Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-03 18:33:26 -0400 (Mon, 03 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4669
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4404
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4431
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 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-03 14:03:53 -0400 (Mon, 03 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on palomino4

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: 1.9.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-06-03 14:25:38 -0400 (Mon, 03 Jun 2024)
EndedAt: 2024-06-03 14:26:28 -0400 (Mon, 03 Jun 2024)
EllapsedTime: 50.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-03 14:26:19.562][biodb::testContext]
biodb.INFO [2024-06-03 14:26:19.565][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:26:19.567][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-03 14:26:19.568][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:26:19.569][biodb::testContext]
biodb.INFO [2024-06-03 14:26:19.576][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:26:19.579][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-03 14:26:19.588][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:26:19.589][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-03 14:26:19.591][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-03 14:26:19.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.596][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-03 14:26:19.626][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-03 14:26:19.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.631][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-03 14:26:19.632][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-03 14:26:19.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.637][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-03 14:26:19.638][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-03 14:26:19.639][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-03 14:26:19.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.644][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-03 14:26:19.645][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-03 14:26:19.646][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-03 14:26:19.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.651][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-03 14:26:19.652][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-03 14:26:19.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.655][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[2024-06-03 14:26:19.657][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-03 14:26:19.658][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-03 14:26:19.659][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-03 14:26:19.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.663][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-03 14:26:19.665][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-03 14:26:19.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.669][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-03 14:26:19.670][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-03 14:26:19.672][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-03 14:26:19.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.676][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:26:19.677][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-03 14:26:19.678][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-03 14:26:19.680][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-03 14:26:19.681][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-03 14:26:19.682][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-03 14:26:19.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.685][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[2024-06-03 14:26:19.687][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-03 14:26:19.688][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-03 14:26:19.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.692][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-03 14:26:19.694][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-03 14:26:19.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.698][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-03 14:26:19.699][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-03 14:26:19.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.704][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-03 14:26:19.705][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-03 14:26:19.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.710][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-03 14:26:19.711][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-03 14:26:19.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.715][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:26:19.716][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-03 14:26:19.720][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-03 14:26:19.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.725][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-03 14:26:19.726][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-03 14:26:19.727][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-03 14:26:19.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.733][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-03 14:26:19.760][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.773][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-03 14:26:19.775][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.776][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:19.777][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.780][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.781][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.785][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:26:19.786][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:19.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.789][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-03 14:26:19.790][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:19.792][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.793][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.794][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:26:19.794][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:26:19.794][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:26:19.794][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:26:19.794][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:26:19.796][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:19.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.799][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:19.801][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.808][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.809][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:19.812][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:19.813][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.814][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.815][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-03 14:26:19.817][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.819][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:26:19.820][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.821][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:19.822][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.825][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.826][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.827][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:26:19.828][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:19.829][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.831][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-03 14:26:19.832][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:19.833][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.834][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.835][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:26:19.835][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:26:19.835][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:26:19.835][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:26:19.835][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:26:19.837][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:19.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.840][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:19.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.842][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.843][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.845][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:19.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:19.848][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.849][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.851][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-03 14:26:19.853][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.854][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-03 14:26:19.855][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.856][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:19.858][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.859][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.860][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.861][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.862][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:26:19.864][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:19.865][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.866][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-03 14:26:19.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:19.868][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.870][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.871][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:19.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.875][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:19.877][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.878][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.879][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.880][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.881][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:19.882][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:19.884][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.885][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.886][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-03 14:26:19.888][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.889][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:26:19.890][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.892][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:19.893][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.894][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.895][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.898][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:26:19.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:19.900][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.901][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-03 14:26:19.903][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:19.904][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.905][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:19.906][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.907][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:19.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.911][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:19.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:19.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:19.914][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:19.915][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.917][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:19.918][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:19.919][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:19.920][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:19.923][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:26:19.924][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.938][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[2024-06-03 14:26:19.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:19.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:19.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:19.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:19.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:19.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.006][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[2024-06-03 14:26:20.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.012][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[2024-06-03 14:26:20.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.017][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[2024-06-03 14:26:20.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.030][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-03 14:26:20.034][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-03 14:26:20.035][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-03 14:26:20.037][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-03 14:26:20.038][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-03 14:26:20.040][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-03 14:26:20.041][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-03 14:26:20.043][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-03 14:26:20.045][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:26:20.046][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-03 14:26:20.048][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-03 14:26:20.049][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-03 14:26:20.051][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-03 14:26:20.052][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-03 14:26:20.054][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-03 14:26:20.055][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-03 14:26:20.057][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-03 14:26:20.059][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-03 14:26:20.060][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-03 14:26:20.062][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-03 14:26:20.063][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-03 14:26:20.065][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-03 14:26:20.067][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-03 14:26:20.068][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-03 14:26:20.070][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-03 14:26:20.071][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-03 14:26:20.073][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-03 14:26:20.074][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-03 14:26:20.076][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-03 14:26:20.078][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-03 14:26:20.079][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-03 14:26:20.081][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-03 14:26:20.082][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-03 14:26:20.084][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-03 14:26:20.085][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-03 14:26:20.087][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-03 14:26:20.089][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-03 14:26:20.090][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-03 14:26:20.092][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-03 14:26:20.093][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-03 14:26:20.095][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-03 14:26:20.096][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-03 14:26:20.098][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-03 14:26:20.100][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-03 14:26:20.101][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-03 14:26:20.103][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-03 14:26:20.104][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-03 14:26:20.106][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-03 14:26:20.107][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-03 14:26:20.109][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-03 14:26:20.111][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-03 14:26:20.112][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-03 14:26:20.114][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-03 14:26:20.115][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-03 14:26:20.117][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-03 14:26:20.118][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-03 14:26:20.120][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-03 14:26:20.122][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-03 14:26:20.123][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-03 14:26:20.125][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-03 14:26:20.126][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-03 14:26:20.128][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-03 14:26:20.129][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-03 14:26:20.131][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-03 14:26:20.133][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-03 14:26:20.134][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-03 14:26:20.136][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-03 14:26:20.137][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-03 14:26:20.139][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-03 14:26:20.140][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-03 14:26:20.142][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-03 14:26:20.144][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-03 14:26:20.145][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-03 14:26:20.147][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-03 14:26:20.148][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-03 14:26:20.150][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-03 14:26:20.151][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-03 14:26:20.153][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-03 14:26:20.154][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-03 14:26:20.156][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-03 14:26:20.158][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-03 14:26:20.159][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-03 14:26:20.161][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-03 14:26:20.195][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-03 14:26:20.197][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:26:20.200][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:26:20.201][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.203][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.298][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[2024-06-03 14:26:20.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.337][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[2024-06-03 14:26:20.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:20.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:20.348][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-03 14:26:20.357][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:26:20.359][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:20.361][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-03 14:26:20.362][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:20.363][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:20.364][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:20.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:20.367][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:20.368][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:20.369][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-03 14:26:20.370][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:20.372][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:20.373][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-03 14:26:20.374][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:20.375][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-03 14:26:20.375][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:26:20.375][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:26:20.375][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:26:20.376][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:20.378][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:26:20.379][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-03 14:26:20.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:20.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:20.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:20.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:20.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:20.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:20.387][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-03 14:26:20.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:20.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:20.391][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:20.392][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:20.397][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:26:20.418][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:26:20.420][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-03 14:26:20.424][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:26:20.428][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-03 14:26:20.431][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:26:20.433][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:26:20.434][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-03 14:26:20.444][biodb::testThat]
biodb.INFO [2024-06-03 14:26:20.445][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-03 14:26:20.446][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:20.448][biodb::testThat]
biodb.TRACE[2024-06-03 14:26:20.454][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-03 14:26:20.456][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-03 14:26:20.460][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-03 14:26:20.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:26:20.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:20.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:20.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:20.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:20.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:20.496][FUN] Functions in observer BiodbConfig: [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[2024-06-03 14:26:20.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.531][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.547][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.557][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:26:20.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.562][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.567][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.572][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.577][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:26:20.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.596][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.601][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.684][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.689][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.699][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:20.733][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-03 14:26:20.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:20.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.741][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:20.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:20.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.746][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:20.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:20.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:20.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.794][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.842][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.847][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.852][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:20.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.883][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.884][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.886][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:20.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:20.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.907][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.917][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.918][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:20.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:20.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.937][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.942][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.947][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.951][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.953][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.955][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.956][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:20.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.971][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.976][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.981][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.986][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.987][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:20.990][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:20.991][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:20.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.011][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.012][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.014][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.023][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.024][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.033][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-03 14:26:21.034][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:21.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.037][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.044][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.045][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.047][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.067][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-03 14:26:21.096][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-03 14:26:21.098][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-03 14:26:21.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:26:21.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:21.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:21.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:21.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:21.112][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:21.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-03 14:26:21.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.120][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.130][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:26:21.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:21.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.135][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.140][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.155][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:21.193][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-03 14:26:21.211][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:21.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:21.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.217][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:21.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:21.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:21.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:21.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.226][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:21.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:21.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.243][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.286][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.291][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.296][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:21.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.340][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.341][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.344][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.375][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.376][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.394][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.399][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.404][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.409][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.411][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.413][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.414][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.429][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:21.430][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:21.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.433][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.440][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.441][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:21.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.443][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:21.450][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:21.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:21.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:21.454][ef$get] fields variable is a list.
biodb.INFO [2024-06-03 14:26:21.466][biodb::testThat]
biodb.INFO [2024-06-03 14:26:21.467][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-03 14:26:21.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:21.470][biodb::testThat]
biodb.DEBUG[2024-06-03 14:26:21.473][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-03 14:26:21.479][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-03 14:26:21.499][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-03 14:26:21.502][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-03 14:26:21.504][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-03 14:26:21.505][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-03 14:26:21.507][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-03 14:26:21.508][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-03 14:26:21.509][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-03 14:26:21.511][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-03 14:26:21.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:26:21.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:21.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:21.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:21.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:21.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:21.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:21.536][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-03 14:26:21.554][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-03 14:26:21.555][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-03 14:26:21.557][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-03 14:26:22.234][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-06-03 14:26:22.235][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-03 14:26:22.237][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-03 14:26:22.238][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-03 14:26:22.866][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-03 14:26:22.869][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-03 14:26:22.884][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-03 14:26:22.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:26:22.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:22.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:22.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:22.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:22.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:22.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:22.928][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-03 14:26:22.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-03 14:26:22.960][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-03 14:26:22.983][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-03 14:26:23.196][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-06-03 14:26:23.197][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-03 14:26:23.198][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-03 14:26:23.200][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-03 14:26:23.803][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-03 14:26:23.806][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-03 14:26:23.811][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-03 14:26:23.814][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-03 14:26:23.817][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-03 14:26:23.819][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-03 14:26:23.820][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-03 14:26:23.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:26:23.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:23.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:23.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:23.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:23.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:23.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-03 14:26:23.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.843][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:23.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:23.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.853][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:26:23.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:23.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.883][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.888][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.898][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:23.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-03 14:26:23.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:23.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:23.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:23.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:23.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:23.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-03 14:26:23.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.942][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:23.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-03 14:26:23.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:23.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:23.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.952][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-03 14:26:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-03 14:26:23.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.957][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.972][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-03 14:26:23.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:23.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:23.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:24.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:24.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:24.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:24.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:24.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:24.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-03 14:26:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-03 14:26:24.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:24.020][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-03 14:26:24.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-03 14:26:24.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-03 14:26:24.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:26:24.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:26:24.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:26:24.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:26:24.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-03 14:26:24.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-03 14:26:24.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:26:24.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-03 14:26:24.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:26:24.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-03 14:26:24.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-03 14:26:24.081][biodb::testThat]
biodb.INFO [2024-06-03 14:26:24.083][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-03 14:26:24.084][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:24.085][biodb::testThat]
biodb.TRACE[2024-06-03 14:26:24.088][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:24.090][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:24.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.092][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:24.094][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-03 14:26:24.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:24.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:24.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:24.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:24.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:24.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:24.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:24.144][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-03 14:26:24.147][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-03 14:26:24.150][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-03 14:26:24.151][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-03 14:26:24.152][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-03 14:26:24.365][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-06-03 14:26:24.366][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-03 14:26:24.368][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-03 14:26:24.369][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-03 14:26:24.979][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-03 14:26:24.984][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-03 14:26:24.993][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-03 14:26:25.002][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-03 14:26:25.027][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.029][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-03 14:26:25.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:25.031][biodb::testThat]
biodb.TRACE[2024-06-03 14:26:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:25.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:25.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:25.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:25.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:25.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-03 14:26:25.105][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-03 14:26:25.108][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-03 14:26:25.122][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-03 14:26:25.124][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-03 14:26:25.128][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-03 14:26:25.160][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.161][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-03 14:26:25.162][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:25.163][biodb::testThat]
biodb.TRACE[2024-06-03 14:26:25.176][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:25.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:25.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:25.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:25.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.224][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.229][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-03 14:26:25.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:25.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-03 14:26:25.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:25.239][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:25.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-03 14:26:25.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:25.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-03 14:26:25.252][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.253][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-03 14:26:25.254][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:25.255][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.273][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.274][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-03 14:26:25.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:25.276][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.288][biodb::testThat]
biodb.INFO [2024-06-03 14:26:25.289][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-03 14:26:25.290][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:25.292][biodb::testThat]
biodb.DEBUG[2024-06-03 14:26:25.305][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[2024-06-03 14:26:25.519][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-06-03 14:26:26.178][biodb::testThat]
biodb.INFO [2024-06-03 14:26:26.180][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-03 14:26:26.181][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-03 14:26:26.182][biodb::testThat]
biodb.DEBUG[2024-06-03 14:26:26.409][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-03 14:26:27.822][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:27.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:27.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:27.826][ef$get] fields variable is a list.
biodb.TRACE[2024-06-03 14:26:27.827][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-03 14:26:27.828][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-03 14:26:27.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-03 14:26:27.831][ef$get] fields variable is a list.
biodb.INFO [2024-06-03 14:26:27.832][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-03 14:26:27.834][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-03 14:26:27.835][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-03 14:26:27.836][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-03 14:26:27.837][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:27.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:27.839][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:27.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:27.841][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-03 14:26:27.853][biodb::testContext]
biodb.INFO [2024-06-03 14:26:27.854][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:26:27.855][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-03 14:26:27.856][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-03 14:26:27.858][biodb::testContext]
biodb.INFO [2024-06-03 14:26:27.860][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:26:27.863][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-03 14:26:27.868][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:26:27.869][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-03 14:26:27.871][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-03 14:26:27.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.875][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-03 14:26:27.877][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-03 14:26:27.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.888][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-03 14:26:27.889][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-03 14:26:27.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.894][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-03 14:26:27.895][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-03 14:26:27.896][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-03 14:26:27.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.901][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-03 14:26:27.902][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-03 14:26:27.904][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-03 14:26:27.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.908][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-03 14:26:27.910][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-03 14:26:27.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.914][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-03 14:26:27.916][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-03 14:26:27.917][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-03 14:26:27.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.922][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-03 14:26:27.923][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-03 14:26:27.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.928][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-03 14:26:27.929][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-03 14:26:27.931][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-03 14:26:27.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.935][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:26:27.936][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-03 14:26:27.938][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-03 14:26:27.939][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-03 14:26:27.940][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-03 14:26:27.942][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-03 14:26:27.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.946][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-03 14:26:27.948][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-03 14:26:27.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.952][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-03 14:26:27.954][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-03 14:26:27.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.958][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-03 14:26:27.960][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-03 14:26:27.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.965][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-03 14:26:27.967][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-03 14:26:27.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.972][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-03 14:26:27.973][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-03 14:26:27.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.978][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-03 14:26:27.979][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-03 14:26:27.983][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-03 14:26:27.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:27.988][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-03 14:26:27.989][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-03 14:26:27.990][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-03 14:26:27.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:27.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:27.994][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[2024-06-03 14:26:27.995][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-03 14:26:27.997][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:27.999][self$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[2024-06-03 14:26:28.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.001][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:28.002][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.007][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:26:28.009][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:28.010][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.011][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-03 14:26:28.012][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:28.014][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.021][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.022][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:26:28.022][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:26:28.022][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:26:28.022][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:26:28.022][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:26:28.024][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:28.025][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.026][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.027][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:28.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.030][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.031][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.032][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.033][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:28.034][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:28.036][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.037][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.038][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-03 14:26:28.040][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.042][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:26:28.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:28.045][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.046][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.048][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.049][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.050][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:26:28.051][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:28.053][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.054][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-03 14:26:28.055][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:28.057][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.058][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.059][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:26:28.059][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-03 14:26:28.059][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-03 14:26:28.059][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-03 14:26:28.059][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-03 14:26:28.061][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:28.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.065][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:28.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.068][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.069][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.070][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:28.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:28.073][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.074][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.076][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-03 14:26:28.078][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.079][self$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[2024-06-03 14:26:28.081][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.082][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:28.083][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.084][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.086][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.087][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.088][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-03 14:26:28.090][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:28.091][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.092][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-03 14:26:28.094][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:28.095][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.097][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.098][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.099][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:28.100][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.101][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.103][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:28.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.106][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.108][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.109][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:28.110][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:28.111][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.113][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.114][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-03 14:26:28.116][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.117][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-03 14:26:28.119][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.120][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:28.121][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.122][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.124][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.125][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.126][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-03 14:26:28.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:28.129][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.130][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-03 14:26:28.131][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:28.132][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.134][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.135][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.136][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-03 14:26:28.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:28.141][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.143][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.144][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.151][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:28.152][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:28.153][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.154][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.156][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:26:28.157][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.193][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.DEBUG[2024-06-03 14:26:28.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.228][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[2024-06-03 14:26:28.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.258][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-03 14:26:28.259][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-03 14:26:28.261][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-03 14:26:28.263][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-03 14:26:28.265][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-03 14:26:28.266][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-03 14:26:28.268][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-03 14:26:28.269][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-03 14:26:28.271][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:26:28.272][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-03 14:26:28.279][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-03 14:26:28.281][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-03 14:26:28.283][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-03 14:26:28.284][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-03 14:26:28.286][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-03 14:26:28.288][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-03 14:26:28.289][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-03 14:26:28.291][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-03 14:26:28.294][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-03 14:26:28.297][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-03 14:26:28.298][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-03 14:26:28.300][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-03 14:26:28.302][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-03 14:26:28.303][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-03 14:26:28.305][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-03 14:26:28.306][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-03 14:26:28.308][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-03 14:26:28.310][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-03 14:26:28.312][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-03 14:26:28.313][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-03 14:26:28.315][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-03 14:26:28.317][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-03 14:26:28.318][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-03 14:26:28.320][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-03 14:26:28.321][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-03 14:26:28.323][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-03 14:26:28.325][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-03 14:26:28.326][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-03 14:26:28.330][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-03 14:26:28.332][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-03 14:26:28.334][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-03 14:26:28.336][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-03 14:26:28.337][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-03 14:26:28.339][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-03 14:26:28.341][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-03 14:26:28.342][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-03 14:26:28.344][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-03 14:26:28.346][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-03 14:26:28.347][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-03 14:26:28.349][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-03 14:26:28.350][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-03 14:26:28.352][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-03 14:26:28.353][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-03 14:26:28.355][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-03 14:26:28.357][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-03 14:26:28.358][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-03 14:26:28.360][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-03 14:26:28.361][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-03 14:26:28.363][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-03 14:26:28.364][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-03 14:26:28.366][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-03 14:26:28.368][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-03 14:26:28.369][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-03 14:26:28.371][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-03 14:26:28.372][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-03 14:26:28.374][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-03 14:26:28.375][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-03 14:26:28.377][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-03 14:26:28.379][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-03 14:26:28.380][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-03 14:26:28.382][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-03 14:26:28.383][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-03 14:26:28.385][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-03 14:26:28.387][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-03 14:26:28.388][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-03 14:26:28.390][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-03 14:26:28.391][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-03 14:26:28.393][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-03 14:26:28.400][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-03 14:26:28.402][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-03 14:26:28.403][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-03 14:26:28.405][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-03 14:26:28.406][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-03 14:26:28.408][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-03 14:26:28.410][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-03 14:26:28.412][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-03 14:26:28.413][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-03 14:26:28.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-03 14:26:28.555][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-03 14:26:28.557][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:26:28.559][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.560][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-03 14:26:28.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.563][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-03 14:26:28.564][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.565][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.567][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.568][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.569][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-03 14:26:28.570][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-03 14:26:28.572][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.573][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-03 14:26:28.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-03 14:26:28.575][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-03 14:26:28.575][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:26:28.575][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:26:28.575][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-03 14:26:28.576][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-03 14:26:28.578][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-03 14:26:28.579][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-03 14:26:28.580][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.581][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.582][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-03 14:26:28.584][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-03 14:26:28.585][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-03 14:26:28.586][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-03 14:26:28.587][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-03 14:26:28.588][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-03 14:26:28.589][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-03 14:26:28.591][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-03 14:26:28.592][self$setPropertyValue]
biodb.DEBUG[2024-06-03 14:26:28.593][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-03 14:26:28.597][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:26:28.598][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-03 14:26:28.599][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-03 14:26:28.601][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-03 14:26:28.603][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:26:28.604][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-03 14:26:28.605][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-03 14:26:28.606][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-03 14:26:28.608][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-03 14:26:28.609][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-03 14:26:28.610][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-03 14:26:28.611][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-03 14:26:28.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-03 14:26:28.613][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-03 14:26:28.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-03 14:26:28.616][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-03 14:26:28.617][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 86 ]
> 
> proc.time()
   user  system elapsed 
   5.03    0.60   10.86

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbExpasy/DESCRIPTION' ... OK
* this is package 'biodbExpasy' version '1.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'biodbExpasy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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'
 OK
* DONE

Status: 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log'
for details.

Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package 'biodbExpasy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)