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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --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 16:02:57 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 16:03:49 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 52.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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Platform: x86_64-w64-mingw32/x64

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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 16:03:41.781][biodb::testContext]
biodb.INFO [2025-03-22 16:03:41.784][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:41.785][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-22 16:03:41.787][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:41.788][biodb::testContext]
biodb.INFO [2025-03-22 16:03:41.795][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:41.798][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:41.820][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:41.822][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:03:41.823][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:03:41.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.827][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:03:41.844][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:03:41.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:41.848][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:03:41.850][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:03:41.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.854][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:03:41.855][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:03:41.857][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:03:41.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:41.861][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:03:41.862][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:03:41.863][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:03:41.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.868][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:03:41.869][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:03:41.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.873][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:03:41.874][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:03:41.876][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:03:41.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.880][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:03:41.881][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:03:41.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.886][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:03:41.887][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:03:41.888][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:03:41.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.892][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:41.894][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:03:41.895][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:03:41.896][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:03:41.897][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:03:41.898][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:03:41.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.903][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:03:41.904][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:03:41.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.908][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:03:41.910][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:03:41.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.913][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 16:03:41.914][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:03:41.915][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:03:41.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.920][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:03:41.921][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:03:41.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.924][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 16:03:41.925][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:03:41.927][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:03:41.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.931][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:41.932][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:03:41.936][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:03:41.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:41.940][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:03:41.941][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:03:41.942][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:03:41.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:41.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:41.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:41.949][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:03:41.976][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:41.990][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:03:41.997][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:41.998][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:41.999][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.001][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.002][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.003][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.004][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:42.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:42.007][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.008][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:03:42.009][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:42.010][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.011][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.013][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:42.013][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:42.013][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:42.013][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:42.013][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:42.014][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:42.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:42.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.021][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.022][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.023][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:42.024][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:42.025][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.026][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.028][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:03:42.030][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.031][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:42.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:42.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.036][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.037][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.039][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:42.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:42.042][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.043][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:03:42.044][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:42.045][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.046][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.048][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:42.048][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:42.048][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:42.048][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:42.048][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:42.049][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:42.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.051][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.052][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:42.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.056][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.057][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.058][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:42.059][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:42.060][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.061][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.063][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:03:42.065][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.066][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:03:42.067][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.068][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:42.070][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.071][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.072][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.073][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.074][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:42.076][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:42.077][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.078][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:03:42.079][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:42.080][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.081][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.083][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:42.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:42.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.090][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.091][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.092][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.093][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:42.094][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:42.095][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.096][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.098][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:03:42.100][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.101][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:42.102][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.103][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:42.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.106][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.107][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.108][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.109][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:42.111][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:42.112][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.113][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:03:42.114][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:42.115][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.117][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.118][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.119][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:42.120][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.122][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:42.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.126][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.127][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:42.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:42.130][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.132][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.135][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:42.136][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.140][FUN] 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 16:03:42.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.146][FUN] 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 16:03:42.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.151][FUN] 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 16:03:42.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.157][FUN] 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 16:03:42.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.162][FUN] 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 16:03:42.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.168][FUN] 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 16:03:42.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:42.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.178][FUN] 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 16:03:42.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.184][FUN] 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 16:03:42.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:42.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.195][FUN] 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 16:03:42.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.201][FUN] 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 16:03:42.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.211][FUN] 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 16:03:42.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.216][FUN] 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 16:03:42.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.221][FUN] 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 16:03:42.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.227][FUN] 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 16:03:42.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:42.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.235][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:03:42.240][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:03:42.241][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:03:42.243][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:03:42.244][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:03:42.246][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:03:42.248][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:42.249][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:42.251][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:03:42.252][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:03:42.254][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:03:42.255][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:03:42.257][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:42.259][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:42.260][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:03:42.262][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:03:42.263][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:03:42.265][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:03:42.266][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:03:42.268][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:03:42.269][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:03:42.271][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:03:42.273][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:03:42.274][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:03:42.276][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:03:42.277][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:03:42.279][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:03:42.280][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:03:42.282][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:03:42.283][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:03:42.285][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:03:42.287][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:03:42.288][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:03:42.290][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:03:42.291][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:03:42.293][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:03:42.294][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:03:42.296][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:03:42.297][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:03:42.299][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:03:42.301][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:03:42.302][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:03:42.304][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:03:42.305][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:03:42.307][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:03:42.308][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:03:42.310][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:03:42.312][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:03:42.313][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:03:42.315][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:03:42.316][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:03:42.318][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:03:42.319][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:03:42.321][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:03:42.323][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:03:42.324][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:03:42.326][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:03:42.327][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:03:42.329][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:03:42.330][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:03:42.332][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:03:42.334][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:03:42.335][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:03:42.337][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:03:42.338][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:03:42.340][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:03:42.341][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:03:42.343][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:03:42.344][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:03:42.346][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:03:42.348][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:03:42.349][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:03:42.351][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:03:42.352][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:03:42.354][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:03:42.355][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:03:42.357][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:03:42.358][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:03:42.360][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:03:42.362][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:03:42.363][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:03:42.365][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:03:42.366][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:03:42.402][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:03:42.404][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:42.407][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:42.408][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.410][FUN] 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 16:03:42.411][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.432][FUN] 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 16:03:42.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.442][FUN] 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 16:03:42.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.451][FUN] 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 16:03:42.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.458][FUN] 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 16:03:42.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.466][FUN] 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 16:03:42.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:42.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.481][FUN] 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 16:03:42.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.483][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 16:03:42.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.488][FUN] 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 16:03:42.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.496][FUN] 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 16:03:42.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.498][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 16:03:42.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.503][FUN] 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 16:03:42.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.510][FUN] 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 16:03:42.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.518][FUN] 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 16:03:42.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.525][FUN] 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 16:03:42.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.533][FUN] 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 16:03:42.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.540][FUN] 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 16:03:42.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.547][FUN] 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 16:03:42.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:42.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:42.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:42.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:42.560][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:42.569][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:03:42.571][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.572][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-22 16:03:42.573][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.575][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:42.576][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.577][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.578][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.579][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.580][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-22 16:03:42.582][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:42.583][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.584][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-22 16:03:42.585][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:42.586][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-22 16:03:42.586][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:03:42.586][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:03:42.586][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:03:42.588][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:42.589][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:42.590][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:03:42.591][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.592][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.593][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:42.594][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:42.595][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:42.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:42.598][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:03:42.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:42.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:42.601][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:42.602][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:42.608][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:03:42.633][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:03:42.634][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-22 16:03:42.638][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:03:42.642][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-22 16:03:42.645][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:42.646][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:42.648][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-22 16:03:42.658][biodb::testThat]
biodb.INFO [2025-03-22 16:03:42.661][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-22 16:03:42.662][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:42.663][biodb::testThat]
biodb.TRACE[2025-03-22 16:03:42.668][loadFileContents] Loaded 1 files from cache: [1]: "F:/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 16:03:42.670][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:03:42.673][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:03:42.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:42.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:42.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:42.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:42.699][FUN] 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 16:03:42.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:42.701][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.TRACE[2025-03-22 16:03:42.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.737][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:42.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:42.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.752][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:42.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:42.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.762][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:03:42.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.767][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.772][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.777][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.782][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:03:42.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:42.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:42.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:42.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:42.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:42.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:42.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:42.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.890][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:42.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:42.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.895][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:42.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:42.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.899][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:42.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:42.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.909][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:42.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:42.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:42.943][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-03-22 16:03:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:42.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:42.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:42.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:42.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:42.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:42.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.960][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:42.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:42.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:42.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:42.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:42.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:42.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.008][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.050][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.055][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.060][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.088][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.090][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.092][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.123][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.126][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.142][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.152][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.157][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.161][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.163][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.165][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.166][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.181][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.186][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.191][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.195][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.197][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.200][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.215][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.216][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.218][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.225][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.226][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.227][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.229][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.235][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.236][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.245][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.246][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.266][loadFileContents] Loaded 1 files from cache: [1]: "F:/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 16:03:43.300][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:03:43.302][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:03:43.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:43.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:43.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:43.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:43.314][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 16:03:43.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:43.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:03:43.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.324][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.334][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:03:43.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:43.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.339][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.344][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.353][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:43.387][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-03-22 16:03:43.406][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:43.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:43.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.412][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:43.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:43.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.417][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:43.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:43.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.421][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:43.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:43.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.442][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.483][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.488][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.493][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:43.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.529][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.562][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.563][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.566][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.581][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.586][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.601][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.602][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.606][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.620][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:43.622][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:43.623][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.624][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.631][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.632][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:43.633][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:43.641][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:43.642][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:43.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:43.644][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:43.656][biodb::testThat]
biodb.INFO [2025-03-22 16:03:43.657][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-22 16:03:43.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:43.660][biodb::testThat]
biodb.DEBUG[2025-03-22 16:03:43.662][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-03-22 16:03:43.669][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-22 16:03:43.691][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-03-22 16:03:43.694][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-03-22 16:03:43.696][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-22 16:03:43.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-22 16:03:43.698][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-03-22 16:03:43.700][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:03:43.701][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-22 16:03:43.702][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-22 16:03:43.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:43.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:43.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:43.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:43.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:43.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:43.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:43.721][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-03-22 16:03:43.739][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:03:43.741][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:03:43.742][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-03-22 16:03:44.286][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2025-03-22 16:03:44.287][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-22 16:03:44.289][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-22 16:03:44.290][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-03-22 16:03:44.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:03:44.885][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-03-22 16:03:44.900][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-03-22 16:03:44.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:44.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:44.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:44.921][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:44.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:44.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:44.925][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 16:03:44.943][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-03-22 16:03:44.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:03:44.959][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:03:44.972][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-03-22 16:03:45.192][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2025-03-22 16:03:45.193][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-22 16:03:45.195][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-22 16:03:45.196][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-03-22 16:03:45.596][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:03:45.599][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-03-22 16:03:45.604][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-03-22 16:03:45.607][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2025-03-22 16:03:45.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-22 16:03:45.611][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-03-22 16:03:45.613][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:03:45.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:45.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:45.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:45.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:45.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:45.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:45.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:03:45.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.640][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:45.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:45.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.650][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:03:45.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:45.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.679][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.684][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.693][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:45.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:03:45.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:45.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:45.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:45.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:45.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:45.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:03:45.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.733][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:45.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:03:45.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.748][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:03:45.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:03:45.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.753][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.758][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.767][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:03:45.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:03:45.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:03:45.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:45.816][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-03-22 16:03:45.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:45.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:45.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:45.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:45.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:45.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:45.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:45.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:03:45.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:45.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:03:45.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:45.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:03:45.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:45.862][biodb::testThat]
biodb.INFO [2025-03-22 16:03:45.863][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-22 16:03:45.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:45.866][biodb::testThat]
biodb.TRACE[2025-03-22 16:03:45.874][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.877][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.878][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:45.880][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-03-22 16:03:45.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:45.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:45.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:45.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:45.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:45.927][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:03:45.929][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:03:45.932][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:03:45.934][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:03:45.935][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-03-22 16:03:46.148][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2025-03-22 16:03:46.150][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-03-22 16:03:46.151][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-03-22 16:03:46.153][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-03-22 16:03:46.583][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:03:46.585][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-03-22 16:03:46.590][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-03-22 16:03:46.597][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-03-22 16:03:46.619][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.621][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-22 16:03:46.622][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:46.623][biodb::testThat]
biodb.TRACE[2025-03-22 16:03:46.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:46.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:46.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:46.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:46.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:46.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:46.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:03:46.696][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:03:46.699][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-22 16:03:46.713][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-03-22 16:03:46.715][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-22 16:03:46.721][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-03-22 16:03:46.752][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.753][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-22 16:03:46.754][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:46.756][biodb::testThat]
biodb.TRACE[2025-03-22 16:03:46.768][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.773][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.778][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:46.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:46.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:46.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:46.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:03:46.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.826][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:46.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:03:46.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:46.831][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:46.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:03:46.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:46.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:46.849][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.850][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-22 16:03:46.851][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:46.852][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.864][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.866][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-22 16:03:46.867][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:46.868][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.879][biodb::testThat]
biodb.INFO [2025-03-22 16:03:46.881][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-22 16:03:46.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:46.883][biodb::testThat]
biodb.DEBUG[2025-03-22 16:03:46.897][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 16:03:47.111][getUrlContent] Use base::url() 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 16:03:47.546][biodb::testThat]
biodb.INFO [2025-03-22 16:03:47.548][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-22 16:03:47.549][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:03:47.550][biodb::testThat]
biodb.DEBUG[2025-03-22 16:03:47.778][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 16:03:48.215][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:48.217][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:48.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:48.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:03:48.220][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:03:48.222][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:03:48.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:03:48.224][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:03:48.225][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:03:48.227][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-22 16:03:48.228][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-22 16:03:48.229][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:03:48.230][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.238][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.240][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-22 16:03:48.252][biodb::testContext]
biodb.INFO [2025-03-22 16:03:48.253][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:48.254][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-22 16:03:48.255][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:03:48.257][biodb::testContext]
biodb.INFO [2025-03-22 16:03:48.259][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:48.262][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:48.267][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:48.268][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:03:48.269][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:03:48.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.274][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:03:48.275][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:03:48.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.280][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:03:48.281][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:03:48.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.285][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:03:48.287][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:03:48.288][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:03:48.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.292][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:03:48.293][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:03:48.295][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:03:48.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.299][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:03:48.300][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:03:48.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.305][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:03:48.306][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:03:48.307][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:03:48.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.311][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:03:48.313][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:03:48.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.317][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:03:48.318][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:03:48.320][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:03:48.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.324][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:48.325][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:03:48.327][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:03:48.328][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:03:48.329][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:03:48.330][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:03:48.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.335][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:03:48.336][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:03:48.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.340][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:03:48.342][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:03:48.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.351][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:03:48.353][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:03:48.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.357][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:03:48.358][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:03:48.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.363][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:03:48.364][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:03:48.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.368][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:03:48.370][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:03:48.373][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:03:48.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.378][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:03:48.379][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:03:48.380][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:03:48.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.385][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:03:48.387][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.388][self$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 16:03:48.389][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:48.392][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.393][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.394][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.395][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.397][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:48.398][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:48.399][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.400][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:03:48.402][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:48.403][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.404][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.405][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:48.405][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:48.405][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:48.405][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:48.405][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:48.406][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:48.408][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:48.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.413][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.415][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.417][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:48.418][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:48.419][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.420][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.422][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:03:48.424][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.425][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:48.426][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.427][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:48.428][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.430][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.431][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.432][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.433][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:48.435][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:48.436][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.437][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:03:48.438][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:48.439][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.441][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.442][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:48.442][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:03:48.442][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:03:48.442][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:03:48.442][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:03:48.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:48.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:48.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.449][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.451][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.452][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:48.453][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:48.455][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.456][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.457][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:03:48.459][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.460][self$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 16:03:48.467][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.468][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:48.469][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.472][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.473][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.474][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:03:48.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:48.477][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.478][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:03:48.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:48.481][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.482][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.483][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.484][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:48.485][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.488][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:48.489][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.490][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.492][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.494][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:48.495][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:48.496][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.497][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.498][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:03:48.500][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.502][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:03:48.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:48.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.509][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.510][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:03:48.511][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:48.513][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.514][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:03:48.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:48.516][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.517][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.519][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:03:48.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:48.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.528][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.529][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:48.530][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:48.531][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.533][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.534][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:48.535][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.540][FUN] 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 16:03:48.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.545][FUN] 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 16:03:48.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.551][FUN] 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 16:03:48.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.556][FUN] 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 16:03:48.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.562][FUN] 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 16:03:48.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.583][FUN] 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 16:03:48.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.589][FUN] 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 16:03:48.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.606][FUN] 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 16:03:48.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.622][FUN] 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 16:03:48.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.628][FUN] 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 16:03:48.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.633][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 16:03:48.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.636][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:03:48.638][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:03:48.640][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:03:48.641][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:03:48.643][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:03:48.645][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:03:48.646][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:48.648][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:48.649][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:03:48.651][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:03:48.652][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:03:48.654][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:03:48.656][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:03:48.657][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:03:48.659][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:03:48.660][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:03:48.662][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:03:48.664][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:03:48.665][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:03:48.667][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:03:48.668][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:03:48.670][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:03:48.671][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:03:48.673][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:03:48.675][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:03:48.676][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:03:48.678][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:03:48.679][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:03:48.686][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:03:48.688][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:03:48.689][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:03:48.691][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:03:48.692][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:03:48.694][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:03:48.696][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:03:48.697][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:03:48.699][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:03:48.700][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:03:48.702][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:03:48.704][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:03:48.705][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:03:48.707][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:03:48.708][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:03:48.710][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:03:48.712][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:03:48.713][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:03:48.715][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:03:48.716][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:03:48.718][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:03:48.720][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:03:48.721][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:03:48.723][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:03:48.724][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:03:48.726][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:03:48.728][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:03:48.729][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:03:48.731][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:03:48.732][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:03:48.734][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:03:48.736][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:03:48.737][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:03:48.739][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:03:48.740][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:03:48.742][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:03:48.743][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:03:48.745][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:03:48.747][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:03:48.748][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:03:48.750][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:03:48.751][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:03:48.753][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:03:48.755][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:03:48.756][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:03:48.758][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:03:48.759][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:03:48.761][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:03:48.762][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:03:48.764][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:03:48.766][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:03:48.767][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:03:48.769][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:03:48.770][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:03:48.772][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:03:48.774][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:03:48.776][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:03:48.777][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:03:48.778][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.779][FUN] 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 16:03:48.781][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.793][FUN] 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 16:03:48.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.800][FUN] 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 16:03:48.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.808][FUN] 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 16:03:48.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.815][FUN] 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 16:03:48.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.823][FUN] 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 16:03:48.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.830][FUN] 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 16:03:48.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.838][FUN] 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 16:03:48.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.846][FUN] 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 16:03:48.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.853][FUN] 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 16:03:48.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:48.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.861][FUN] 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 16:03:48.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.868][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 16:03:48.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.870][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 16:03:48.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.876][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 16:03:48.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.878][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 16:03:48.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.883][FUN] 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 16:03:48.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.885][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 16:03:48.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.891][FUN] 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 16:03:48.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:03:48.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.905][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 16:03:48.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.911][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 16:03:48.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.913][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 16:03:48.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:03:48.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.918][FUN] 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 16:03:48.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.921][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 16:03:48.924][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-22 16:03:48.926][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:03:48.928][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.929][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-22 16:03:48.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:03:48.933][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.934][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.935][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.936][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.937][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-22 16:03:48.939][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:03:48.940][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.941][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-22 16:03:48.942][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:03:48.943][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-22 16:03:48.943][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:03:48.943][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:03:48.943][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:03:48.945][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:03:48.946][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:03:48.947][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:03:48.948][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.949][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.950][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:03:48.952][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:03:48.953][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:03:48.954][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:03:48.955][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:03:48.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:03:48.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:03:48.958][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:03:48.960][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:03:48.961][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:03:48.965][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:03:48.966][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-22 16:03:48.967][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:03:48.969][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-22 16:03:48.971][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:48.972][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:03:48.973][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-22 16:03:48.974][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:03:48.976][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-22 16:03:48.977][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-22 16:03:48.978][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:03:48.979][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:03:48.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:03:48.981][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:03:48.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:03:48.983][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:03:48.985][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".
[ 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --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 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'biodbExpasy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/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)