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.361][biodb::testThat]
biodb.INFO [2025-03-29 16:02:16.362][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-29 16:02:16.363][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:16.364][biodb::testThat]
biodb.DEBUG[2025-03-29 16:02:16.384][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2025-03-29 16:02:16.861][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2025-03-29 16:02:17.345][biodb::testThat]
biodb.INFO [2025-03-29 16:02:17.346][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-29 16:02:17.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-29 16:02:17.348][biodb::testThat]
biodb.DEBUG[2025-03-29 16:02:17.813][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-03-29 16:02:18.301][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:18.302][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:18.303][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:18.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-29 16:02:18.306][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-29 16:02:18.307][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-29 16:02:18.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-29 16:02:18.310][ef$get] fields variable is a list.
biodb.INFO [2025-03-29 16:02:18.311][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:02:18.312][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-29 16:02:18.314][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-29 16:02:18.315][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:02:18.316][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.318][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.320][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-29 16:02:18.343][biodb::testContext]
biodb.INFO [2025-03-29 16:02:18.344][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:02:18.346][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-29 16:02:18.347][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-29 16:02:18.348][biodb::testContext]
biodb.INFO [2025-03-29 16:02:18.350][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:02:18.352][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-29 16:02:18.356][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:18.358][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-29 16:02:18.359][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-29 16:02:18.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.363][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-29 16:02:18.365][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-29 16:02:18.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.369][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-29 16:02:18.371][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-29 16:02:18.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.375][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-29 16:02:18.376][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-29 16:02:18.378][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-29 16:02:18.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.382][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-29 16:02:18.383][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-29 16:02:18.385][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-29 16:02:18.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.389][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-29 16:02:18.390][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-29 16:02:18.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.395][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-29 16:02:18.396][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-29 16:02:18.397][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-29 16:02:18.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.401][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[2025-03-29 16:02:18.402][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-29 16:02:18.403][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-29 16:02:18.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.407][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-29 16:02:18.409][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-29 16:02:18.410][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-29 16:02:18.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.413][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[2025-03-29 16:02:18.414][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:02:18.416][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-29 16:02:18.417][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-29 16:02:18.418][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-29 16:02:18.419][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-29 16:02:18.421][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-29 16:02:18.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.425][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-29 16:02:18.427][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-29 16:02:18.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.430][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[2025-03-29 16:02:18.431][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-29 16:02:18.432][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-29 16:02:18.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.437][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-29 16:02:18.438][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-29 16:02:18.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.443][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-29 16:02:18.444][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-29 16:02:18.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.448][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-29 16:02:18.450][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-29 16:02:18.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.458][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-29 16:02:18.459][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-29 16:02:18.470][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-29 16:02:18.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.474][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-29 16:02:18.476][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-29 16:02:18.477][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-29 16:02:18.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.481][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-29 16:02:18.484][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.485][self$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[2025-03-29 16:02:18.486][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:18.489][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.490][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.491][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.494][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:02:18.495][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:18.496][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.498][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-29 16:02:18.499][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:18.500][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.501][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.502][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:18.502][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:02:18.502][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:02:18.502][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:02:18.502][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:02:18.504][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:18.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.507][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:18.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.511][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.512][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:18.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:18.516][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.517][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.518][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-29 16:02:18.521][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.522][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:02:18.523][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.524][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:18.525][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.527][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.528][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:02:18.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:18.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.534][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-29 16:02:18.536][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:18.537][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.538][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.539][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:18.539][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-29 16:02:18.539][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-29 16:02:18.539][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-29 16:02:18.539][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-29 16:02:18.541][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:18.542][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:18.546][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.547][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.548][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.549][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.550][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:18.551][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:18.553][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.554][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.555][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-29 16:02:18.558][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.559][self$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[2025-03-29 16:02:18.560][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.561][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:18.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.568][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-29 16:02:18.569][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:18.570][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.571][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-29 16:02:18.573][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:18.574][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.575][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.577][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.578][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:18.579][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.580][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.581][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:18.583][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.584][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.585][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.590][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.592][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:18.593][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:18.594][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.595][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.596][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-29 16:02:18.599][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.600][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-29 16:02:18.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:18.604][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.605][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.606][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.608][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-29 16:02:18.610][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:18.611][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.612][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-29 16:02:18.614][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:18.615][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.616][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:18.617][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.619][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-29 16:02:18.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:18.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:18.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:18.625][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:18.627][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:18.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:18.630][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:18.631][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:18.633][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:18.634][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.641][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[2025-03-29 16:02:18.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.657][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[2025-03-29 16:02:18.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.673][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[2025-03-29 16:02:18.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.733][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-29 16:02:18.735][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-29 16:02:18.737][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-29 16:02:18.738][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-29 16:02:18.740][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-29 16:02:18.742][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-29 16:02:18.744][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-29 16:02:18.745][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-29 16:02:18.747][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:02:18.749][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-29 16:02:18.750][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-29 16:02:18.752][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-29 16:02:18.754][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-29 16:02:18.755][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-29 16:02:18.757][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-29 16:02:18.759][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-29 16:02:18.760][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-29 16:02:18.762][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-29 16:02:18.764][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-29 16:02:18.766][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-29 16:02:18.767][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-29 16:02:18.769][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-29 16:02:18.771][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-29 16:02:18.772][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-29 16:02:18.774][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-29 16:02:18.776][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-29 16:02:18.777][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-29 16:02:18.779][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-29 16:02:18.781][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-29 16:02:18.783][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-29 16:02:18.784][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-29 16:02:18.786][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-29 16:02:18.788][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-29 16:02:18.789][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-29 16:02:18.791][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-29 16:02:18.793][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-29 16:02:18.794][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-29 16:02:18.796][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-29 16:02:18.798][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-29 16:02:18.799][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-29 16:02:18.801][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-29 16:02:18.803][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-29 16:02:18.805][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-29 16:02:18.806][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-29 16:02:18.808][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-29 16:02:18.810][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-29 16:02:18.811][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-29 16:02:18.813][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-29 16:02:18.815][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-29 16:02:18.816][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-29 16:02:18.818][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-29 16:02:18.820][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-29 16:02:18.822][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-29 16:02:18.828][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-29 16:02:18.829][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-29 16:02:18.831][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-29 16:02:18.833][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-29 16:02:18.835][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-29 16:02:18.836][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-29 16:02:18.838][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-29 16:02:18.840][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-29 16:02:18.841][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-29 16:02:18.843][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-29 16:02:18.845][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-29 16:02:18.846][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-29 16:02:18.848][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-29 16:02:18.850][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-29 16:02:18.852][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-29 16:02:18.853][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-29 16:02:18.855][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-29 16:02:18.857][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-29 16:02:18.858][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-29 16:02:18.860][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-29 16:02:18.862][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-29 16:02:18.864][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-29 16:02:18.865][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-29 16:02:18.867][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-29 16:02:18.869][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-29 16:02:18.870][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-29 16:02:18.872][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-29 16:02:18.874][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-29 16:02:18.876][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-29 16:02:18.877][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-29 16:02:18.879][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-29 16:02:18.881][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-29 16:02:18.882][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-29 16:02:18.883][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.885][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.917][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[2025-03-29 16:02:18.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:18.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:18.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:18.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:18.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:18.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:18.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:18.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:19.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:19.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:19.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:19.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:19.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:19.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:19.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:19.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:19.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:19.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:19.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:19.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:19.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:19.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:19.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-29 16:02:19.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:19.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:19.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:19.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:19.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:19.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-29 16:02:19.024][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-29 16:02:19.025][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:02:19.028][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:19.029][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-29 16:02:19.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:19.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-29 16:02:19.033][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:19.034][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-29 16:02:19.035][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:19.036][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-29 16:02:19.037][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-29 16:02:19.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-29 16:02:19.040][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:19.041][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-29 16:02:19.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-29 16:02:19.044][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-29 16:02:19.044][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:02:19.044][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:02:19.044][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-29 16:02:19.045][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-29 16:02:19.046][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-29 16:02:19.047][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-29 16:02:19.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:19.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:19.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-29 16:02:19.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-29 16:02:19.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-29 16:02:19.054][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-29 16:02:19.055][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-29 16:02:19.057][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-29 16:02:19.058][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-29 16:02:19.063][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-29 16:02:19.065][self$setPropertyValue]
biodb.DEBUG[2025-03-29 16:02:19.066][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-29 16:02:19.070][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:02:19.071][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-29 16:02:19.073][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-29 16:02:19.075][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-29 16:02:19.076][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:02:19.077][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-29 16:02:19.078][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-29 16:02:19.080][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-29 16:02:19.081][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-29 16:02:19.082][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-29 16:02:19.083][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-29 16:02:19.084][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-29 16:02:19.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-29 16:02:19.087][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-29 16:02:19.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-29 16:02:19.089][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-29 16:02:19.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.10.0’
* 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 ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 whether startup messages can be suppressed ... 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 ... OK
* 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 files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log’
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** 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
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)