Back to Long Tests report for BioC 3.20

This page was generated on 2025-01-04 23:55 -0500 (Sat, 04 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
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: 2025-01-04 09:55 -0500 (Sat, 04 Jan 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: 2025-01-04 16:01:19 -0500 (Sat, 04 Jan 2025)
EndedAt: 2025-01-04 16:02:24 -0500 (Sat, 04 Jan 2025)
EllapsedTime: 64.4 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 [2025-01-04 16:02:14.694][biodb::testContext]
biodb.INFO [2025-01-04 16:02:14.699][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-04 16:02:14.701][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-04 16:02:14.702][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-04 16:02:14.704][biodb::testContext]
biodb.INFO [2025-01-04 16:02:14.712][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-04 16:02:14.715][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-04 16:02:14.724][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-04 16:02:14.725][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-04 16:02:14.727][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-04 16:02:14.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.733][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-04 16:02:14.778][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-04 16:02:14.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.783][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-04 16:02:14.784][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-04 16:02:14.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.789][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-04 16:02:14.790][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-04 16:02:14.792][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-04 16:02:14.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.796][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-04 16:02:14.798][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-04 16:02:14.799][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-04 16:02:14.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.803][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-04 16:02:14.805][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-04 16:02:14.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.810][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-04 16:02:14.811][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-04 16:02:14.812][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-04 16:02:14.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.817][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-04 16:02:14.818][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-04 16:02:14.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.823][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-04 16:02:14.824][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-04 16:02:14.825][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-04 16:02:14.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.830][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-04 16:02:14.832][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-04 16:02:14.833][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-04 16:02:14.834][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-04 16:02:14.836][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-04 16:02:14.837][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-04 16:02:14.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.843][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-04 16:02:14.844][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-04 16:02:14.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.849][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-04 16:02:14.850][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-04 16:02:14.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.855][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-04 16:02:14.857][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-04 16:02:14.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.862][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-04 16:02:14.863][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-04 16:02:14.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.868][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-04 16:02:14.870][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-04 16:02:14.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.874][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-04 16:02:14.875][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-04 16:02:14.887][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-04 16:02:14.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.892][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-04 16:02:14.894][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-04 16:02:14.895][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-04 16:02:14.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:14.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:14.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:14.902][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-04 16:02:14.947][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:14.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-04 16:02:14.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:14.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:14.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:14.975][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:14.976][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:14.977][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:14.979][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-04 16:02:14.980][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:14.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:14.983][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-04 16:02:14.984][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:14.985][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:14.987][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:14.988][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-04 16:02:14.988][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-04 16:02:14.988][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-04 16:02:14.988][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-04 16:02:14.988][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-04 16:02:14.989][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:14.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:14.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:14.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:14.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:14.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:14.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:14.998][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:14.999][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:15.000][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:15.001][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.003][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.004][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-04 16:02:15.007][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.008][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-04 16:02:15.009][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.011][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:15.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.015][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.022][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.023][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-04 16:02:15.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:15.025][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.027][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-04 16:02:15.028][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:15.029][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.030][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.032][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-04 16:02:15.032][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-04 16:02:15.032][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-04 16:02:15.032][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-04 16:02:15.032][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-04 16:02:15.033][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:15.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.035][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:15.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.040][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.041][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.042][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:15.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:15.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.046][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.047][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-04 16:02:15.050][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.051][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-04 16:02:15.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:15.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.057][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.058][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.060][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-04 16:02:15.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:15.062][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.063][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-04 16:02:15.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:15.066][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.068][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.069][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:15.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.073][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:15.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.078][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:15.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:15.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.082][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.084][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-04 16:02:15.086][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.087][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-04 16:02:15.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:15.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.092][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.096][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-04 16:02:15.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:15.099][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.100][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-04 16:02:15.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:15.102][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.103][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.105][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.106][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:15.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.109][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:15.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.113][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.114][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.115][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:15.116][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:15.118][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.119][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.123][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-04 16:02:15.124][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.159][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[2025-01-04 16:02:15.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.170][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[2025-01-04 16:02:15.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.181][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[2025-01-04 16:02:15.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.192][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[2025-01-04 16:02:15.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.221][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-04 16:02:15.226][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-04 16:02:15.228][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-04 16:02:15.230][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-04 16:02:15.232][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-04 16:02:15.233][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-04 16:02:15.235][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-04 16:02:15.237][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-04 16:02:15.239][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-04 16:02:15.240][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-04 16:02:15.242][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-04 16:02:15.244][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-04 16:02:15.246][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-04 16:02:15.252][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-04 16:02:15.253][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-04 16:02:15.255][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-04 16:02:15.257][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-04 16:02:15.259][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-04 16:02:15.260][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-04 16:02:15.262][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-04 16:02:15.264][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-04 16:02:15.266][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-04 16:02:15.268][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-04 16:02:15.269][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-04 16:02:15.271][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-04 16:02:15.273][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-04 16:02:15.274][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-04 16:02:15.276][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-04 16:02:15.278][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-04 16:02:15.280][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-04 16:02:15.281][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-04 16:02:15.283][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-04 16:02:15.285][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-04 16:02:15.287][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-04 16:02:15.288][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-04 16:02:15.290][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-04 16:02:15.292][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-04 16:02:15.294][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-04 16:02:15.295][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-04 16:02:15.297][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-04 16:02:15.299][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-04 16:02:15.301][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-04 16:02:15.302][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-04 16:02:15.304][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-04 16:02:15.306][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-04 16:02:15.308][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-04 16:02:15.310][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-04 16:02:15.311][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-04 16:02:15.313][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-04 16:02:15.315][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-04 16:02:15.317][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-04 16:02:15.318][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-04 16:02:15.320][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-04 16:02:15.322][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-04 16:02:15.324][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-04 16:02:15.325][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-04 16:02:15.327][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-04 16:02:15.329][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-04 16:02:15.330][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-04 16:02:15.332][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-04 16:02:15.334][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-04 16:02:15.336][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-04 16:02:15.337][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-04 16:02:15.339][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-04 16:02:15.341][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-04 16:02:15.342][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-04 16:02:15.344][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-04 16:02:15.346][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-04 16:02:15.348][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-04 16:02:15.349][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-04 16:02:15.351][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-04 16:02:15.353][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-04 16:02:15.355][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-04 16:02:15.356][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-04 16:02:15.358][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-04 16:02:15.360][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-04 16:02:15.361][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-04 16:02:15.363][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-04 16:02:15.365][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-04 16:02:15.367][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-04 16:02:15.369][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-04 16:02:15.370][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-04 16:02:15.372][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-04 16:02:15.380][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-04 16:02:15.382][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-04 16:02:15.385][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-04 16:02:15.387][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.389][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.477][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[2025-01-04 16:02:15.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.492][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[2025-01-04 16:02:15.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:15.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:15.534][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-01-04 16:02:15.547][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-01-04 16:02:15.549][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.551][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-01-04 16:02:15.552][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.553][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:15.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.556][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.557][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.558][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.560][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-01-04 16:02:15.561][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:15.562][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.563][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-01-04 16:02:15.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:15.566][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-01-04 16:02:15.566][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-01-04 16:02:15.566][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-01-04 16:02:15.566][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-01-04 16:02:15.567][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:15.568][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-04 16:02:15.570][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-04 16:02:15.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:15.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:15.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:15.577][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:15.578][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-01-04 16:02:15.579][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:15.580][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:15.582][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:15.583][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:15.591][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-04 16:02:15.615][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-01-04 16:02:15.616][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-01-04 16:02:15.621][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-01-04 16:02:15.625][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-01-04 16:02:15.630][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-04 16:02:15.631][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-04 16:02:15.632][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-01-04 16:02:15.643][biodb::testThat]
biodb.INFO [2025-01-04 16:02:15.644][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-04 16:02:15.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:15.646][biodb::testThat]
biodb.TRACE[2025-01-04 16:02:15.650][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[2025-01-04 16:02:15.653][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-01-04 16:02:15.657][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-01-04 16:02:15.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-04 16:02:15.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:15.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:15.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:15.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:15.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:15.688][FUN] Functions in observer BiodbConfig: [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[2025-01-04 16:02:15.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.749][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:15.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:15.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.771][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:15.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:15.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.781][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-04 16:02:15.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.786][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.791][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.796][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.801][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-04 16:02:15.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:15.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:15.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:15.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:15.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.885][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:15.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:15.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.919][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:15.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:15.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:15.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:15.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.929][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:15.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:15.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.934][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:15.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:15.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:15.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:15.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:15.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:15.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:15.979][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-01-04 16:02:15.982][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:15.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:15.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:15.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:15.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:15.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:15.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:15.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:16.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.042][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.086][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.091][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.096][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.130][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.131][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.134][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.165][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.166][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.169][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.185][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.190][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.195][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.200][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.202][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.204][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.205][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.220][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.226][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.231][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.236][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.237][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.240][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.241][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.256][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.261][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.267][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.268][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.271][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.277][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.279][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.281][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.288][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.290][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.291][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.292][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.320][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[2025-01-04 16:02:16.369][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-01-04 16:02:16.370][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-01-04 16:02:16.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-04 16:02:16.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:16.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:16.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:16.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:16.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:16.385][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[2025-01-04 16:02:16.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.394][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.404][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-04 16:02:16.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:16.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.410][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.415][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.425][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:16.461][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-01-04 16:02:16.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:16.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:16.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.504][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:16.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:16.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:16.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:16.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.566][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.611][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.616][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.621][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:16.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.663][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.665][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.667][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.683][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.694][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.699][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.700][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.702][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.723][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.728][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.733][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.738][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.739][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.740][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.741][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.743][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.758][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:16.759][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:16.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.762][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.768][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.769][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:16.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.772][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:16.778][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:16.780][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:16.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:16.782][ef$get] fields variable is a list.
biodb.INFO [2025-01-04 16:02:16.793][biodb::testThat]
biodb.INFO [2025-01-04 16:02:16.794][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-04 16:02:16.795][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:16.796][biodb::testThat]
biodb.DEBUG[2025-01-04 16:02:16.799][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-01-04 16:02:16.807][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-01-04 16:02:16.811][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-01-04 16:02:16.814][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-01-04 16:02:16.816][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-01-04 16:02:16.817][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-01-04 16:02:16.818][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-01-04 16:02:16.820][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-01-04 16:02:16.821][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-01-04 16:02:16.822][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-01-04 16:02:16.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-04 16:02:16.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:16.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:16.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:16.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:16.840][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:16.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:16.842][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-01-04 16:02:16.870][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-04 16:02:16.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-04 16:02:16.873][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-01-04 16:02:17.581][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-01-04 16:02:18.026][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-04 16:02:18.029][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-01-04 16:02:18.049][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-01-04 16:02:18.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-04 16:02:18.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:18.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:18.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:18.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:18.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:18.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:18.105][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-01-04 16:02:18.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-04 16:02:18.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-04 16:02:18.150][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-01-04 16:02:18.606][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-01-04 16:02:19.067][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-01-04 16:02:19.070][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-01-04 16:02:19.074][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-01-04 16:02:19.078][private$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[2025-01-04 16:02:19.081][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-01-04 16:02:19.082][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-01-04 16:02:19.084][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-01-04 16:02:19.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-04 16:02:19.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:19.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:19.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:19.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:19.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:19.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-04 16:02:19.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.107][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:19.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:19.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.118][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-04 16:02:19.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:19.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.156][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.161][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.171][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:19.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-04 16:02:19.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:19.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:19.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:19.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:19.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:19.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-04 16:02:19.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.211][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:19.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-01-04 16:02:19.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.222][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-01-04 16:02:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-01-04 16:02:19.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.227][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.232][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.243][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-01-04 16:02:19.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-04 16:02:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-04 16:02:19.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:19.297][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-01-04 16:02:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-04 16:02:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-04 16:02:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-04 16:02:19.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-04 16:02:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-04 16:02:19.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-04 16:02:19.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-04 16:02:19.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-04 16:02:19.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-04 16:02:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-04 16:02:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-04 16:02:19.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-04 16:02:19.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-04 16:02:19.343][biodb::testThat]
biodb.INFO [2025-01-04 16:02:19.344][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-04 16:02:19.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:19.347][biodb::testThat]
biodb.TRACE[2025-01-04 16:02:19.350][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.354][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:19.356][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-01-04 16:02:19.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:19.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:19.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:19.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:19.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:19.409][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-01-04 16:02:19.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-01-04 16:02:19.416][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-01-04 16:02:19.417][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-01-04 16:02:19.419][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-01-04 16:02:19.891][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-01-04 16:02:20.360][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-01-04 16:02:20.363][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-01-04 16:02:20.372][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-01-04 16:02:20.382][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-01-04 16:02:20.403][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.404][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-04 16:02:20.405][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:20.407][biodb::testThat]
biodb.TRACE[2025-01-04 16:02:20.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:20.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:20.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:20.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:20.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:20.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:20.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-04 16:02:20.490][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-01-04 16:02:20.494][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-01-04 16:02:20.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-01-04 16:02:20.522][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-04 16:02:20.524][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-01-04 16:02:20.546][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.547][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-04 16:02:20.549][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:20.550][biodb::testThat]
biodb.TRACE[2025-01-04 16:02:20.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.572][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:20.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:20.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.577][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:20.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:20.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.628][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.633][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-04 16:02:20.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:20.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-04 16:02:20.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:20.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:20.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-04 16:02:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-04 16:02:20.659][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.660][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-04 16:02:20.661][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:20.663][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.674][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.676][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-04 16:02:20.677][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:20.678][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.689][biodb::testThat]
biodb.INFO [2025-01-04 16:02:20.691][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-04 16:02:20.692][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:20.693][biodb::testThat]
biodb.DEBUG[2025-01-04 16:02:20.713][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[2025-01-04 16:02:21.171][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 [2025-01-04 16:02:21.644][biodb::testThat]
biodb.INFO [2025-01-04 16:02:21.646][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-04 16:02:21.647][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-04 16:02:21.648][biodb::testThat]
biodb.DEBUG[2025-01-04 16:02:22.102][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-01-04 16:02:22.583][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:22.584][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:22.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:22.587][ef$get] fields variable is a list.
biodb.TRACE[2025-01-04 16:02:22.588][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-04 16:02:22.589][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-04 16:02:22.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-04 16:02:22.592][ef$get] fields variable is a list.
biodb.INFO [2025-01-04 16:02:22.593][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-04 16:02:22.595][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-01-04 16:02:22.596][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-01-04 16:02:22.597][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-04 16:02:22.598][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:22.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:22.600][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.603][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-04 16:02:22.616][biodb::testContext]
biodb.INFO [2025-01-04 16:02:22.618][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-04 16:02:22.619][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-01-04 16:02:22.629][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-04 16:02:22.630][biodb::testContext]
biodb.INFO [2025-01-04 16:02:22.632][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-04 16:02:22.634][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-04 16:02:22.638][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-04 16:02:22.640][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-04 16:02:22.641][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-04 16:02:22.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.645][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-04 16:02:22.647][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-04 16:02:22.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.651][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-04 16:02:22.652][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-04 16:02:22.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.657][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-04 16:02:22.658][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-04 16:02:22.659][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-04 16:02:22.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.664][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-04 16:02:22.665][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-04 16:02:22.666][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-04 16:02:22.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.669][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[2025-01-04 16:02:22.670][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-04 16:02:22.672][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-04 16:02:22.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.676][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-04 16:02:22.677][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-04 16:02:22.679][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-04 16:02:22.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.683][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-04 16:02:22.684][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-04 16:02:22.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.689][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-04 16:02:22.690][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-04 16:02:22.691][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-04 16:02:22.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.696][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-04 16:02:22.697][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-04 16:02:22.698][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-04 16:02:22.699][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-04 16:02:22.701][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-04 16:02:22.702][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-04 16:02:22.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.706][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-04 16:02:22.708][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-04 16:02:22.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.712][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-04 16:02:22.713][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-04 16:02:22.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.718][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-04 16:02:22.719][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-04 16:02:22.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.723][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-04 16:02:22.725][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-04 16:02:22.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.729][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-04 16:02:22.731][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-04 16:02:22.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.735][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-04 16:02:22.736][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-04 16:02:22.747][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-04 16:02:22.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.751][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-04 16:02:22.753][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-04 16:02:22.754][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-04 16:02:22.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.759][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-04 16:02:22.761][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.762][self$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[2025-01-04 16:02:22.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:22.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.776][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-04 16:02:22.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:22.778][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.779][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-04 16:02:22.781][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:22.782][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.783][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.784][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-04 16:02:22.784][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-04 16:02:22.784][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-04 16:02:22.784][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-04 16:02:22.784][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-04 16:02:22.786][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:22.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.789][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:22.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.793][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.794][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.795][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:22.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:22.797][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.799][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.800][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-04 16:02:22.802][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.804][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-04 16:02:22.805][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.806][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:22.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.810][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.811][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.812][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-04 16:02:22.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:22.815][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.816][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-04 16:02:22.817][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:22.818][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.819][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.821][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-04 16:02:22.821][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-04 16:02:22.821][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-04 16:02:22.821][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-04 16:02:22.821][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-04 16:02:22.822][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:22.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:22.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.829][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.830][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.831][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:22.832][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:22.834][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.835][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.836][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-04 16:02:22.838][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.840][self$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[2025-01-04 16:02:22.841][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.842][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:22.843][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.846][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.847][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.848][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-04 16:02:22.849][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:22.851][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.852][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-04 16:02:22.853][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:22.854][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.855][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.857][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.858][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:22.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.861][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:22.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.866][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:22.868][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:22.869][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.870][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.872][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-04 16:02:22.874][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.875][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-04 16:02:22.876][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.878][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:22.879][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.880][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.881][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.883][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.884][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-04 16:02:22.885][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:22.886][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.888][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-04 16:02:22.889][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:22.890][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.891][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:22.892][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.894][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-04 16:02:22.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:22.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:22.903][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:22.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:22.906][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.907][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:22.908][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:22.910][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:22.912][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:22.914][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-04 16:02:22.915][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:22.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:22.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:22.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:22.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:22.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.011][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-04 16:02:23.013][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-04 16:02:23.014][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-04 16:02:23.016][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-04 16:02:23.018][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-04 16:02:23.020][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-04 16:02:23.021][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-04 16:02:23.023][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-04 16:02:23.025][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-04 16:02:23.030][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-04 16:02:23.032][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-04 16:02:23.034][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-04 16:02:23.036][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-04 16:02:23.037][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-04 16:02:23.039][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-04 16:02:23.041][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-04 16:02:23.042][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-04 16:02:23.044][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-04 16:02:23.046][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-04 16:02:23.047][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-04 16:02:23.049][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-04 16:02:23.051][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-04 16:02:23.052][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-04 16:02:23.054][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-04 16:02:23.056][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-04 16:02:23.057][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-04 16:02:23.059][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-04 16:02:23.061][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-04 16:02:23.063][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-04 16:02:23.064][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-04 16:02:23.066][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-04 16:02:23.068][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-04 16:02:23.069][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-04 16:02:23.071][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-04 16:02:23.073][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-04 16:02:23.074][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-04 16:02:23.076][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-04 16:02:23.078][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-04 16:02:23.079][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-04 16:02:23.081][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-04 16:02:23.083][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-04 16:02:23.085][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-04 16:02:23.086][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-04 16:02:23.088][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-04 16:02:23.090][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-04 16:02:23.091][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-04 16:02:23.093][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-04 16:02:23.095][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-04 16:02:23.096][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-04 16:02:23.098][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-04 16:02:23.100][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-04 16:02:23.101][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-04 16:02:23.103][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-04 16:02:23.105][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-04 16:02:23.107][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-04 16:02:23.108][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-04 16:02:23.110][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-04 16:02:23.112][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-04 16:02:23.113][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-04 16:02:23.115][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-04 16:02:23.117][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-04 16:02:23.118][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-04 16:02:23.120][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-04 16:02:23.122][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-04 16:02:23.123][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-04 16:02:23.125][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-04 16:02:23.127][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-04 16:02:23.129][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-04 16:02:23.130][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-04 16:02:23.132][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-04 16:02:23.134][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-04 16:02:23.135][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-04 16:02:23.137][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-04 16:02:23.139][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-04 16:02:23.141][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-04 16:02:23.142][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-04 16:02:23.144][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-04 16:02:23.146][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-04 16:02:23.147][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-04 16:02:23.149][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-04 16:02:23.155][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-04 16:02:23.157][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-04 16:02:23.159][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-04 16:02:23.160][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-04 16:02:23.162][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-04 16:02:23.164][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-04 16:02:23.165][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.167][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.198][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[2025-01-04 16:02:23.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.229][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[2025-01-04 16:02:23.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-04 16:02:23.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-04 16:02:23.306][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-01-04 16:02:23.307][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-01-04 16:02:23.310][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:23.311][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-01-04 16:02:23.312][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:23.313][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-04 16:02:23.315][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:23.316][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-04 16:02:23.317][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:23.318][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-04 16:02:23.320][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-01-04 16:02:23.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-04 16:02:23.322][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:23.323][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-01-04 16:02:23.325][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-04 16:02:23.326][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-01-04 16:02:23.326][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-01-04 16:02:23.326][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-01-04 16:02:23.326][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-01-04 16:02:23.327][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-04 16:02:23.328][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-04 16:02:23.330][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-04 16:02:23.331][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:23.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:23.333][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-04 16:02:23.334][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-04 16:02:23.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-04 16:02:23.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-04 16:02:23.338][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-01-04 16:02:23.339][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-04 16:02:23.340][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-04 16:02:23.341][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-04 16:02:23.343][self$setPropertyValue]
biodb.DEBUG[2025-01-04 16:02:23.344][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-04 16:02:23.348][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-01-04 16:02:23.350][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-01-04 16:02:23.351][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-01-04 16:02:23.353][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-01-04 16:02:23.354][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-04 16:02:23.355][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-04 16:02:23.357][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-01-04 16:02:23.358][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-04 16:02:23.360][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-01-04 16:02:23.361][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-01-04 16:02:23.362][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-04 16:02:23.363][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-04 16:02:23.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-04 16:02:23.365][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-04 16:02:23.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-04 16:02:23.368][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-04 16:02:23.369][FUN] Functions in observer 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)