Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-01 23:55 -0500 (Sat, 01 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4768
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4503
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4526
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: 2025-03-01 09:55 -0500 (Sat, 01 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 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on merida1

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

raw results


Summary

Package: biodbExpasy
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
StartedAt: 2025-03-01 16:01:22 -0500 (Sat, 01 Mar 2025)
EndedAt: 2025-03-01 16:02:26 -0500 (Sat, 01 Mar 2025)
EllapsedTime: 64.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
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 [2025-03-01 16:02:16.719][biodb::testContext]
biodb.INFO [2025-03-01 16:02:16.724][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:02:16.725][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-01 16:02:16.727][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:02:16.728][biodb::testContext]
biodb.INFO [2025-03-01 16:02:16.736][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:02:16.739][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:02:16.747][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:02:16.749][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:02:16.764][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:02:16.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.770][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:02:16.795][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:02:16.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.800][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:02:16.801][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:02:16.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.806][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:02:16.807][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:02:16.809][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:02:16.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.814][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:02:16.815][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:02:16.816][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:02:16.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.821][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:02:16.822][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:02:16.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.825][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[2025-03-01 16:02:16.826][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:02:16.828][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:02:16.829][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:02:16.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.833][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:02:16.835][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:02:16.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.839][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:02:16.841][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:02:16.842][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:02:16.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.847][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:02:16.848][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:02:16.849][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:02:16.850][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:02:16.852][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:02:16.853][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:02:16.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.857][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:02:16.859][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:02:16.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.863][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:02:16.865][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:02:16.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.869][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:02:16.871][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:02:16.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.875][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:02:16.876][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:02:16.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.881][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:02:16.882][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:02:16.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.887][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:02:16.888][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:02:16.899][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:02:16.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.904][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:02:16.905][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:02:16.906][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:02:16.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:16.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:16.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:16.914][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:02:16.958][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:16.980][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:02:16.981][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:16.983][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:16.984][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:16.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:16.987][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:16.993][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:16.994][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:02:16.996][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:16.997][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:16.998][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:02:16.999][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:17.000][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.002][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.003][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:02:17.003][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:02:17.003][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:02:17.003][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:02:17.003][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:02:17.004][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:17.005][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.008][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:17.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.011][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.012][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.014][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:17.015][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:17.016][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.017][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.018][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:02:17.021][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.022][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:02:17.023][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.024][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:17.026][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.030][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:02:17.032][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:17.033][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.034][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:02:17.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:17.037][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.039][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:02:17.039][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:02:17.039][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:02:17.039][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:02:17.039][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:02:17.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:17.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.044][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:17.045][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.046][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.047][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.049][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.050][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:17.051][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:17.052][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.053][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.055][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:02:17.057][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.058][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:02:17.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.061][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:17.062][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.063][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.064][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.066][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.067][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:02:17.068][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:17.069][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.071][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:02:17.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:17.073][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.074][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.075][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.077][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:17.078][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.079][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.080][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:17.081][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.084][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.085][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.086][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:17.087][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:17.088][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.090][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.091][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:02:17.093][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.094][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:02:17.096][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.097][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:17.098][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.099][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.101][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.102][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.103][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:02:17.104][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:17.105][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.107][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:02:17.108][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:17.109][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.112][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.113][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:17.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.116][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:17.117][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.118][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.120][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.121][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.122][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:17.123][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:17.124][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.125][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.130][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:02:17.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.143][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[2025-03-01 16:02:17.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.154][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[2025-03-01 16:02:17.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.159][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[2025-03-01 16:02:17.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.170][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[2025-03-01 16:02:17.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.213][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[2025-03-01 16:02:17.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.229][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[2025-03-01 16:02:17.230][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:02:17.236][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:02:17.238][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:02:17.239][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:02:17.241][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:02:17.243][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:02:17.244][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:02:17.246][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:02:17.248][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:02:17.250][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:02:17.251][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:02:17.253][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:02:17.255][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:02:17.256][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:02:17.258][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:02:17.260][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:02:17.262][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:02:17.263][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:02:17.265][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:02:17.267][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:02:17.268][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:02:17.270][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:02:17.272][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:02:17.273][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:02:17.275][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:02:17.277][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:02:17.278][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:02:17.280][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:02:17.282][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:02:17.284][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:02:17.285][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:02:17.287][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:02:17.289][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:02:17.290][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:02:17.292][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:02:17.294][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:02:17.296][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:02:17.297][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:02:17.299][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:02:17.301][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:02:17.303][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:02:17.304][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:02:17.306][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:02:17.308][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:02:17.309][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:02:17.311][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:02:17.313][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:02:17.315][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:02:17.317][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:02:17.318][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:02:17.320][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:02:17.322][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:02:17.323][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:02:17.325][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:02:17.327][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:02:17.328][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:02:17.330][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:02:17.332][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:02:17.334][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:02:17.336][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:02:17.338][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:02:17.340][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:02:17.341][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:02:17.343][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:02:17.345][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:02:17.346][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:02:17.348][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:02:17.350][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:02:17.352][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:02:17.353][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:02:17.355][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:02:17.357][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:02:17.358][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:02:17.360][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:02:17.362][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:02:17.363][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:02:17.365][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:02:17.367][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:02:17.368][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:02:17.370][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:02:17.372][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:02:17.373][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:02:17.375][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:02:17.382][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:02:17.384][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:02:17.388][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:02:17.389][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.391][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:17.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:17.532][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-01 16:02:17.544][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-01 16:02:17.547][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.548][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-01 16:02:17.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:17.552][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.553][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.554][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.555][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.556][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-01 16:02:17.558][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:17.559][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.560][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-01 16:02:17.561][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:17.562][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-01 16:02:17.562][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-01 16:02:17.562][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-01 16:02:17.562][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-01 16:02:17.564][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:17.565][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:02:17.566][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:02:17.567][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.570][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:17.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:17.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:17.573][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:17.575][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-01 16:02:17.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:17.577][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:17.578][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:17.579][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:17.587][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:02:17.611][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-01 16:02:17.613][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-01 16:02:17.617][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-01 16:02:17.622][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-01 16:02:17.632][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:02:17.633][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:02:17.635][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-01 16:02:17.645][biodb::testThat]
biodb.INFO [2025-03-01 16:02:17.646][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:02:17.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:17.649][biodb::testThat]
biodb.TRACE[2025-03-01 16:02:17.653][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2025-03-01 16:02:17.655][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:02:17.659][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-01 16:02:17.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:02:17.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:17.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:17.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:17.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:17.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:17.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:02:17.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.741][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:17.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.768][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:17.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:17.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.773][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-01 16:02:17.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.778][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.783][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.793][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-01 16:02:17.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:17.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:17.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:17.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:17.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:17.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:17.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:17.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:17.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.927][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:17.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:17.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.932][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:17.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:17.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:17.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:17.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:17.977][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-03-01 16:02:17.980][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:17.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.986][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:17.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:17.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.991][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:17.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:17.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:17.996][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:17.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:17.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:17.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.094][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.099][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.128][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.129][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.163][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.167][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.188][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.198][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.200][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.202][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.203][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.222][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.227][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.232][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.237][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.238][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.241][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.242][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.257][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.267][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.269][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.271][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.277][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.279][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.281][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.288][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.289][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.291][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.314][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2025-03-01 16:02:18.363][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:02:18.365][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-01 16:02:18.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:02:18.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:18.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:18.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:18.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:18.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:18.383][FUN] Functions in observer BiodbConfig: [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[2025-03-01 16:02:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.401][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-01 16:02:18.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:18.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.412][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.421][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:18.457][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-03-01 16:02:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:18.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.490][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:18.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:18.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:18.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.500][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:18.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.516][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.568][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:18.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.615][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.617][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.619][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.650][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.652][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.670][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.676][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.681][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.686][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.687][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.691][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.705][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:18.707][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:18.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.715][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.717][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:18.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:18.729][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:18.731][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:18.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:18.733][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:02:18.743][biodb::testThat]
biodb.INFO [2025-03-01 16:02:18.745][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:02:18.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:18.747][biodb::testThat]
biodb.DEBUG[2025-03-01 16:02:18.749][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-03-01 16:02:18.757][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-01 16:02:18.762][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-03-01 16:02:18.763][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-03-01 16:02:18.765][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-01 16:02:18.766][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-01 16:02:18.767][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:02:18.769][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-01 16:02:18.770][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-01 16:02:18.771][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-01 16:02:18.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:02:18.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:18.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:18.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:18.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:18.788][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:18.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:18.791][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-03-01 16:02:18.819][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:02:18.820][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:02:18.822][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-03-01 16:02:19.512][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-03-01 16:02:19.951][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-01 16:02:19.954][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-03-01 16:02:20.077][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-03-01 16:02:20.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:02:20.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:20.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:20.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:20.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:20.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:20.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:20.234][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-03-01 16:02:20.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:02:20.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:02:20.276][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-03-01 16:02:20.733][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-03-01 16:02:21.203][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-01 16:02:21.206][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-03-01 16:02:21.285][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-03-01 16:02:21.366][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2025-03-01 16:02:21.368][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-01 16:02:21.370][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-03-01 16:02:21.371][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-01 16:02:21.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:02:21.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:21.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:21.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:21.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:21.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:21.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:02:21.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.394][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:21.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:21.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.404][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-01 16:02:21.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.446][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.456][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:21.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:02:21.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:21.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:21.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:21.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:21.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:21.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:02:21.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.496][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:21.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-01 16:02:21.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.502][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.507][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-01 16:02:21.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-01 16:02:21.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.512][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.517][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.527][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-01 16:02:21.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:02:21.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:02:21.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:21.582][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-03-01 16:02:21.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:02:21.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:02:21.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:02:21.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:02:21.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:02:21.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:02:21.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:02:21.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:02:21.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:02:21.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:02:21.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:02:21.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:02:21.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:02:21.628][biodb::testThat]
biodb.INFO [2025-03-01 16:02:21.629][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:02:21.630][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:21.631][biodb::testThat]
biodb.TRACE[2025-03-01 16:02:21.635][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.636][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.637][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.639][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:21.640][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-03-01 16:02:21.675][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:21.690][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:21.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:21.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:21.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:21.698][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-03-01 16:02:21.700][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-01 16:02:21.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-01 16:02:21.705][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-01 16:02:21.707][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-03-01 16:02:22.181][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-03-01 16:02:22.657][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-01 16:02:22.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-03-01 16:02:22.705][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-03-01 16:02:22.754][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-03-01 16:02:22.774][biodb::testThat]
biodb.INFO [2025-03-01 16:02:22.775][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:02:22.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:22.778][biodb::testThat]
biodb.TRACE[2025-03-01 16:02:22.811][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:22.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:22.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:22.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:22.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:22.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:22.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:22.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:22.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:02:22.869][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-01 16:02:22.872][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-01 16:02:22.894][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-03-01 16:02:22.896][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-01 16:02:22.897][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-03-01 16:02:22.920][biodb::testThat]
biodb.INFO [2025-03-01 16:02:22.921][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:02:22.922][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:22.923][biodb::testThat]
biodb.TRACE[2025-03-01 16:02:22.936][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:22.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:22.941][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:22.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:22.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:22.946][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:22.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:22.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:22.951][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:22.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:22.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:22.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:23.007][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:23.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:23.012][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:02:23.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:02:23.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:23.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:23.017][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:23.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:02:23.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:23.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:23.023][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:23.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:02:23.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:23.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:02:23.034][biodb::testThat]
biodb.INFO [2025-03-01 16:02:23.035][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:02:23.037][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:23.038][biodb::testThat]
biodb.INFO [2025-03-01 16:02:23.050][biodb::testThat]
biodb.INFO [2025-03-01 16:02:23.051][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:02:23.053][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:23.054][biodb::testThat]
biodb.INFO [2025-03-01 16:02:23.065][biodb::testThat]
biodb.INFO [2025-03-01 16:02:23.066][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:02:23.067][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:23.068][biodb::testThat]
biodb.DEBUG[2025-03-01 16:02:23.088][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[2025-03-01 16:02:23.554][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2025-03-01 16:02:24.031][biodb::testThat]
biodb.INFO [2025-03-01 16:02:24.033][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:02:24.034][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:02:24.035][biodb::testThat]
biodb.DEBUG[2025-03-01 16:02:24.486][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-03-01 16:02:24.952][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:24.953][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:24.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:24.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:02:24.957][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:02:24.958][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:02:24.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:02:24.961][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:02:24.962][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:02:24.964][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-01 16:02:24.965][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-01 16:02:24.966][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:02:24.967][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:24.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:24.969][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:24.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:24.972][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:24.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:02:24.985][biodb::testContext]
biodb.INFO [2025-03-01 16:02:24.986][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:02:24.988][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-01 16:02:24.989][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:02:24.990][biodb::testContext]
biodb.INFO [2025-03-01 16:02:24.993][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:02:24.995][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:02:24.999][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:02:25.000][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:02:25.001][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:02:25.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.006][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:02:25.007][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:02:25.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.012][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:02:25.013][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:02:25.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.018][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:02:25.019][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:02:25.020][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:02:25.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.025][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:02:25.026][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:02:25.027][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:02:25.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.032][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:02:25.033][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:02:25.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.045][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:02:25.046][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:02:25.047][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:02:25.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.052][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:02:25.053][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:02:25.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.058][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:02:25.059][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:02:25.060][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:02:25.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.065][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:02:25.067][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:02:25.069][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:02:25.070][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:02:25.071][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:02:25.073][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:02:25.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.077][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:02:25.079][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:02:25.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.083][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:02:25.084][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:02:25.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.089][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:02:25.090][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:02:25.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.095][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:02:25.096][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:02:25.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.101][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:02:25.102][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:02:25.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.107][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:02:25.108][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:02:25.118][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:02:25.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.123][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:02:25.124][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:02:25.125][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:02:25.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.130][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:02:25.132][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.133][self$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[2025-03-01 16:02:25.135][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.136][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:25.137][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.138][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.140][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.141][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.142][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:02:25.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:25.145][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.146][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:02:25.147][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:25.148][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.149][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.151][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:02:25.151][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:02:25.151][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:02:25.151][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:02:25.151][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:02:25.152][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:25.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:25.157][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.159][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.160][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.161][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:25.162][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:25.164][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.165][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.166][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:02:25.172][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.174][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:02:25.175][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.176][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:25.177][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.179][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.180][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.181][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.182][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:02:25.184][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:25.185][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.186][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:02:25.187][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:25.188][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.190][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.191][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:02:25.191][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:02:25.191][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:02:25.191][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:02:25.191][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:02:25.192][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:25.194][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.195][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.196][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:25.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.199][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.201][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.202][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:25.203][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:25.204][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.205][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.207][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:02:25.209][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.210][self$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[2025-03-01 16:02:25.212][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.213][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:25.214][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.217][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.218][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.219][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:02:25.220][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:25.222][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.223][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:02:25.224][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:25.225][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.227][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.228][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.229][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:25.230][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.233][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:25.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.236][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.237][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.239][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:25.240][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:25.241][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.242][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.244][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:02:25.246][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.247][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:02:25.249][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.250][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:25.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.252][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.254][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.255][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.256][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:02:25.257][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:25.259][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.260][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:02:25.261][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:25.262][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.264][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.265][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.266][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:02:25.267][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.268][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.270][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:25.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.273][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.274][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.276][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:25.277][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:25.278][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.279][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:02:25.282][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.310][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[2025-03-01 16:02:25.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.316][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[2025-03-01 16:02:25.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.333][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[2025-03-01 16:02:25.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.384][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:02:25.386][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:02:25.388][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:02:25.389][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:02:25.391][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:02:25.393][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:02:25.395][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:02:25.397][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:02:25.398][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:02:25.400][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:02:25.402][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:02:25.407][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:02:25.409][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:02:25.411][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:02:25.412][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:02:25.414][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:02:25.416][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:02:25.418][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:02:25.419][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:02:25.421][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:02:25.423][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:02:25.425][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:02:25.426][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:02:25.428][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:02:25.430][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:02:25.432][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:02:25.433][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:02:25.435][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:02:25.437][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:02:25.439][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:02:25.440][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:02:25.442][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:02:25.444][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:02:25.445][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:02:25.447][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:02:25.449][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:02:25.450][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:02:25.452][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:02:25.454][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:02:25.455][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:02:25.457][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:02:25.459][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:02:25.461][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:02:25.462][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:02:25.464][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:02:25.466][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:02:25.467][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:02:25.469][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:02:25.471][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:02:25.472][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:02:25.474][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:02:25.476][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:02:25.477][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:02:25.479][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:02:25.481][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:02:25.483][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:02:25.484][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:02:25.486][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:02:25.488][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:02:25.489][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:02:25.491][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:02:25.493][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:02:25.494][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:02:25.496][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:02:25.498][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:02:25.499][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:02:25.501][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:02:25.503][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:02:25.504][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:02:25.506][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:02:25.508][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:02:25.510][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:02:25.511][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:02:25.513][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:02:25.515][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:02:25.521][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:02:25.523][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:02:25.525][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:02:25.526][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:02:25.528][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:02:25.530][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:02:25.531][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:02:25.533][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:02:25.535][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:02:25.537][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:02:25.538][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:02:25.539][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.541][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.542][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[2025-03-01 16:02:25.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.557][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[2025-03-01 16:02:25.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.580][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[2025-03-01 16:02:25.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.619][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[2025-03-01 16:02:25.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:02:25.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:02:25.679][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-01 16:02:25.681][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-01 16:02:25.683][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.684][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-01 16:02:25.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:02:25.688][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.689][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.690][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.691][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.693][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-01 16:02:25.694][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:02:25.695][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.696][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-01 16:02:25.698][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:02:25.699][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-01 16:02:25.699][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-01 16:02:25.699][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-01 16:02:25.699][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-01 16:02:25.700][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:02:25.701][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:02:25.702][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:02:25.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.706][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:02:25.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:02:25.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:02:25.709][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:02:25.710][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-01 16:02:25.712][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:02:25.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:02:25.714][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:02:25.715][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:02:25.717][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:02:25.721][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-01 16:02:25.722][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-01 16:02:25.723][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-01 16:02:25.725][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-01 16:02:25.726][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:02:25.728][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:02:25.729][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-01 16:02:25.730][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:02:25.731][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-01 16:02:25.733][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-01 16:02:25.734][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:02:25.735][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:02:25.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:02:25.737][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:02:25.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:02:25.739][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:02:25.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

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


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

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