Back to Long Tests report for BioC 3.20

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

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

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

CHECK results for biodbExpasy on merida1

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

raw results


Summary

Package: biodbExpasy
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.10.0.tar.gz
StartedAt: 2025-03-22 16:01:25 -0400 (Sat, 22 Mar 2025)
EndedAt: 2025-03-22 16:02:27 -0400 (Sat, 22 Mar 2025)
EllapsedTime: 61.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.3 (2025-02-28) -- "Trophy Case"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbExpasy' is deprecated and will be removed from
  Bioconductor version 3.21
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2025-03-22 16:02:18.522][biodb::testContext]
biodb.INFO [2025-03-22 16:02:18.526][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:18.527][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-22 16:02:18.529][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:18.530][biodb::testContext]
biodb.INFO [2025-03-22 16:02:18.538][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:18.540][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:18.549][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:18.551][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:02:18.552][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:02:18.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.558][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:02:18.596][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:02:18.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.600][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:02:18.602][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:02:18.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.606][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:02:18.607][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:02:18.609][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:02:18.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.613][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:02:18.614][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:02:18.616][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:02:18.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.620][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:02:18.621][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:02:18.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.626][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:02:18.627][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:02:18.628][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:02:18.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.633][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:02:18.634][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:02:18.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.639][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:02:18.640][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:02:18.641][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:02:18.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.646][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:18.647][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:02:18.648][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:02:18.649][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:02:18.651][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:02:18.652][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:02:18.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.655][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[2025-03-22 16:02:18.656][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:02:18.658][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:02:18.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.662][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:02:18.663][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:02:18.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.669][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:02:18.670][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:02:18.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.674][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:02:18.676][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:02:18.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.680][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:02:18.682][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:02:18.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.687][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:18.688][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:02:18.698][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:02:18.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.703][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:02:18.705][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:02:18.706][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:02:18.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.714][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:02:18.760][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.783][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:02:18.785][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.786][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:18.787][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.789][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.790][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.791][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.792][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:18.794][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:18.795][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.796][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:02:18.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:18.799][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.801][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.802][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:18.802][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:18.802][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:18.802][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:18.802][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:18.808][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:18.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.812][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:18.813][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.814][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.815][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.817][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:18.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:18.820][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.821][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.823][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:02:18.825][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.826][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:18.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:18.830][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.831][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.832][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.835][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:18.836][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:18.837][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.838][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:02:18.840][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:18.841][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.842][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.843][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:18.843][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:18.843][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:18.843][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:18.843][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:18.845][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:18.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.847][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:18.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.852][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.853][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.854][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:18.855][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:18.856][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.858][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.859][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:02:18.861][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.862][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:02:18.864][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.865][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:18.866][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.867][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.869][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.870][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.871][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:18.872][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:18.874][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.875][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:02:18.876][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:18.878][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.879][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.880][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.881][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:18.883][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.885][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:18.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.888][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.890][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.891][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:18.892][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:18.893][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.894][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.896][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:02:18.898][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.899][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:18.901][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:18.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.905][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.906][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.907][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.908][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:18.910][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:18.911][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.912][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:02:18.914][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:18.915][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.916][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:18.917][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.919][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:18.920][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.921][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.922][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:18.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:18.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:18.926][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:18.927][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.928][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:18.929][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:18.930][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:18.932][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:18.936][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:18.937][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.938][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[2025-03-22 16:02:18.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.944][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[2025-03-22 16:02:18.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.966][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[2025-03-22 16:02:18.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:18.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:18.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:18.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:18.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:18.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.041][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:02:19.046][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:02:19.048][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:02:19.049][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:02:19.051][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:02:19.053][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:02:19.054][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:19.056][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:19.058][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:19.059][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:02:19.061][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:02:19.063][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:02:19.065][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:19.066][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:19.068][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:02:19.070][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:02:19.071][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:02:19.073][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:02:19.075][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:02:19.077][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:02:19.079][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:02:19.080][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:02:19.082][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:02:19.084][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:02:19.086][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:02:19.088][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:02:19.089][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:02:19.091][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:02:19.093][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:02:19.095][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:02:19.096][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:02:19.098][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:02:19.100][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:02:19.101][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:02:19.103][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:02:19.105][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:02:19.107][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:02:19.108][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:02:19.110][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:02:19.112][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:02:19.114][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:02:19.115][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:02:19.117][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:02:19.119][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:02:19.121][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:02:19.122][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:02:19.124][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:02:19.126][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:02:19.128][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:02:19.129][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:02:19.131][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:02:19.133][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:02:19.134][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:02:19.136][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:02:19.138][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:02:19.140][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:02:19.142][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:02:19.143][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:02:19.145][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:02:19.147][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:02:19.149][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:02:19.151][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:02:19.152][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:02:19.154][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:02:19.156][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:02:19.158][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:02:19.159][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:02:19.161][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:02:19.163][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:02:19.164][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:02:19.166][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:02:19.168][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:02:19.170][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:02:19.171][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:02:19.173][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:02:19.175][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:02:19.177][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:02:19.179][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:02:19.181][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:02:19.183][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:02:19.185][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:02:19.187][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:02:19.189][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:02:19.197][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:02:19.199][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:19.202][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:19.204][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.206][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.220][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[2025-03-22 16:02:19.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.244][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[2025-03-22 16:02:19.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.288][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[2025-03-22 16:02:19.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:19.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:19.353][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:19.367][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:19.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:19.371][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-22 16:02:19.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:19.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:19.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:19.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:19.377][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:19.379][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:19.380][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-22 16:02:19.381][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:19.383][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:19.384][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-22 16:02:19.385][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:19.386][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-22 16:02:19.386][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:19.386][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:19.386][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:19.388][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:19.389][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:19.390][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:02:19.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:19.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:19.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:19.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:19.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:19.397][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:19.399][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:02:19.400][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:19.401][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:19.402][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:19.403][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:19.411][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:19.433][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:19.435][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-22 16:02:19.439][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:19.444][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-22 16:02:19.448][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:19.449][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:19.451][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-22 16:02:19.461][biodb::testThat]
biodb.INFO [2025-03-22 16:02:19.462][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-22 16:02:19.464][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:19.465][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:19.469][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2025-03-22 16:02:19.471][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:02:19.482][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:02:19.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:19.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:19.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:19.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:19.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:19.509][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:19.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:19.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.561][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:19.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:19.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.583][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.594][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:19.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.599][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.604][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.609][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.614][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:19.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.741][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.746][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.751][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.761][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:19.795][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2025-03-22 16:02:19.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.803][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:19.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:19.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:19.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:19.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:19.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:19.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.856][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.903][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.908][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.913][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:19.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.941][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.942][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:19.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.976][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.979][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:19.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:19.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:19.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:19.996][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:19.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.001][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.006][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.011][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.013][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.015][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.016][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.037][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.041][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.047][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.052][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.055][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.056][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.071][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.081][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.083][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.092][ef$get] Asked field names are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.093][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.102][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.129][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2025-03-22 16:02:20.177][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2025-03-22 16:02:20.179][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:02:20.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:20.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:20.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:20.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:20.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:20.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:20.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:20.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.201][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.211][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:20.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:20.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.216][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.225][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.236][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:20.271][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2025-03-22 16:02:20.299][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:20.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:20.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.304][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:20.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:20.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.309][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:20.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:20.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.314][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:20.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:20.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.330][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.373][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.379][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.384][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:20.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.428][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.430][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.432][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.453][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.462][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.464][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.465][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.466][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.482][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.487][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.492][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.497][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.498][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.502][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.517][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:20.518][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:20.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.521][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.527][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.528][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:20.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:20.537][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:20.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:20.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:20.540][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:20.551][biodb::testThat]
biodb.INFO [2025-03-22 16:02:20.552][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-22 16:02:20.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:20.554][biodb::testThat]
biodb.DEBUG[2025-03-22 16:02:20.557][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2025-03-22 16:02:20.564][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2025-03-22 16:02:20.569][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2025-03-22 16:02:20.570][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2025-03-22 16:02:20.572][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2025-03-22 16:02:20.573][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-22 16:02:20.574][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2025-03-22 16:02:20.580][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:02:20.582][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-22 16:02:20.583][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-22 16:02:20.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:20.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:20.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:20.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:20.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:20.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:20.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:20.601][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2025-03-22 16:02:20.629][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:02:20.631][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:02:20.632][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2025-03-22 16:02:21.200][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2025-03-22 16:02:21.640][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:02:21.643][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2025-03-22 16:02:21.662][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2025-03-22 16:02:21.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:21.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:21.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:21.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:21.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:21.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:21.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:21.706][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2025-03-22 16:02:21.727][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:02:21.732][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:02:21.756][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2025-03-22 16:02:22.194][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2025-03-22 16:02:22.643][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:02:22.646][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2025-03-22 16:02:22.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2025-03-22 16:02:22.653][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2025-03-22 16:02:22.655][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-22 16:02:22.657][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2025-03-22 16:02:22.658][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2025-03-22 16:02:22.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:22.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:22.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:22.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:22.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:22.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:22.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:22.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.681][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:22.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.686][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:22.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:22.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.722][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.727][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.737][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:22.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-22 16:02:22.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:22.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:22.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:22.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:22.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:22.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-22 16:02:22.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.783][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:22.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2025-03-22 16:02:22.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.793][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2025-03-22 16:02:22.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2025-03-22 16:02:22.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.798][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.803][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.813][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2025-03-22 16:02:22.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-22 16:02:22.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-22 16:02:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:22.862][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2025-03-22 16:02:22.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:22.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:22.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:22.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:22.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:22.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:22.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-22 16:02:22.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:22.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-22 16:02:22.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:22.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-22 16:02:22.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:22.911][biodb::testThat]
biodb.INFO [2025-03-22 16:02:22.912][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-22 16:02:22.913][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:22.914][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:22.918][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.919][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.922][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:22.923][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2025-03-22 16:02:22.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:22.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:22.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:22.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:22.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:22.976][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:02:22.978][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:02:22.982][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-22 16:02:22.983][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-22 16:02:22.984][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2025-03-22 16:02:23.462][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2025-03-22 16:02:23.985][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-22 16:02:23.988][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2025-03-22 16:02:23.993][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2025-03-22 16:02:24.000][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2025-03-22 16:02:24.027][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.028][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-22 16:02:24.029][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:24.030][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:24.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:24.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:24.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:24.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:24.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.073][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:24.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:24.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-22 16:02:24.112][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2025-03-22 16:02:24.116][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-22 16:02:24.138][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2025-03-22 16:02:24.140][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-22 16:02:24.141][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2025-03-22 16:02:24.169][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.170][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-22 16:02:24.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:24.173][biodb::testThat]
biodb.TRACE[2025-03-22 16:02:24.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:24.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:24.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:24.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:24.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.257][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-22 16:02:24.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.262][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-22 16:02:24.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:24.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:24.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-22 16:02:24.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:24.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:24.283][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.285][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-22 16:02:24.286][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:24.287][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.299][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.300][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-22 16:02:24.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:24.303][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.313][biodb::testThat]
biodb.INFO [2025-03-22 16:02:24.315][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-22 16:02:24.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:24.317][biodb::testThat]
biodb.DEBUG[2025-03-22 16:02:24.337][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2025-03-22 16:02:24.836][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2025-03-22 16:02:25.308][biodb::testThat]
biodb.INFO [2025-03-22 16:02:25.309][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-22 16:02:25.310][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-22 16:02:25.311][biodb::testThat]
biodb.DEBUG[2025-03-22 16:02:25.763][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2025-03-22 16:02:26.229][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:26.231][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:26.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:26.233][ef$get] fields variable is a list.
biodb.TRACE[2025-03-22 16:02:26.235][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-22 16:02:26.236][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-22 16:02:26.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-22 16:02:26.238][ef$get] fields variable is a list.
biodb.INFO [2025-03-22 16:02:26.240][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:02:26.241][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-22 16:02:26.242][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-22 16:02:26.244][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:02:26.245][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.247][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.249][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-22 16:02:26.272][biodb::testContext]
biodb.INFO [2025-03-22 16:02:26.273][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:26.274][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-22 16:02:26.276][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-22 16:02:26.277][biodb::testContext]
biodb.INFO [2025-03-22 16:02:26.279][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:26.281][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:26.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:26.287][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-22 16:02:26.288][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-22 16:02:26.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.293][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-22 16:02:26.294][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-22 16:02:26.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.299][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-22 16:02:26.300][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-22 16:02:26.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.305][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-22 16:02:26.306][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-22 16:02:26.307][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-22 16:02:26.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.312][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-22 16:02:26.313][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-22 16:02:26.314][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-22 16:02:26.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.319][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-22 16:02:26.320][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-22 16:02:26.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.325][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-22 16:02:26.326][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-22 16:02:26.328][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-22 16:02:26.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.333][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-22 16:02:26.334][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-22 16:02:26.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.338][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-22 16:02:26.340][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-22 16:02:26.341][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-22 16:02:26.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.345][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:26.347][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-22 16:02:26.348][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-22 16:02:26.349][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-22 16:02:26.350][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-22 16:02:26.352][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-22 16:02:26.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.356][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-22 16:02:26.357][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-22 16:02:26.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.362][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-22 16:02:26.363][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-22 16:02:26.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.368][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-22 16:02:26.369][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-22 16:02:26.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.373][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-22 16:02:26.375][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-22 16:02:26.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.379][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-22 16:02:26.380][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-22 16:02:26.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.389][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-22 16:02:26.390][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-22 16:02:26.400][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-22 16:02:26.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.405][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-22 16:02:26.406][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-22 16:02:26.408][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-22 16:02:26.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.412][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-22 16:02:26.414][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.416][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-22 16:02:26.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:26.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.421][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.424][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:26.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:26.427][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.428][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-22 16:02:26.429][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:26.431][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.432][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.433][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:26.433][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:26.433][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:26.433][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:26.433][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:26.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:26.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:26.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.441][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.443][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:26.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:26.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.447][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.449][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-22 16:02:26.451][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.452][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:26.454][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.455][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:26.456][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.457][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.458][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.460][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.461][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:26.462][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:26.463][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.465][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-22 16:02:26.466][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:26.467][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.468][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.470][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:26.470][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-22 16:02:26.470][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-22 16:02:26.470][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-22 16:02:26.470][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-22 16:02:26.471][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:26.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.474][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:26.476][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.478][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.479][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.480][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:26.481][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:26.483][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.484][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.485][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-22 16:02:26.488][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.489][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-22 16:02:26.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.491][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:26.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.496][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.498][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-22 16:02:26.499][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:26.500][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.501][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-22 16:02:26.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:26.504][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.505][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.506][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.507][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:26.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.511][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:26.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.514][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.520][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:26.522][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:26.523][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.524][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.526][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-22 16:02:26.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.529][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-22 16:02:26.530][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.532][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:26.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.534][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.535][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.537][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.538][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-22 16:02:26.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:26.540][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.542][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-22 16:02:26.543][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:26.544][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.545][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.547][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.548][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-22 16:02:26.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.551][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:26.553][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.554][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.555][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.556][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.557][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:26.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:26.560][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.561][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.562][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:26.564][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.662][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[2025-03-22 16:02:26.664][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-22 16:02:26.665][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-22 16:02:26.667][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-22 16:02:26.669][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-22 16:02:26.671][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-22 16:02:26.672][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-22 16:02:26.674][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:26.676][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:26.678][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:26.680][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-22 16:02:26.681][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-22 16:02:26.683][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-22 16:02:26.685][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-22 16:02:26.687][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-22 16:02:26.688][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-22 16:02:26.690][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-22 16:02:26.692][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-22 16:02:26.693][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-22 16:02:26.695][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-22 16:02:26.697][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-22 16:02:26.698][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-22 16:02:26.700][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-22 16:02:26.702][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-22 16:02:26.703][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-22 16:02:26.705][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-22 16:02:26.707][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-22 16:02:26.709][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-22 16:02:26.710][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-22 16:02:26.712][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-22 16:02:26.714][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-22 16:02:26.715][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-22 16:02:26.717][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-22 16:02:26.719][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-22 16:02:26.720][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-22 16:02:26.722][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-22 16:02:26.724][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-22 16:02:26.725][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-22 16:02:26.727][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-22 16:02:26.729][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-22 16:02:26.731][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-22 16:02:26.732][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-22 16:02:26.734][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-22 16:02:26.736][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-22 16:02:26.737][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-22 16:02:26.739][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-22 16:02:26.741][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-22 16:02:26.743][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-22 16:02:26.744][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-22 16:02:26.746][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-22 16:02:26.748][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-22 16:02:26.749][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-22 16:02:26.751][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-22 16:02:26.753][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-22 16:02:26.759][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-22 16:02:26.761][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-22 16:02:26.762][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-22 16:02:26.764][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-22 16:02:26.766][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-22 16:02:26.767][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-22 16:02:26.769][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-22 16:02:26.771][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-22 16:02:26.772][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-22 16:02:26.774][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-22 16:02:26.776][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-22 16:02:26.777][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-22 16:02:26.779][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-22 16:02:26.781][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-22 16:02:26.782][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-22 16:02:26.784][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-22 16:02:26.786][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-22 16:02:26.787][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-22 16:02:26.789][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-22 16:02:26.791][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-22 16:02:26.792][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-22 16:02:26.794][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-22 16:02:26.796][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-22 16:02:26.797][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-22 16:02:26.799][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-22 16:02:26.801][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-22 16:02:26.802][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-22 16:02:26.804][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-22 16:02:26.806][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-22 16:02:26.807][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-22 16:02:26.809][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-22 16:02:26.811][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-22 16:02:26.812][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-22 16:02:26.813][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.815][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.818][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-22 16:02:26.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:26.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:26.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:26.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:26.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:26.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-22 16:02:26.953][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2025-03-22 16:02:26.954][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:26.957][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.958][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2025-03-22 16:02:26.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-22 16:02:26.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.963][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.964][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.965][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.966][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2025-03-22 16:02:26.968][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-22 16:02:26.969][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.970][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2025-03-22 16:02:26.971][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-22 16:02:26.972][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2025-03-22 16:02:26.972][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:26.972][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:26.972][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2025-03-22 16:02:26.974][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-22 16:02:26.975][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-22 16:02:26.976][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-22 16:02:26.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.979][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.980][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-22 16:02:26.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-22 16:02:26.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-22 16:02:26.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-22 16:02:26.984][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2025-03-22 16:02:26.986][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-22 16:02:26.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-22 16:02:26.992][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-22 16:02:26.993][self$setPropertyValue]
biodb.DEBUG[2025-03-22 16:02:26.995][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-22 16:02:26.998][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:26.999][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2025-03-22 16:02:27.001][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2025-03-22 16:02:27.003][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2025-03-22 16:02:27.004][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:27.005][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-22 16:02:27.006][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2025-03-22 16:02:27.007][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-22 16:02:27.009][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2025-03-22 16:02:27.010][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2025-03-22 16:02:27.011][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-22 16:02:27.012][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-22 16:02:27.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-22 16:02:27.014][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-22 16:02:27.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-22 16:02:27.017][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-22 16:02:27.018][FUN] Functions in observer 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 4.4.3 (2025-02-28)
* 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)