Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4408
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4407
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 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-29 09:55 -0400 (Sat, 29 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino6Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on lconway

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: 1.9.0
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_1.9.0.tar.gz
StartedAt: 2024-06-29 16:01:07 -0400 (Sat, 29 Jun 2024)
EndedAt: 2024-06-29 16:01:51 -0400 (Sat, 29 Jun 2024)
EllapsedTime: 43.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-29 16:01:42.819][biodb::testContext]
biodb.INFO [2024-06-29 16:01:42.822][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:01:42.823][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-29 16:01:42.823][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:01:42.824][biodb::testContext]
biodb.INFO [2024-06-29 16:01:42.830][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:01:42.831][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:01:42.837][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:01:42.838][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:01:42.839][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:01:42.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.842][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:01:42.867][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:01:42.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.870][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:01:42.871][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:01:42.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.873][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:01:42.874][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:01:42.875][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:01:42.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.877][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:01:42.878][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:01:42.879][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:01:42.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.881][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:01:42.882][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:01:42.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.885][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:01:42.886][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:01:42.886][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:01:42.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.889][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:01:42.890][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:01:42.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.893][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:01:42.893][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:01:42.894][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:01:42.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.897][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:01:42.897][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:01:42.898][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:01:42.899][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:01:42.900][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:01:42.900][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:01:42.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.902][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[2024-06-29 16:01:42.903][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:01:42.904][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:01:42.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.906][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:01:42.907][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:01:42.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.909][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[2024-06-29 16:01:42.910][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:01:42.911][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:01:42.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.914][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:01:42.914][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:01:42.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.917][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:01:42.918][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:01:42.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.921][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:01:42.921][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:01:42.938][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:01:42.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.940][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[2024-06-29 16:01:42.941][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:01:42.942][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:01:42.943][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:01:42.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:42.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:42.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:42.947][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:01:42.970][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:42.981][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-29 16:01:42.982][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:42.983][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:42.984][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:42.984][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:42.985][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:42.986][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:42.986][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:01:42.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:42.988][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:42.989][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:01:42.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:42.990][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:42.991][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:42.992][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:01:42.992][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:01:42.992][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:01:42.992][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:01:42.992][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:01:42.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:42.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:42.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:42.994][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:42.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:42.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:42.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:42.997][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:42.998][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:42.999][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:43.000][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.000][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.001][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:01:43.003][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.003][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:01:43.004][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.005][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:43.006][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.006][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.007][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.008][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:01:43.009][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:43.010][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.011][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:01:43.012][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:43.012][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.018][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.019][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:01:43.019][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:01:43.019][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:01:43.019][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:01:43.019][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:01:43.019][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:43.020][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.021][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:43.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.024][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:43.025][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:43.026][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.027][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.028][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:01:43.029][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.030][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-29 16:01:43.030][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.031][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:43.032][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.033][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.034][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:01:43.035][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:43.036][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.037][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:01:43.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:43.038][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.039][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.039][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:43.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.042][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:43.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.044][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.045][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:43.046][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:43.047][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.048][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.049][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:01:43.050][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.051][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:01:43.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:43.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.054][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.055][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.056][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.057][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:01:43.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:43.058][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.059][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:01:43.060][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:43.061][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.061][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.062][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.063][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:43.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.064][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:43.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.068][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.069][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:43.070][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:43.070][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.071][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.074][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:01:43.075][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.133][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:01:43.136][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:01:43.137][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:01:43.138][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:01:43.139][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:01:43.140][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:01:43.141][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:01:43.142][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:01:43.143][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:01:43.144][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:01:43.145][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:01:43.146][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:01:43.147][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:01:43.148][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:01:43.149][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:01:43.150][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:01:43.151][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:01:43.152][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:01:43.153][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:01:43.154][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:01:43.155][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:01:43.161][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:01:43.162][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:01:43.162][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:01:43.163][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:01:43.164][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:01:43.165][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:01:43.166][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:01:43.167][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:01:43.168][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:01:43.169][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:01:43.170][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:01:43.171][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:01:43.172][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:01:43.173][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:01:43.174][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:01:43.175][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:01:43.176][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:01:43.177][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:01:43.178][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:01:43.179][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:01:43.180][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:01:43.181][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:01:43.182][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:01:43.183][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:01:43.184][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:01:43.185][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:01:43.186][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:01:43.187][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:01:43.188][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:01:43.189][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:01:43.190][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:01:43.191][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:01:43.192][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:01:43.193][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:01:43.194][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:01:43.195][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:01:43.196][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:01:43.197][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:01:43.198][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:01:43.199][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:01:43.200][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:01:43.201][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:01:43.202][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:01:43.203][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:01:43.204][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:01:43.205][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:01:43.206][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:01:43.207][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:01:43.208][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:01:43.209][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:01:43.210][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:01:43.211][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:01:43.212][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:01:43.213][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:01:43.214][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:01:43.215][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:01:43.216][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:01:43.217][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:01:43.218][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:01:43.219][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:01:43.220][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:01:43.221][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:01:43.226][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:01:43.227][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:01:43.229][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:01:43.230][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.231][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.249][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[2024-06-29 16:01:43.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.280][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[2024-06-29 16:01:43.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:43.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:43.318][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-29 16:01:43.324][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:01:43.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.327][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-29 16:01:43.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.328][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:43.329][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.330][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.330][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.331][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.332][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-29 16:01:43.333][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:43.333][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.334][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-29 16:01:43.335][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:43.335][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-29 16:01:43.335][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:01:43.335][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:01:43.335][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:01:43.336][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:43.337][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:01:43.338][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:01:43.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:43.341][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:43.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:43.342][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:43.343][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:01:43.344][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:43.344][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:43.345][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:43.346][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:43.350][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:01:43.367][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:01:43.368][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-29 16:01:43.372][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:01:43.374][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-29 16:01:43.377][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:01:43.378][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:01:43.379][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-29 16:01:43.387][biodb::testThat]
biodb.INFO [2024-06-29 16:01:43.388][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-29 16:01:43.389][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:43.389][biodb::testThat]
biodb.TRACE[2024-06-29 16:01:43.392][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[2024-06-29 16:01:43.393][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:01:43.396][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:01:43.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:01:43.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:01:43.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.474][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.481][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:01:43.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.484][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.487][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.490][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.494][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:01:43.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.539][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.549][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.552][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.558][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:43.606][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-29 16:01:43.608][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:43.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:43.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.616][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:43.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.645][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.673][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.677][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.680][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.699][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.700][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.701][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.727][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.728][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.729][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.740][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.744][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.750][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.751][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.753][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.764][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.768][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.771][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.774][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.775][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.777][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.787][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.789][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.793][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.794][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.796][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.800][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.801][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.803][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.807][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.808][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.809][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.823][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[2024-06-29 16:01:43.853][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:01:43.854][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:01:43.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:01:43.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:43.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:43.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:43.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:43.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:43.863][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:01:43.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.868][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:43.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:43.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:43.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.875][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:01:43.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.878][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.881][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.887][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:43.909][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-29 16:01:43.925][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:43.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.931][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:43.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:43.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.934][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:43.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:43.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.944][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.973][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.977][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.980][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:43.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:43.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:43.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:43.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:43.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:44.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:44.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:44.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:44.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.005][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:44.006][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:44.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.007][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:44.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:44.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:44.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:44.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:44.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:44.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:44.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:44.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.026][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:44.027][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:44.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.028][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:44.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:44.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.039][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.042][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.045][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.048][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.049][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.051][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.061][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:44.062][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:44.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.063][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.067][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.068][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:44.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.070][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:44.078][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:44.078][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:44.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:44.080][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:01:44.087][biodb::testThat]
biodb.INFO [2024-06-29 16:01:44.088][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-29 16:01:44.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:44.089][biodb::testThat]
biodb.DEBUG[2024-06-29 16:01:44.091][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-29 16:01:44.096][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-29 16:01:44.100][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-29 16:01:44.101][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-29 16:01:44.102][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-29 16:01:44.103][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-29 16:01:44.104][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-29 16:01:44.104][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:01:44.105][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-29 16:01:44.106][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-29 16:01:44.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:01:44.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:44.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:44.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:44.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:44.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:44.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:44.119][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-29 16:01:44.135][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:01:44.135][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:01:44.136][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-29 16:01:44.888][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-29 16:01:45.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:01:45.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-29 16:01:45.272][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-29 16:01:45.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:01:45.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:45.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:45.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:45.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:45.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:45.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:45.297][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-29 16:01:45.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:01:45.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:01:45.327][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-29 16:01:45.692][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-29 16:01:46.229][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:01:46.231][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-29 16:01:46.234][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-29 16:01:46.236][private$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[2024-06-29 16:01:46.237][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-29 16:01:46.238][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-29 16:01:46.239][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:01:46.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:01:46.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:46.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:46.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:46.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:46.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:46.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:01:46.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.254][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:46.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:46.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.261][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:01:46.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:46.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.280][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.284][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.290][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:46.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:01:46.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:46.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:46.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:46.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:46.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:46.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:01:46.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.321][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:46.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:01:46.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.327][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:01:46.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:01:46.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.330][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.334][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.340][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:01:46.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:01:46.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:01:46.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:46.372][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-29 16:01:46.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:01:46.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:01:46.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:01:46.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:01:46.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:01:46.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:01:46.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:01:46.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:01:46.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:01:46.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:01:46.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:01:46.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:01:46.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:01:46.402][biodb::testThat]
biodb.INFO [2024-06-29 16:01:46.406][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-29 16:01:46.407][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:46.408][biodb::testThat]
biodb.TRACE[2024-06-29 16:01:46.410][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.411][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.413][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:46.414][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-29 16:01:46.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:46.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:46.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:46.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:46.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:46.445][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:01:46.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:01:46.448][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:01:46.449][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:01:46.450][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-29 16:01:46.848][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-29 16:01:47.243][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:01:47.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-29 16:01:47.247][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-29 16:01:47.252][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-29 16:01:47.267][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.267][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-29 16:01:47.268][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:47.269][biodb::testThat]
biodb.TRACE[2024-06-29 16:01:47.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:47.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:47.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:01:47.326][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:01:47.328][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-29 16:01:47.340][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-29 16:01:47.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-29 16:01:47.342][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-29 16:01:47.358][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.359][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-29 16:01:47.360][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:47.360][biodb::testThat]
biodb.TRACE[2024-06-29 16:01:47.369][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.372][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.375][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:47.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:47.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.378][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:47.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:47.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.408][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:01:47.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:47.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:01:47.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:47.418][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:47.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:01:47.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:47.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:01:47.426][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.427][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-29 16:01:47.427][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:47.428][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.436][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.436][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-29 16:01:47.437][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:47.438][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.444][biodb::testThat]
biodb.INFO [2024-06-29 16:01:47.445][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-29 16:01:47.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:47.446][biodb::testThat]
biodb.DEBUG[2024-06-29 16:01:47.457][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[2024-06-29 16:01:48.013][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 [2024-06-29 16:01:48.417][biodb::testThat]
biodb.INFO [2024-06-29 16:01:48.418][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-29 16:01:48.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:01:48.419][biodb::testThat]
biodb.DEBUG[2024-06-29 16:01:48.799][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-29 16:01:49.205][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:49.206][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:49.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:49.207][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:01:49.208][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:01:49.209][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:01:49.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:01:49.211][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:01:49.211][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:01:49.212][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-29 16:01:49.213][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-29 16:01:49.214][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:01:49.214][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.216][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.217][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-29 16:01:49.225][biodb::testContext]
biodb.INFO [2024-06-29 16:01:49.226][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:01:49.227][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-29 16:01:49.227][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:01:49.228][biodb::testContext]
biodb.INFO [2024-06-29 16:01:49.230][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:01:49.231][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:01:49.234][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:01:49.234][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:01:49.235][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:01:49.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.238][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:01:49.239][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:01:49.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.241][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:01:49.242][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:01:49.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.245][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:01:49.245][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:01:49.246][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:01:49.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.249][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:01:49.249][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:01:49.250][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:01:49.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.253][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:01:49.254][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:01:49.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.256][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:01:49.257][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:01:49.258][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:01:49.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.261][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:01:49.261][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:01:49.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.264][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:01:49.265][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:01:49.266][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:01:49.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.268][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:01:49.269][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:01:49.274][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:01:49.276][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:01:49.277][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:01:49.278][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:01:49.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.281][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:01:49.281][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:01:49.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.284][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:01:49.284][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:01:49.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.287][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:01:49.288][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:01:49.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.290][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:01:49.291][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:01:49.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.294][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:01:49.295][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:01:49.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.296][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[2024-06-29 16:01:49.297][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:01:49.298][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:01:49.316][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:01:49.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.319][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:01:49.320][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:01:49.320][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:01:49.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.323][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:01:49.324][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.325][self$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[2024-06-29 16:01:49.326][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.327][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:49.327][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.328][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.329][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.330][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.330][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:01:49.331][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:49.332][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.332][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:01:49.333][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:49.334][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.335][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.335][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:01:49.335][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:01:49.335][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:01:49.335][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:01:49.335][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:01:49.336][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:49.337][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.338][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:49.339][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.340][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.340][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.341][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.342][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:49.342][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:49.343][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.344][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.345][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:01:49.346][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.347][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:01:49.348][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.348][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:49.349][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.350][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.350][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.351][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.352][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:01:49.353][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:49.353][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.354][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:01:49.355][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:49.355][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.356][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.357][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:01:49.357][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:01:49.357][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:01:49.357][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:01:49.357][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:01:49.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:49.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.360][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:49.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.361][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.362][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.362][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.363][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:49.364][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:49.365][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.365][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.366][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:01:49.367][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.368][self$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[2024-06-29 16:01:49.369][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.370][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:49.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.377][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:01:49.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:49.379][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.379][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:01:49.380][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:49.381][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.381][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.382][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:49.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.385][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:49.385][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.386][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.387][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.387][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:49.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:49.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.390][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.391][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:01:49.392][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.393][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:01:49.394][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.394][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:49.395][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.396][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.396][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.397][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.398][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:01:49.399][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:49.399][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.400][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:01:49.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:49.401][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.402][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.403][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.404][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:01:49.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.405][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.406][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:49.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.408][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.409][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:49.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:49.410][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.411][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.412][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:01:49.413][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.424][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[2024-06-29 16:01:49.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.441][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[2024-06-29 16:01:49.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.465][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.DEBUG[2024-06-29 16:01:49.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.475][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:01:49.476][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:01:49.477][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:01:49.478][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:01:49.479][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:01:49.481][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:01:49.482][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:01:49.483][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:01:49.484][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:01:49.485][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:01:49.487][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:01:49.488][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:01:49.489][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:01:49.490][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:01:49.491][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:01:49.492][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:01:49.493][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:01:49.494][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:01:49.495][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:01:49.496][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:01:49.497][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:01:49.498][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:01:49.499][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:01:49.500][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:01:49.501][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:01:49.502][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:01:49.503][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:01:49.504][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:01:49.505][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:01:49.506][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:01:49.507][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:01:49.508][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:01:49.509][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:01:49.510][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:01:49.511][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:01:49.512][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:01:49.513][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:01:49.514][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:01:49.515][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:01:49.516][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:01:49.517][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:01:49.518][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:01:49.519][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:01:49.521][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:01:49.522][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:01:49.523][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:01:49.523][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:01:49.524][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:01:49.525][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:01:49.526][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:01:49.527][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:01:49.528][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:01:49.529][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:01:49.530][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:01:49.531][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:01:49.533][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:01:49.538][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:01:49.539][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:01:49.540][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:01:49.540][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:01:49.541][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:01:49.542][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:01:49.543][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:01:49.544][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:01:49.545][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:01:49.546][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:01:49.547][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:01:49.548][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:01:49.549][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:01:49.550][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:01:49.551][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:01:49.552][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:01:49.553][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:01:49.554][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:01:49.555][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:01:49.556][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:01:49.557][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:01:49.557][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:01:49.558][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:01:49.560][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:01:49.561][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:01:49.562][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:01:49.563][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:01:49.564][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:01:49.565][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:01:49.566][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:01:49.567][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.568][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.573][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[2024-06-29 16:01:49.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.600][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[2024-06-29 16:01:49.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.641][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[2024-06-29 16:01:49.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.646][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[2024-06-29 16:01:49.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:01:49.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:01:49.652][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-29 16:01:49.653][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:01:49.655][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.656][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-29 16:01:49.657][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.657][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:01:49.658][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.659][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.660][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.661][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-29 16:01:49.662][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:01:49.663][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.664][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-29 16:01:49.664][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:01:49.665][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-29 16:01:49.665][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:01:49.665][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:01:49.665][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:01:49.666][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:01:49.667][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:01:49.667][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:01:49.668][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.669][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:01:49.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:01:49.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:01:49.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:01:49.672][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:01:49.673][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:01:49.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:01:49.674][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:01:49.675][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:01:49.676][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:01:49.678][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:01:49.679][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-29 16:01:49.680][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:01:49.681][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-29 16:01:49.682][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:01:49.683][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:01:49.683][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-29 16:01:49.684][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:01:49.685][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-29 16:01:49.686][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-29 16:01:49.686][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:01:49.687][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:01:49.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:01:49.688][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:01:49.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:01:49.690][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:01:49.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ 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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 12.7.1
* 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 ‘1.9.0’
* 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 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)