Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-22 23:55 -0400 (Sat, 22 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4763
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4494
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4521
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/32HostnameOS / ArchCHECK
biodbExpasy 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-22 09:55 -0400 (Sat, 22 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_20
git_last_commit: 4403c2f
git_last_commit_date: 2024-10-29 11:09:35 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on nebbiolo2

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

raw results


Summary

Package: biodbExpasy
Version: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
StartedAt: 2025-03-22 16:01:52 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 16:02:36 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 44.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2025-03-22 16:02:28.363][biodb::testContext]
biodb.INFO [2025-03-22 16:02:28.365][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:28.366][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-22 16:02:28.367][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:28.368][biodb::testContext]
biodb.INFO [2025-03-22 16:02:28.375][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:28.377][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:28.384][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:28.385][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:02:28.386][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:02:28.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.390][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:02:28.410][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:02:28.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.414][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:02:28.415][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:02:28.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.419][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:02:28.420][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:02:28.421][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:02:28.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.424][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:02:28.425][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:02:28.426][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:02:28.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.430][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:02:28.431][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:02:28.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.435][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:02:28.436][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:02:28.437][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:02:28.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.441][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:02:28.442][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:02:28.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.444][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[2025-03-22 16:02:28.445][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:02:28.446][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:02:28.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:02:28.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.451][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:28.452][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:02:28.453][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:02:28.454][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:02:28.455][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:02:28.456][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:02:28.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.460][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:02:28.461][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:02:28.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.465][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:02:28.466][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:02:28.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.470][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:02:28.471][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:02:28.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.475][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:02:28.476][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:02:28.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.479][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:02:28.480][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:02:28.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.484][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:28.485][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:02:28.489][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:02:28.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.493][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:02:28.494][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:02:28.495][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:02:28.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.502][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:02:28.538][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.561][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:02:28.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:28.563][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.564][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.565][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.567][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:28.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:28.569][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.570][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:02:28.571][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:28.571][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.572][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.573][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:28.573][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:28.573][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:28.573][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:28.573][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:28.574][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:28.575][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.577][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:28.577][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.578][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.579][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.580][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.581][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:28.582][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:28.583][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.583][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.584][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:02:28.586][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.587][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:28.588][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.589][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:28.590][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.590][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.591][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.592][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.593][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:28.594][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:28.595][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.596][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:02:28.597][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:28.597][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.598][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.599][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:28.599][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:28.599][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:28.599][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:28.599][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:28.600][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:28.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:28.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.605][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.606][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.607][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:28.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:28.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.609][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.610][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:02:28.612][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.613][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:02:28.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:28.615][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.616][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.617][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.619][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:28.620][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:28.621][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.621][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:02:28.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:28.623][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.625][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.626][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:28.627][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:28.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.631][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.632][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:28.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:28.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.635][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.636][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:02:28.638][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.638][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:28.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:28.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.645][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:28.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:28.646][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.647][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:02:28.648][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:28.649][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.650][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:28.651][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.652][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:28.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:28.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:28.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:28.657][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:28.657][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:28.659][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:28.660][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:28.661][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:28.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:28.665][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.678][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.733][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:02:28.737][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:02:28.739][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:02:28.740][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:02:28.741][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:02:28.749][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:02:28.752][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:28.754][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:28.755][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:28.757][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:02:28.758][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:02:28.759][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:02:28.761][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:28.762][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:28.764][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:02:28.765][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:02:28.766][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:02:28.768][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:02:28.769][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:02:28.770][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:02:28.772][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:02:28.773][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:02:28.775][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:02:28.776][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:02:28.777][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:02:28.779][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:02:28.780][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:02:28.781][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:02:28.783][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:02:28.784][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:02:28.786][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:02:28.787][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:02:28.788][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:02:28.790][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:02:28.809][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:02:28.810][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:02:28.811][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:02:28.813][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:02:28.814][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:02:28.815][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:02:28.817][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:02:28.818][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:02:28.820][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:02:28.821][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:02:28.823][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:02:28.824][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:02:28.825][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:02:28.827][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:02:28.828][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:02:28.830][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:02:28.831][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:02:28.832][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:02:28.834][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:02:28.835][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:02:28.837][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:02:28.838][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:02:28.840][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:02:28.841][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:02:28.843][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:02:28.845][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:02:28.846][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:02:28.847][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:02:28.849][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:02:28.850][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:02:28.851][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:02:28.853][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:02:28.854][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:02:28.855][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:02:28.857][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:02:28.858][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:02:28.860][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:02:28.861][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:02:28.862][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:02:28.864][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:02:28.865][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:02:28.866][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:02:28.868][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:02:28.869][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:02:28.870][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:02:28.872][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:02:28.873][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:02:28.874][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:02:28.876][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:02:28.882][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:02:28.884][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:28.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:28.888][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.890][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:28.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:28.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:28.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:28.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:28.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:28.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:28.998][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:29.008][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:29.010][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:29.011][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-22 16:02:29.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:29.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:29.013][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:29.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:29.015][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:29.016][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:29.017][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-22 16:02:29.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:29.019][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:29.020][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-22 16:02:29.020][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:29.021][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-22 16:02:29.021][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:29.021][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:29.021][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:29.022][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:29.023][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:29.024][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:02:29.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:29.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:29.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:29.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:29.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:29.029][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:29.030][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:02:29.031][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:29.032][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:29.032][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:29.033][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:29.039][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:29.064][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:29.065][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-22 16:02:29.069][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:29.072][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-22 16:02:29.076][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:29.077][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:29.078][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-22 16:02:29.086][biodb::testThat]
biodb.INFO [2025-03-22 16:02:29.087][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-22 16:02:29.087][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:29.088][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:29.091][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2025-03-22 16:02:29.093][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:02:29.096][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:02:29.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:29.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:29.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:29.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:29.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:29.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:29.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:29.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.156][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.170][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.178][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:29.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.181][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.185][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.189][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.192][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:29.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.211][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.260][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.263][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.271][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:29.304][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-03-22 16:02:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.314][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.349][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.378][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.381][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.385][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.405][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.406][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.406][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.407][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.429][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.430][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.442][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.445][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.449][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.452][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.453][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.455][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.456][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.465][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.469][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.472][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.476][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.477][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.478][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.479][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.479][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.512][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.513][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.518][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.519][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.521][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.524][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.525][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.531][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.532][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.532][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.548][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2025-03-22 16:02:29.579][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:02:29.581][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:02:29.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:29.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:29.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:29.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:29.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:29.589][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:29.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.603][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:29.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:29.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.607][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.610][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.617][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:29.642][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-03-22 16:02:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:29.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:29.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:29.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.681][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.714][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.721][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:29.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.749][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.773][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.774][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.775][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.786][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.789][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.793][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.796][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.797][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.798][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.800][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.809][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:29.810][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:29.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.812][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.816][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.817][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:29.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.818][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:29.822][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:29.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:29.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:29.824][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:29.830][biodb::testThat]
biodb.INFO [2025-03-22 16:02:29.831][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-22 16:02:29.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:29.833][biodb::testThat]
biodb.DEBUG[2025-03-22 16:02:29.835][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-03-22 16:02:29.841][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-22 16:02:29.845][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-03-22 16:02:29.846][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-03-22 16:02:29.847][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-22 16:02:29.848][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-22 16:02:29.849][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-03-22 16:02:29.850][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:02:29.851][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-22 16:02:29.852][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-22 16:02:29.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:29.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:29.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:29.862][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:29.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:29.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:29.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:29.866][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-03-22 16:02:29.889][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:02:29.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:02:29.891][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-03-22 16:02:30.807][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-03-22 16:02:31.340][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:02:31.342][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-03-22 16:02:31.355][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-03-22 16:02:31.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:31.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:31.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:31.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:31.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:31.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:31.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:31.384][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-03-22 16:02:31.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:02:31.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:02:31.423][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-03-22 16:02:31.858][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-03-22 16:02:32.219][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:02:32.221][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-03-22 16:02:32.223][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-03-22 16:02:32.226][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2025-03-22 16:02:32.227][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-22 16:02:32.228][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-03-22 16:02:32.229][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:02:32.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:32.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:32.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:32.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:32.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:32.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:32.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.248][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:32.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.259][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:32.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:32.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.283][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.286][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:32.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:32.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:32.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:32.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:32.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:32.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:32.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:32.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.321][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:32.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:32.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.328][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:32.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:32.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.332][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.335][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.342][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:32.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:32.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:32.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:32.378][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-03-22 16:02:32.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:32.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:32.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:32.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:32.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:32.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:32.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:32.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:32.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:32.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:32.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:32.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:32.415][biodb::testThat]
biodb.INFO [2025-03-22 16:02:32.416][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-22 16:02:32.417][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:32.418][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:32.420][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.421][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.423][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:32.424][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-03-22 16:02:32.446][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.449][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:32.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:32.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:32.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:32.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:32.459][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:02:32.460][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:02:32.463][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:02:32.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:02:32.465][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-03-22 16:02:32.931][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-03-22 16:02:33.326][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:02:33.331][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-03-22 16:02:33.338][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-03-22 16:02:33.351][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-03-22 16:02:33.377][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.379][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-22 16:02:33.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:33.382][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:33.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:33.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:33.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:33.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:33.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:33.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:33.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:33.444][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:02:33.447][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-22 16:02:33.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-03-22 16:02:33.470][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-22 16:02:33.471][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-03-22 16:02:33.485][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.486][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-22 16:02:33.487][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:33.488][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:33.496][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.503][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:33.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:33.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:33.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.539][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.543][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:33.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.546][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:33.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:33.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:33.550][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:33.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:33.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:33.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:33.557][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.558][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-22 16:02:33.559][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:33.560][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.575][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.576][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-22 16:02:33.576][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:33.577][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.584][biodb::testThat]
biodb.INFO [2025-03-22 16:02:33.585][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-22 16:02:33.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:33.586][biodb::testThat]
biodb.DEBUG[2025-03-22 16:02:33.599][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2025-03-22 16:02:34.143][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2025-03-22 16:02:34.579][biodb::testThat]
biodb.INFO [2025-03-22 16:02:34.581][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-22 16:02:34.582][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:34.584][biodb::testThat]
biodb.DEBUG[2025-03-22 16:02:34.961][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-03-22 16:02:35.617][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:35.618][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:35.619][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:35.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:35.621][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:35.622][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:35.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:35.624][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:35.626][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:02:35.627][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-22 16:02:35.628][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-22 16:02:35.629][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:02:35.630][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:35.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:35.632][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.634][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-22 16:02:35.645][biodb::testContext]
biodb.INFO [2025-03-22 16:02:35.646][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:35.647][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-22 16:02:35.648][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:35.649][biodb::testContext]
biodb.INFO [2025-03-22 16:02:35.651][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:35.652][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:35.656][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:35.657][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:02:35.658][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:02:35.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.661][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:02:35.662][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:02:35.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.666][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:02:35.667][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:02:35.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.671][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:02:35.672][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:02:35.673][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:02:35.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.676][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:02:35.677][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:02:35.678][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:02:35.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.682][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:02:35.683][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:02:35.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.686][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:02:35.687][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:02:35.688][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:02:35.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.692][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:02:35.693][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:02:35.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.696][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:02:35.697][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:02:35.698][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:02:35.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.702][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:35.703][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:02:35.704][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:02:35.705][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:02:35.706][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:02:35.707][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:02:35.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.710][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:02:35.711][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:02:35.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.715][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:02:35.716][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:02:35.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.719][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:02:35.720][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:02:35.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.724][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:02:35.725][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:02:35.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.728][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:02:35.729][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:02:35.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.733][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:35.734][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:02:35.738][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:02:35.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.741][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:02:35.742][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:02:35.743][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:02:35.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.747][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:02:35.749][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.750][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:02:35.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.752][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:35.753][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.755][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.757][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:35.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:35.758][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.759][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:02:35.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:35.761][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:35.763][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:35.764][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:35.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.767][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:35.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.770][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.776][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:35.778][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:35.779][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.780][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.781][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:02:35.783][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.784][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:35.785][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.785][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:35.786][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.788][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.789][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.790][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:35.791][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:35.792][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.793][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:02:35.794][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:35.795][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.795][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.796][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:35.796][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:35.796][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:35.796][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:35.796][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:35.797][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:35.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.799][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:35.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.802][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.803][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.804][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:35.805][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:35.806][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.807][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.808][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:02:35.809][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.810][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:02:35.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:35.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.815][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.816][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:35.817][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:35.818][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.819][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:02:35.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:35.821][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.823][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:35.824][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.825][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.826][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:35.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.828][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.829][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.830][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:35.831][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:35.832][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.833][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.834][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:02:35.835][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.836][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:35.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.838][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:35.839][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.840][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.841][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.842][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.842][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:35.843][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:35.844][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.845][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:02:35.846][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:35.847][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:35.849][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.850][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:35.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.852][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:35.853][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:35.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:35.855][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:35.855][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.856][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:35.857][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:35.858][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:35.859][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:35.860][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:35.861][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.881][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[2025-03-22 16:02:35.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:35.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:35.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:35.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:35.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:35.930][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:02:35.931][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:02:35.933][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:02:35.934][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:02:35.939][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:02:35.940][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:02:35.942][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:35.943][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:35.944][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:35.945][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:02:35.947][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:02:35.948][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:02:35.949][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:35.951][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:35.952][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:02:35.953][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:02:35.954][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:02:35.956][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:02:35.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:02:35.958][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:02:35.959][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:02:35.961][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:02:35.962][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:02:35.963][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:02:35.964][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:02:35.966][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:02:35.967][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:02:35.968][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:02:35.969][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:02:35.971][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:02:35.972][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:02:35.973][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:02:35.974][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:02:35.976][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:02:35.977][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:02:35.978][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:02:35.979][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:02:35.981][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:02:35.982][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:02:35.983][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:02:35.984][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:02:35.986][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:02:35.987][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:02:35.988][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:02:35.989][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:02:35.991][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:02:35.992][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:02:35.993][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:02:35.994][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:02:35.996][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:02:35.997][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:02:35.998][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:02:35.999][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:02:36.001][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:02:36.002][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:02:36.003][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:02:36.004][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:02:36.006][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:02:36.007][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:02:36.008][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:02:36.009][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:02:36.010][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:02:36.012][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:02:36.013][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:02:36.014][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:02:36.015][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:02:36.017][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:02:36.018][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:02:36.019][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:02:36.020][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:02:36.022][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:02:36.023][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:02:36.024][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:02:36.025][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:02:36.027][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:02:36.028][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:02:36.029][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:02:36.030][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:02:36.032][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:02:36.033][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:02:36.034][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:02:36.035][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:02:36.037][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:02:36.038][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:02:36.039][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:36.040][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:36.041][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.043][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.075][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[2025-03-22 16:02:36.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.118][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[2025-03-22 16:02:36.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.129][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[2025-03-22 16:02:36.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:36.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:36.147][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:36.148][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:36.150][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:36.151][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-22 16:02:36.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:36.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:36.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:36.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:36.156][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:36.156][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:36.157][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-22 16:02:36.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:36.159][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:36.160][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-22 16:02:36.161][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:36.162][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-22 16:02:36.162][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:36.162][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:36.162][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:36.163][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:36.164][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:36.165][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:02:36.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:36.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:36.167][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:36.168][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:36.169][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:36.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:36.170][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:02:36.171][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:36.172][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:36.173][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:36.174][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:36.175][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:36.178][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:36.179][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-22 16:02:36.180][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:36.182][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-22 16:02:36.183][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:36.183][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:36.184][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-22 16:02:36.185][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:02:36.186][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-22 16:02:36.187][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-22 16:02:36.188][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:02:36.189][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:36.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:36.190][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:36.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:36.192][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:36.193][FUN] Functions in observer 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:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)