Long Tests report for BioC 3.22 - CHECK results for biodbNcbi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4883
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
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*

CHECK results for biodbNcbi on merida1

To the developers/maintainers of the biodbNcbi 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: biodbNcbi

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz

StartedAt: 2025-12-20 16:01:19 -0500 (Sat, 20 Dec 2025)

EndedAt: 2025-12-20 16:02:30 -0500 (Sat, 20 Dec 2025)

EllapsedTime: 71.2 seconds

RetCode: 1

Status: ERROR

CheckDir: biodbNcbi.Rcheck

Warnings: NA

Tests output

biodbNcbi.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNcbi")
Loading required package: biodbNcbi
biodb.INFO [2025-12-20 16:02:17.869][biodb::testContext]
biodb.INFO [2025-12-20 16:02:17.873][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:17.874][biodb::testContext] Test context - CCDS long tests
biodb.INFO [2025-12-20 16:02:17.876][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:17.877][biodb::testContext]
biodb.INFO [2025-12-20 16:02:17.884][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:17.886][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:17.894][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:17.895][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:02:17.897][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:02:17.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.902][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:02:17.927][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:02:17.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.941][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:02:17.943][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:02:17.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.947][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:02:17.948][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:02:17.950][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:02:17.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.954][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:02:17.956][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:02:17.957][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:02:17.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.962][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:02:17.963][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:02:17.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.968][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:02:17.969][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:02:17.970][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:02:17.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.975][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:02:17.976][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:02:17.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.979][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[2025-12-20 16:02:17.980][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:02:17.982][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:02:17.983][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:02:17.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.988][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:17.989][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:02:17.990][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:02:17.991][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:02:17.993][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:02:17.994][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:02:17.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:17.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:17.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:17.998][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:02:18.000][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:02:18.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.004][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:02:18.006][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:02:18.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.010][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:02:18.012][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:02:18.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.016][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:02:18.017][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:02:18.019][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:02:18.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.023][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:18.025][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:02:18.035][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:02:18.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.040][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:02:18.041][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:02:18.043][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:02:18.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.049][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:02:18.092][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.113][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-20 16:02:18.115][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.116][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.117][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.119][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.120][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.121][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.122][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:18.124][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.125][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.126][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:02:18.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.129][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.130][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.131][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:18.131][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:18.131][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:18.131][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:18.131][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:18.132][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:18.134][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.139][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.141][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.142][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.143][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.144][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.145][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.147][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:02:18.149][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.150][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:18.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.154][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.160][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.161][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.162][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.163][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:18.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.166][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.167][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:02:18.168][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.170][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.171][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.172][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:18.172][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:18.172][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:18.172][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:18.172][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:18.174][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:18.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.176][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.177][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.178][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.181][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.182][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.183][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.185][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.187][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.188][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:02:18.190][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.192][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-20 16:02:18.193][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.194][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.195][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.196][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.198][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.199][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.200][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:18.201][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.203][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.204][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:02:18.205][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.206][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.208][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.209][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.210][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:18.211][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.212][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.214][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.217][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.218][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.220][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.221][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.222][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.223][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.225][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:02:18.227][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.228][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:18.229][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.231][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.232][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.233][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.234][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.236][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.237][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:18.238][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.239][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.241][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:02:18.242][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.243][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.244][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.246][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.247][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:18.248][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.249][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.250][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.252][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.253][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.254][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.255][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.257][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.258][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.259][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.260][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.264][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:18.265][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.357][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:02:18.361][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:02:18.363][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:02:18.365][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:02:18.371][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:02:18.373][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:18.374][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:18.376][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:18.378][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:02:18.379][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:18.381][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:18.383][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:02:18.384][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:18.386][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:18.388][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:18.389][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:18.391][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:02:18.393][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:02:18.395][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:02:18.396][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:02:18.398][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:02:18.400][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:02:18.401][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:02:18.403][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:02:18.405][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:02:18.406][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:02:18.408][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:02:18.410][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:02:18.412][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:02:18.413][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:02:18.415][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:02:18.417][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:02:18.419][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:02:18.421][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:02:18.422][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:02:18.424][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:02:18.426][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:02:18.427][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:02:18.429][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:02:18.431][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:02:18.433][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:02:18.434][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:02:18.436][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:02:18.438][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:02:18.439][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:02:18.441][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:18.443][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:02:18.445][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:02:18.447][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:02:18.448][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:02:18.450][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:02:18.452][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:02:18.453][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:02:18.455][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:02:18.457][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:02:18.458][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:02:18.460][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:02:18.462][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:02:18.464][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:02:18.465][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:02:18.467][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:02:18.469][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:02:18.470][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:02:18.472][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:02:18.474][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:02:18.476][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:02:18.477][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:02:18.479][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:02:18.481][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:02:18.482][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:02:18.484][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:02:18.486][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:02:18.488][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:02:18.489][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:02:18.491][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:02:18.493][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:02:18.494][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:02:18.496][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:02:18.498][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:02:18.500][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:02:18.501][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:02:18.503][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:02:18.505][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:02:18.512][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:02:18.514][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:18.518][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:18.519][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.521][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.594][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[2025-12-20 16:02:18.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.649][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[2025-12-20 16:02:18.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:18.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:18.659][bdb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:18.672][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-20 16:02:18.674][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.675][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-20 16:02:18.677][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.678][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.679][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.680][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.681][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.683][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.684][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-20 16:02:18.685][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.686][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.688][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-20 16:02:18.689][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.690][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-20 16:02:18.690][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-20 16:02:18.691][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.693][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.694][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:18.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.697][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.698][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.699][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.701][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.702][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:18.702][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-20 16:02:18.703][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.704][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.705][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.707][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.708][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-20 16:02:18.710][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.712][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-20 16:02:18.713][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.714][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.715][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.717][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.718][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.719][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.720][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:18.721][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.723][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.724][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-20 16:02:18.725][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.726][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-20 16:02:18.726][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-20 16:02:18.726][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-20 16:02:18.726][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-20 16:02:18.726][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-20 16:02:18.726][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-20 16:02:18.728][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.729][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:18.730][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:18.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.734][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.737][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.739][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:18.739][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:18.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.742][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.743][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.745][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-20 16:02:18.747][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.749][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-20 16:02:18.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.755][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.757][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:18.759][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.760][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.761][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-20 16:02:18.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.764][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:18.769][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.771][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:18.771][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:18.771][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:18.772][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:18.773][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.775][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.779][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.780][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:18.780][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:18.780][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:18.781][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.782][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.784][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.785][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:18.787][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-20 16:02:18.789][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.790][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-20 16:02:18.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:18.794][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.795][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.796][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.798][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.799][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:18.800][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:18.801][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.803][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-20 16:02:18.804][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:18.805][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-20 16:02:18.805][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:18.806][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:18.808][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:18.809][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:18.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.811][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.812][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:18.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:18.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:18.816][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:18.817][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:18.817][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:18.817][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:18.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:18.819][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:18.821][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:18.822][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:18.830][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-20 16:02:18.832][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:18.833][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:18.835][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-20 16:02:18.837][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:18.839][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-20 16:02:18.860][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-12-20 16:02:18.876][bdb$getFactory()$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.INFO [2025-12-20 16:02:18.886][biodb::testThat]
biodb.INFO [2025-12-20 16:02:18.887][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:02:18.888][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:18.890][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:18.894][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS12227.1-content.html".
biodb.DEBUG[2025-12-20 16:02:18.897][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:18.901][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-12-20 16:02:18.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:18.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:18.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:18.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:18.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:18.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:18.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:18.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:18.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:18.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:18.975][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:18.992][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:18.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:18.994][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.039][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.045][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.059][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:19.140][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS12227.1.
biodb.TRACE[2025-12-20 16:02:19.143][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.148][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.226][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.232][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.237][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:19.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:19.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:19.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:19.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.270][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.314][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.320][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.325][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.358][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.359][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.361][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.378][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.383][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.388][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.393][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.394][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.396][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.398][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.413][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.414][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.416][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.417][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.423][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.425][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.427][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.450][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.ccds-CCDS43240.1-content.html".
biodb.DEBUG[2025-12-20 16:02:19.498][biodb$getFactory()$createEntryFromCo ...] Creating NCBI CCDS entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:19.499][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI CCDS entries.
biodb.DEBUG[2025-12-20 16:02:19.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:19.502][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:19.503][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:19.513][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:19.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:19.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:19.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:19.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.560][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.561][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.562][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.564][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.565][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.576][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.586][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:19.621][biodb$getFactory()$createEntryFromCo ...] Accession numbers: CCDS43240.1.
biodb.TRACE[2025-12-20 16:02:19.648][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.653][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.658][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.668][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.674][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:19.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:19.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:19.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:19.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.695][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.738][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.743][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.748][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:19.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.791][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.792][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.795][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.811][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.821][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.826][ef$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.827][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.828][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.830][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.835][self$getBiodb()$getEntryFields()$get] Asked field names are: sequence.
biodb.TRACE[2025-12-20 16:02:19.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.850][ef$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.852][ef$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:19.853][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.854][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:19.861][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:19.862][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:19.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:19.864][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:19.875][biodb::testThat]
biodb.INFO [2025-12-20 16:02:19.876][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:02:19.877][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:19.878][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:19.881][private$loadEntries] Creating entries from ids [2]: "CCDS12227.1, CCDS43240.1".
biodb.DEBUG[2025-12-20 16:02:19.884][conn$getEntryContent] Get NCBI CCDS entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:19.888][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-20 16:02:19.890][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:19.891][conn$getEntryContent] 2 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:19.893][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:19.894][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-20 16:02:20.078][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.079][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:02:20.080][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.082][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.090][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.091][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:02:20.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.094][biodb::testThat]
biodb.WARN [2025-12-20 16:02:20.119][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-20 16:02:20.149][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-20 16:02:20.161][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.162][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:02:20.163][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.164][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:20.188][private$loadEntries] Creating entries from ids [1]: "CCDS12227.1".
biodb.DEBUG[2025-12-20 16:02:20.252][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:20.297][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-20 16:02:20.299][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:20.300][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:20.301][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:20.302][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-20 16:02:20.396][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.397][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:02:20.398][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.400][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-20 16:02:20.459][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.461][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:02:20.462][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.463][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.474][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.476][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:20.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.478][biodb::testThat]
Saving _problems/test_long_100_ccds-38.R
biodb.INFO [2025-12-20 16:02:20.544][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.545][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:20.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:20.548][biodb::testThat]
biodb.INFO [2025-12-20 16:02:20.556][bdb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:02:20.558][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-12-20 16:02:20.559][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:02:20.560][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:20.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:20.562][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.564][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-20 16:02:20.579][biodb::testContext]
biodb.INFO [2025-12-20 16:02:20.580][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:20.581][biodb::testContext] Test context - Gene long tests
biodb.INFO [2025-12-20 16:02:20.583][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:20.584][biodb::testContext]
biodb.INFO [2025-12-20 16:02:20.587][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:20.589][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:20.593][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:20.594][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:02:20.596][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:02:20.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.600][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:02:20.601][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:02:20.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.606][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:02:20.607][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:02:20.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.612][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:02:20.613][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:02:20.615][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:02:20.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.619][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:02:20.620][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:02:20.622][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:02:20.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.626][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:02:20.628][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:02:20.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.632][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:02:20.634][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:02:20.635][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:02:20.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.640][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:02:20.641][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:02:20.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.645][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:02:20.647][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:02:20.648][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:02:20.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.652][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:20.654][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:02:20.655][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:02:20.656][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:02:20.657][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:02:20.659][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:02:20.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.663][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:02:20.664][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:02:20.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.668][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[2025-12-20 16:02:20.669][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:02:20.670][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:02:20.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.679][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:02:20.681][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:02:20.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.685][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:02:20.687][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:02:20.688][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:02:20.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.693][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:20.695][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:02:20.707][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:02:20.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.712][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:02:20.713][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:02:20.714][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:02:20.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.719][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:02:20.722][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.723][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-20 16:02:20.724][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.726][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:20.727][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.728][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.730][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.731][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.732][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:20.733][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:20.735][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.736][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:02:20.737][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:20.739][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.740][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.741][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:20.741][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:20.741][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:20.741][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:20.741][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:20.742][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:20.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.746][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:20.747][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.748][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.750][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.751][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.752][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:20.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:20.755][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.756][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.758][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:02:20.760][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.761][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:20.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.764][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:20.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.768][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.769][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.770][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:20.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:20.773][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.774][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:02:20.776][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:20.777][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.778][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.779][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:20.779][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:20.779][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:20.779][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:20.779][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:20.781][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:20.782][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.784][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:20.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.788][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.789][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:20.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:20.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.794][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.796][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:02:20.798][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.800][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-20 16:02:20.801][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.802][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:20.803][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.805][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.806][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.807][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.808][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:20.810][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:20.811][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.812][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:02:20.813][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:20.815][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.816][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.817][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.819][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:20.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.822][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:20.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.826][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.827][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:20.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:20.831][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.837][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.838][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:02:20.840][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.842][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:20.843][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.844][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:20.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.851][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:20.852][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:20.853][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.854][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:02:20.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:20.857][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.858][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:20.860][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.861][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:20.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.865][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:20.866][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:20.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:20.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:20.870][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.871][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:20.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:20.873][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:20.875][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:20.876][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:20.877][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.901][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[2025-12-20 16:02:20.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:20.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:20.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:20.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:20.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:20.972][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:02:20.974][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:02:20.980][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:02:20.982][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:02:20.984][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:02:20.985][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:20.987][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:20.989][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:20.991][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:02:20.992][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:20.994][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:20.996][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:02:20.998][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:20.999][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:21.001][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:21.003][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:21.004][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:02:21.006][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:02:21.008][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:02:21.010][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:02:21.012][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:02:21.013][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:02:21.015][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:02:21.017][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:02:21.019][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:02:21.020][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:02:21.022][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:02:21.024][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:02:21.025][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:02:21.027][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:02:21.029][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:02:21.031][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:02:21.032][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:02:21.034][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:02:21.036][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:02:21.038][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:02:21.039][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:02:21.041][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:02:21.043][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:02:21.045][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:02:21.046][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:02:21.048][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:02:21.050][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:02:21.052][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:02:21.053][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:02:21.055][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:21.057][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:02:21.059][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:02:21.061][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:02:21.063][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:02:21.065][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:02:21.067][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:02:21.069][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:02:21.071][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:02:21.073][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:02:21.075][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:02:21.077][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:02:21.079][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:02:21.081][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:02:21.083][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:02:21.085][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:02:21.087][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:02:21.089][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:02:21.091][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:02:21.093][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:02:21.095][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:02:21.096][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:02:21.098][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:02:21.100][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:02:21.101][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:02:21.103][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:02:21.105][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:02:21.107][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:02:21.109][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:02:21.110][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:02:21.112][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:02:21.114][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:02:21.116][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:02:21.118][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:02:21.124][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:02:21.126][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:02:21.128][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:02:21.130][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:02:21.132][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:02:21.135][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:21.136][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:21.138][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.140][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.158][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[2025-12-20 16:02:21.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.205][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[2025-12-20 16:02:21.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.251][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[2025-12-20 16:02:21.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:21.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:21.273][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:21.275][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-20 16:02:21.277][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.278][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-20 16:02:21.280][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.281][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:21.282][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.283][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.284][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.286][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.287][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-20 16:02:21.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:21.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.291][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-20 16:02:21.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:21.293][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-20 16:02:21.293][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-20 16:02:21.294][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:21.296][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:21.297][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:21.298][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:21.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.304][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.305][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:21.305][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-20 16:02:21.306][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:21.308][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:21.309][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.310][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:21.312][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-20 16:02:21.314][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.315][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-20 16:02:21.316][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.318][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:21.319][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.320][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.321][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.323][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.324][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:21.325][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:21.326][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.328][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-20 16:02:21.329][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:21.330][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-20 16:02:21.330][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-20 16:02:21.330][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-20 16:02:21.330][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-20 16:02:21.330][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-20 16:02:21.330][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-20 16:02:21.332][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:21.333][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:21.334][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:21.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.338][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.339][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:21.340][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.341][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.343][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.344][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:21.344][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:21.346][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:21.347][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:21.348][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.350][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:21.352][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-20 16:02:21.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:21.355][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-20 16:02:21.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.358][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:21.359][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.360][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.362][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.363][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.365][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:21.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:21.369][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.370][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-20 16:02:21.371][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.373][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:21.375][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:21.376][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:21.376][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:21.376][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:21.378][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:21.379][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.381][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:21.383][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.384][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.387][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:21.387][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:21.387][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:21.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:21.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:21.391][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.392][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:21.394][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-20 16:02:21.396][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.397][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-20 16:02:21.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:21.401][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.402][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.403][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.411][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:21.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:21.413][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.414][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-20 16:02:21.416][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:21.417][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-20 16:02:21.417][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:21.418][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:21.419][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:21.421][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:21.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.423][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.424][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:21.426][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:21.427][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:21.428][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:21.429][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:21.429][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:21.429][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:21.430][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:21.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:21.433][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:21.434][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:21.436][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-20 16:02:21.438][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:21.439][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:21.441][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-20 16:02:21.443][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:21.445][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-20 16:02:21.454][super$initialize] Initialize connector ncbi.gene.
biodb.DEBUG[2025-12-20 16:02:21.497][biodb$getFactory()$createConn] Creating new connector ncbi.gene for database class ncbi.gene .
biodb.INFO [2025-12-20 16:02:21.503][biodb::testThat]
biodb.INFO [2025-12-20 16:02:21.505][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:02:21.507][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:21.509][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:21.516][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.gene-2833-content.xml".
biodb.DEBUG[2025-12-20 16:02:21.517][biodb$getFactory()$createEntryFromCo ...] Creating NCBI Gene entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:21.522][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCBI Gene entries.
biodb.DEBUG[2025-12-20 16:02:21.524][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:21.525][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:21.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:21.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:21.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:21.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:21.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:21.551][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.553][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.554][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.555][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.562][ef$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:21.564][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:21.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.572][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.574][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-12-20 16:02:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-12-20 16:02:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.580][ef$get] Asked field names are: location.
biodb.TRACE[2025-12-20 16:02:21.581][ef$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-12-20 16:02:21.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.584][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.586][self$getBiodb()$getEntryFields()$get] Asked field names are: location.
biodb.TRACE[2025-12-20 16:02:21.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.location.
biodb.TRACE[2025-12-20 16:02:21.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.591][ef$get] Asked field names are: symbol.
biodb.TRACE[2025-12-20 16:02:21.592][ef$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-12-20 16:02:21.594][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.595][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.597][self$getBiodb()$getEntryFields()$get] Asked field names are: symbol.
biodb.TRACE[2025-12-20 16:02:21.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: gene.symbol.
biodb.TRACE[2025-12-20 16:02:21.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.602][ef$get] Asked field names are: synonyms.
biodb.TRACE[2025-12-20 16:02:21.603][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:21.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.606][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.608][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2025-12-20 16:02:21.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:21.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.613][ef$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-12-20 16:02:21.614][ef$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-12-20 16:02:21.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.617][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.620][self$getBiodb()$getEntryFields()$get] Asked field names are: uniprot.id.
biodb.TRACE[2025-12-20 16:02:21.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: uniprot.id.
biodb.TRACE[2025-12-20 16:02:21.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.630][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-20 16:02:21.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-20 16:02:21.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.640][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-20 16:02:21.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-20 16:02:21.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.650][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.gene.id.
biodb.TRACE[2025-12-20 16:02:21.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.gene.id.
biodb.TRACE[2025-12-20 16:02:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:21.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:21.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:21.686][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2833.
biodb.TRACE[2025-12-20 16:02:21.689][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:21.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:21.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.694][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:21.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:21.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.700][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.708][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:21.721][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:21.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:21.726][private$computeField] Compute value for field "aa.seq".
biodb.DEBUG[2025-12-20 16:02:21.766][initialize] Initialize connector ncbi.ccds.
biodb.DEBUG[2025-12-20 16:02:21.786][self$createConn] Creating new connector ncbi.ccds for database class ncbi.ccds .
biodb.DEBUG[2025-12-20 16:02:21.788][private$loadEntries] Creating entries from ids [1]: "CCDS14416.1".
biodb.DEBUG[2025-12-20 16:02:21.791][conn$getEntryContent] Get NCBI CCDS entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:21.793][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.ccds-c3bf0257a03be04fd46e362b99907704.
biodb.DEBUG[2025-12-20 16:02:21.794][conn$getEntryContent] 0 NCBI CCDS entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:21.795][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI CCDS database "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:21.797][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:21.798][conn$getEntryContent] 1 chunk(s) to download.
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:21.860][biodb::testThat]
biodb.INFO [2025-12-20 16:02:21.861][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:02:21.863][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:21.864][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:21.867][private$loadEntries] Creating entries from ids [8]: "2833, 3002, 3627, 4316, 50943, 5551, 916, 9606".
biodb.DEBUG[2025-12-20 16:02:21.868][conn$getEntryContent] Get NCBI Gene entry content(s) for 8 id(s)...
fscache.INFO [2025-12-20 16:02:21.870][cch$loadContents] Load 8 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-20 16:02:21.871][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:21.873][conn$getEntryContent] 8 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:21.874][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:21.875][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:21.876][private$retrieveContents] Get entry content(s) for 8 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:21.937][biodb::testThat]
biodb.INFO [2025-12-20 16:02:21.938][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:02:21.940][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:21.941][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:21.945][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:21.946][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:21.947][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:21.948][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:21.950][function(conn, opt)] Testing searchForEntries() with entry "2833" and field "name".
biodb.DEBUG[2025-12-20 16:02:21.965][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-20 16:02:21.966][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:21.968][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-20 16:02:21.969][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:21.970][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:21.972][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:21.973][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:21.996][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:22.080][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.082][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:02:22.083][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:22.084][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:22.094][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-20 16:02:22.095][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:22.097][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-20 16:02:22.098][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:22.099][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:22.101][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:22.102][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:22.103][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:22.164][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.165][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:02:22.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:22.168][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:22.173][private$loadEntries] Creating entries from ids [1]: "2833".
biodb.DEBUG[2025-12-20 16:02:22.174][conn$getEntryContent] Get NCBI Gene entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:22.176][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.gene-b6d7417e507eb4f1a2e0047bde5295e8.
biodb.DEBUG[2025-12-20 16:02:22.177][conn$getEntryContent] 0 NCBI Gene entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:22.179][conn$getEntryContent] 1 entry content(s) need to be fetched from NCBI Gene database "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:22.180][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:22.181][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:22.182][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:22.261][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.262][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:02:22.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:22.265][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:22.328][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.329][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:02:22.330][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:22.331][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.342][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.343][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:22.344][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:22.346][biodb::testThat]
Saving _problems/test_long_200_gene-38.R
biodb.INFO [2025-12-20 16:02:22.435][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.437][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:22.440][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:22.443][biodb::testThat]
biodb.INFO [2025-12-20 16:02:22.459][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:02:22.462][self$deleteConn] Connector "ncbi.gene" deleted.
biodb.INFO [2025-12-20 16:02:22.464][self$deleteConn] Connector "ncbi.ccds" deleted.
biodb.DEBUG[2025-12-20 16:02:22.466][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:02:22.468][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:22.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:22.472][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.476][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-20 16:02:22.488][biodb::testContext]
biodb.INFO [2025-12-20 16:02:22.490][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:22.492][biodb::testContext] Test context - Pubchem comp long tests
biodb.INFO [2025-12-20 16:02:22.495][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:22.497][biodb::testContext]
biodb.INFO [2025-12-20 16:02:22.501][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:22.505][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:22.513][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:22.516][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:02:22.518][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:02:22.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.534][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:02:22.536][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:02:22.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.544][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:02:22.547][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:02:22.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.553][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:02:22.556][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:02:22.559][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:02:22.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.565][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:02:22.567][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:02:22.568][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:02:22.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.573][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:02:22.574][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:02:22.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.579][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:02:22.580][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:02:22.582][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:02:22.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.590][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:02:22.591][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:02:22.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.596][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:02:22.597][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:02:22.598][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:02:22.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.603][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:22.604][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:02:22.605][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:02:22.607][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:02:22.608][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:02:22.609][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:02:22.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.614][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:02:22.615][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:02:22.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.620][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:02:22.621][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:02:22.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.626][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:02:22.627][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:02:22.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.632][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:02:22.633][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:02:22.635][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:02:22.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.639][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:22.641][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:02:22.651][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:02:22.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.656][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:02:22.657][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:02:22.659][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:02:22.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.663][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:02:22.666][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.667][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-20 16:02:22.668][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.669][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:22.671][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.676][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:22.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:22.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.680][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:02:22.681][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:22.682][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.683][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.685][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:22.685][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:22.685][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:22.685][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:22.685][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:22.686][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:22.691][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.692][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.694][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:22.695][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.696][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.698][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.699][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.700][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:22.701][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:22.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.704][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.705][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:02:22.707][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.709][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:22.710][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.711][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:22.713][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.714][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.715][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.718][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:22.719][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:22.720][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.721][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:02:22.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:22.724][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.725][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.726][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:22.726][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:22.726][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:22.726][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:22.726][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:22.728][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:22.729][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.730][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.731][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:22.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.735][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.736][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.737][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:22.738][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:22.739][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.741][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.742][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:02:22.744][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.746][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-20 16:02:22.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.748][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:22.750][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.751][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.752][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.753][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.754][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:22.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:22.757][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.758][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:02:22.760][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:22.761][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.762][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.763][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:22.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:22.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.770][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.772][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.773][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.774][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:22.775][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:22.776][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.778][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.779][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:02:22.781][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.783][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:22.784][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.785][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:22.786][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.788][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.789][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.790][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.791][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:22.793][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:22.794][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.795][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:02:22.796][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:22.798][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.799][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:22.800][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:22.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.805][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:22.806][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:22.807][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:22.808][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:22.810][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:22.812][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:22.813][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:22.814][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:22.816][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:22.817][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.901][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[2025-12-20 16:02:22.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:22.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:22.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:22.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:22.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:22.914][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:02:22.916][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:02:22.917][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:02:22.919][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:02:22.921][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:02:22.923][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:22.925][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:22.926][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:22.928][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:02:22.930][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:22.932][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:22.934][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:02:22.936][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:22.937][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:22.939][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:22.941][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:22.943][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:02:22.945][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:02:22.947][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:02:22.949][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:02:22.955][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:02:22.957][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:02:22.959][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:02:22.961][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:02:22.962][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:02:22.964][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:02:22.966][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:02:22.968][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:02:22.969][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:02:22.971][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:02:22.973][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:02:22.974][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:02:22.976][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:02:22.978][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:02:22.980][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:02:22.981][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:02:22.983][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:02:22.985][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:02:22.986][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:02:22.988][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:02:22.990][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:02:22.992][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:02:22.993][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:02:22.995][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:02:22.997][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:02:22.999][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:23.000][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:02:23.002][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:02:23.004][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:02:23.006][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:02:23.008][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:02:23.011][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:02:23.014][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:02:23.018][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:02:23.020][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:02:23.022][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:02:23.024][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:02:23.027][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:02:23.031][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:02:23.035][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:02:23.039][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:02:23.042][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:02:23.045][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:02:23.048][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:02:23.051][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:02:23.055][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:02:23.058][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:02:23.061][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:02:23.064][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:02:23.067][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:02:23.070][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:02:23.073][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:02:23.076][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:02:23.079][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:02:23.082][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:02:23.086][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:02:23.089][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:02:23.092][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:02:23.096][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:02:23.099][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:02:23.102][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:02:23.105][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:02:23.108][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:02:23.112][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:02:23.114][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:23.115][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:23.117][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.119][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.193][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[2025-12-20 16:02:23.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:23.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:23.275][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:23.280][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-20 16:02:23.285][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.287][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-20 16:02:23.290][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.292][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:23.295][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.300][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.302][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.305][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-20 16:02:23.309][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:23.312][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.318][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-20 16:02:23.320][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:23.322][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-20 16:02:23.322][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-20 16:02:23.329][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:23.331][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:23.333][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:23.336][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.341][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:23.343][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.346][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.348][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.350][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:23.350][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-20 16:02:23.353][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:23.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:23.357][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.359][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:23.362][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-20 16:02:23.366][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.368][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-20 16:02:23.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:23.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.379][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.381][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.383][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:23.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:23.388][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.390][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-20 16:02:23.392][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:23.394][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-20 16:02:23.394][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-20 16:02:23.394][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-20 16:02:23.394][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-20 16:02:23.394][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-20 16:02:23.394][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-20 16:02:23.396][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:23.399][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:23.401][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:23.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:23.410][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.414][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.416][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:23.416][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:23.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:23.420][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:23.422][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.424][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:23.427][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-20 16:02:23.431][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:23.434][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-20 16:02:23.436][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.439][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:23.441][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.446][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.448][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.451][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:23.453][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:23.456][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.458][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-20 16:02:23.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.464][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:23.467][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:23.470][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:23.470][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:23.470][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:23.472][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:23.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.476][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.478][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:23.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.487][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:23.487][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:23.487][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:23.489][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:23.491][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:23.493][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.496][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:23.499][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-20 16:02:23.504][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.506][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-20 16:02:23.509][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.511][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:23.513][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.515][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.518][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.531][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:23.534][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:23.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.538][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-20 16:02:23.541][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:23.543][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-20 16:02:23.543][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:23.546][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:23.548][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:23.551][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:23.553][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.557][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:23.559][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:23.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:23.564][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:23.566][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:23.566][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:23.566][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:23.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:23.571][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:23.574][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:23.576][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:23.579][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-20 16:02:23.583][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:23.586][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:23.590][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-20 16:02:23.592][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:23.595][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-20 16:02:23.609][super$initialize] Initialize connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-20 16:02:23.621][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.comp for database class ncbi.pubchem.comp .
biodb.INFO [2025-12-20 16:02:23.627][biodb::testThat]
biodb.INFO [2025-12-20 16:02:23.629][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:02:23.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:23.633][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:23.637][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-2-content.xml".
biodb.DEBUG[2025-12-20 16:02:23.639][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:23.643][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-12-20 16:02:23.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:23.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:23.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:23.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:23.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:23.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:23.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:23.668][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.672][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.678][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.680][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.682][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.703][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.705][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.707][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.718][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.720][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.725][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.727][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.738][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.740][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.742][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.744][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.749][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.750][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.753][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.754][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.759][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:23.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:23.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.763][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.765][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:23.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:23.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.770][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:23.772][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:23.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.774][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:23.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:23.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.781][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:23.782][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:23.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.785][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:23.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:23.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.792][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:23.793][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:23.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.795][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:23.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:23.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.802][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:23.804][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:23.805][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.806][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.808][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:23.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:23.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.813][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:23.814][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:23.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.817][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:23.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:23.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.824][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:23.825][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:23.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.827][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.829][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:23.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:23.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.834][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:23.836][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:23.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.838][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.839][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:23.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:23.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.845][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-12-20 16:02:23.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:23.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.865][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-12-20 16:02:23.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.875][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:23.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.880][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-12-20 16:02:23.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.890][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:23.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.895][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-12-20 16:02:23.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:23.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.910][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-12-20 16:02:23.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.920][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:23.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:23.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:23.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.931][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:23.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:23.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.936][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:23.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.946][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:23.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:23.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:23.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:23.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:23.987][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2.
biodb.TRACE[2025-12-20 16:02:23.990][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:23.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:23.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:23.996][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:23.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:23.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.001][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:24.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:24.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:24.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:24.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.011][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:24.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:24.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:24.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:24.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:24.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:24.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.038][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.082][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.087][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.092][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:24.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.124][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.126][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.128][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.145][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:24.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.160][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:24.162][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.164][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.165][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:24.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:24.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.196][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:24.198][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.200][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:24.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.217][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.228][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.233][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.239][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.240][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.241][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.243][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.258][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.268][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.274][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.275][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.277][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.279][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.294][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.300][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.305][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.310][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.311][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.314][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.315][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.331][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.341][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.346][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.348][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.350][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.372][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.378][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.383][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.388][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.389][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.392][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.393][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.409][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.414][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.419][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.424][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.425][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.426][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.428][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.429][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.445][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.450][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.455][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.460][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.462][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.464][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.480][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.496][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.501][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.502][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.504][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.506][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.521][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.527][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.532][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.537][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.538][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.539][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.541][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.542][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:24.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:24.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:24.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:24.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:24.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:24.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.573][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:24.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:24.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.577][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:24.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:24.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.611][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.612][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.613][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.619][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.636][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.651][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.652][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.653][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.654][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.671][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.672][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.675][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.681][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.683][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.685][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.691][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.693][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.695][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.702][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.703][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.706][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.712][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.713][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.716][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.722][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.724][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.726][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.733][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.736][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.743][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.749][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.752][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.758][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.759][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.762][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.768][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.770][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.772][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.779][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.780][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.783][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.789][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.791][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.793][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.800][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:24.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:24.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.804][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.810][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.812][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.814][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.821][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.822][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.823][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.824][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.832][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.comp-65124-content.xml".
biodb.DEBUG[2025-12-20 16:02:24.833][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Compound entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:24.835][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Compound entries.
biodb.DEBUG[2025-12-20 16:02:24.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:24.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:24.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:24.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:24.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:24.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:24.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:24.852][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.857][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:24.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:24.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.863][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.865][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.867][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.874][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.875][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.882][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.884][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:24.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.889][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.891][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.893][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.895][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.900][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.901][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.904][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.905][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:24.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.911][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.912][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.914][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:24.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.921][ef$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:24.922][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.925][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.926][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2025-12-20 16:02:24.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:24.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.932][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.933][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.935][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.942][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.943][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.946][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:24.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:24.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.953][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.954][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.956][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:24.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.963][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.965][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.967][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.969][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:24.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:24.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.974][ef$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:24.976][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.978][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.weight.
biodb.TRACE[2025-12-20 16:02:24.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:24.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.985][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.986][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.989][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.991][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:24.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:24.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:24.996][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.997][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:24.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.000][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.001][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.012][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.PREF.
biodb.TRACE[2025-12-20 16:02:25.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.017][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.027][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.ALLOWED.
biodb.TRACE[2025-12-20 16:02:25.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.032][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.042][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.TRAD.
biodb.TRACE[2025-12-20 16:02:25.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.053][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.SYST.
biodb.TRACE[2025-12-20 16:02:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.063][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.068][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.073][self$getBiodb()$getEntryFields()$get] Asked field names are: COMP.IUPAC.NAME.CAS.
biodb.TRACE[2025-12-20 16:02:25.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.078][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.083][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.093][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.098][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.108][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:25.150][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 65124.
biodb.TRACE[2025-12-20 16:02:25.153][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:25.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:25.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.158][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:25.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:25.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.164][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.169][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:25.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:25.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.174][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:25.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:25.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:25.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:25.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.203][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.247][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.252][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:25.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.297][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.299][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.301][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.334][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.335][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.338][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.372][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.374][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.375][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.376][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:25.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:25.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:25.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:25.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:25.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:25.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.417][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:25.418][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:25.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.420][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.437][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:25.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:25.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.442][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:25.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:25.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.447][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:25.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:25.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.453][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:25.454][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:25.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.456][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.458][self$getBiodb()$getEntryFields()$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:25.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:25.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.473][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.479][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.489][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.491][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.493][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:25.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.510][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.516][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.532][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.533][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.535][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.536][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:25.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.568][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.569][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.571][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.572][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:25.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:25.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:25.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:25.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:25.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:25.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.604][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:25.605][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:25.607][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.608][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:25.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:25.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.625][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.631][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.636][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.641][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.642][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.644][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.646][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.666][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.672][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.677][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.682][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.683][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.684][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.686][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.703][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.708][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.718][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.720][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.721][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.722][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.723][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.740][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.745][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.750][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.756][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.757][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.759][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.761][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.777][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.788][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.799][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.801][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.803][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.805][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.827][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.838][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.840][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.842][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.860][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:25.861][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:25.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.864][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.871][ef$get] Asked field names are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.873][ef$get] Realnames of fields are: comp.iupac.name.allowed.
biodb.TRACE[2025-12-20 16:02:25.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.875][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.882][ef$get] Asked field names are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.884][ef$get] Realnames of fields are: comp.iupac.name.cas.
biodb.TRACE[2025-12-20 16:02:25.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.887][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.893][ef$get] Asked field names are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.895][ef$get] Realnames of fields are: comp.iupac.name.pref.
biodb.TRACE[2025-12-20 16:02:25.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.897][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.904][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.905][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-12-20 16:02:25.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.908][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.914][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.916][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-12-20 16:02:25.917][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.918][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.930][ef$get] Asked field names are: formula.
biodb.TRACE[2025-12-20 16:02:25.932][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-12-20 16:02:25.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.934][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.941][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-12-20 16:02:25.942][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-12-20 16:02:25.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.945][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.951][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.953][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-12-20 16:02:25.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.955][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.962][ef$get] Asked field names are: logp.
biodb.TRACE[2025-12-20 16:02:25.963][ef$get] Realnames of fields are: logp.
biodb.TRACE[2025-12-20 16:02:25.965][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.966][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.972][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.974][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:25.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.976][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.983][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.985][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-12-20 16:02:25.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.987][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:25.994][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:25.996][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:25.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:25.999][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:26.006][ef$get] Asked field names are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:26.007][ef$get] Realnames of fields are: smiles.canonical.
biodb.TRACE[2025-12-20 16:02:26.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.010][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:26.017][ef$get] Asked field names are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:26.018][ef$get] Realnames of fields are: smiles.isomeric.
biodb.TRACE[2025-12-20 16:02:26.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.021][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:26.031][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.032][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:02:26.034][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.035][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.038][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-20 16:02:26.040][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:26.042][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.044][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.045][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.046][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.047][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.049][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.111][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.112][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:02:26.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.115][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:26.119][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:26.120][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:26.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.123][ef$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:26.125][function(conn, opt)] Testing searchForEntries() with entry "2" and field "name".
biodb.DEBUG[2025-12-20 16:02:26.136][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-20 16:02:26.138][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:26.140][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.141][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.142][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.144][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.145][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.146][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.208][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.209][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:02:26.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.211][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.221][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-20 16:02:26.222][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:26.224][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.225][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.227][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.228][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.229][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.230][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.293][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.294][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:02:26.295][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.296][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.302][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-20 16:02:26.303][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:26.305][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.306][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.308][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.309][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.310][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.311][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.369][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.371][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:02:26.372][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.373][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.436][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.438][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:02:26.439][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.440][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.498][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.504][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:26.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.507][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.564][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.566][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:26.567][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.568][biodb::testThat]
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-12-20 16:02:26.639][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:26.641][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:26.642][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.643][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:26.644][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:26.645][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:26.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.648][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:26.650][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.651][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-12-20 16:02:26.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.653][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.663][private$loadEntries] Creating entries from ids [1]: "2".
biodb.DEBUG[2025-12-20 16:02:26.664][conn$getEntryContent] Get PubChem Compound entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:26.666][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.667][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.668][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.670][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.671][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.672][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.734][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.735][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-12-20 16:02:26.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.737][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.741][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-20 16:02:26.743][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:26.745][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.746][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.747][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.749][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.750][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.751][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.810][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.811][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-12-20 16:02:26.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.813][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.817][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-20 16:02:26.818][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:26.820][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.821][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.827][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.829][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.830][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.832][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:26.890][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.892][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-12-20 16:02:26.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.894][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.898][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-20 16:02:26.899][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:26.901][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.902][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.904][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.905][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.906][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.907][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.TRACE[2025-12-20 16:02:26.970][ef$get] Asked field names are: name.
biodb.TRACE[2025-12-20 16:02:26.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-12-20 16:02:26.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.974][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:26.976][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:26.977][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-12-20 16:02:26.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:26.979][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:26.981][biodb::testThat]
biodb.INFO [2025-12-20 16:02:26.983][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-12-20 16:02:26.984][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:26.985][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:26.989][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-20 16:02:26.990][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:26.992][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:26.994][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:26.995][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:26.996][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:26.997][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:26.999][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:27.063][biodb::testThat]
biodb.INFO [2025-12-20 16:02:27.065][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-12-20 16:02:27.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:27.067][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:27.071][private$loadEntries] Creating entries from ids [2]: "2, 65124".
biodb.DEBUG[2025-12-20 16:02:27.072][conn$getEntryContent] Get PubChem Compound entry content(s) for 2 id(s)...
fscache.INFO [2025-12-20 16:02:27.074][cch$loadContents] Load 2 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.comp-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:27.075][conn$getEntryContent] 0 PubChem Compound entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:27.077][conn$getEntryContent] 2 entry content(s) need to be fetched from PubChem Compound database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:27.078][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:27.079][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:27.081][private$retrieveContents] Get entry content(s) for 2 id(s)...
Saving _problems/test_long_300_pubchem.comp-38.R
biodb.INFO [2025-12-20 16:02:27.140][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:02:27.141][self$deleteConn] Connector "ncbi.pubchem.comp" deleted.
biodb.DEBUG[2025-12-20 16:02:27.143][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:02:27.144][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.146][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.148][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-12-20 16:02:27.160][biodb::testContext]
biodb.INFO [2025-12-20 16:02:27.162][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:27.163][biodb::testContext] Test context - Pubchem Subst long tests
biodb.INFO [2025-12-20 16:02:27.164][biodb::testContext] ********************************************************************************
biodb.INFO [2025-12-20 16:02:27.165][biodb::testContext]
biodb.INFO [2025-12-20 16:02:27.168][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:27.170][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:27.175][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:27.176][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-12-20 16:02:27.177][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-12-20 16:02:27.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.182][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-12-20 16:02:27.183][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-12-20 16:02:27.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.188][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-12-20 16:02:27.190][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-12-20 16:02:27.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.193][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[2025-12-20 16:02:27.194][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-12-20 16:02:27.196][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-12-20 16:02:27.197][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-12-20 16:02:27.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.201][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-12-20 16:02:27.203][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-12-20 16:02:27.204][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-12-20 16:02:27.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.209][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-12-20 16:02:27.210][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-12-20 16:02:27.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.215][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-12-20 16:02:27.216][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-12-20 16:02:27.217][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-12-20 16:02:27.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.222][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-12-20 16:02:27.223][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-12-20 16:02:27.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.228][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-12-20 16:02:27.229][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-12-20 16:02:27.230][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-12-20 16:02:27.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.235][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:27.237][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-12-20 16:02:27.238][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-12-20 16:02:27.239][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-12-20 16:02:27.240][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-12-20 16:02:27.242][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-12-20 16:02:27.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.247][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-12-20 16:02:27.248][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-12-20 16:02:27.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.253][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-12-20 16:02:27.254][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-12-20 16:02:27.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.259][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-12-20 16:02:27.260][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-12-20 16:02:27.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.265][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-12-20 16:02:27.266][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-12-20 16:02:27.268][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-12-20 16:02:27.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.405][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-12-20 16:02:27.406][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-12-20 16:02:27.417][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-12-20 16:02:27.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.421][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-12-20 16:02:27.422][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-12-20 16:02:27.424][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-12-20 16:02:27.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.428][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-12-20 16:02:27.430][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.432][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-12-20 16:02:27.433][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:27.435][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.437][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.438][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.439][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.440][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:27.441][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:27.443][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.444][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-12-20 16:02:27.445][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:27.446][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.447][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.449][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:27.449][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:27.449][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:27.449][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:27.449][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:27.450][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:27.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.453][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:27.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.457][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.458][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.459][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:27.460][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:27.462][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.463][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.464][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-12-20 16:02:27.466][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.468][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:27.469][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:27.471][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.472][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.474][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.475][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.476][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:27.477][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:27.479][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.480][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-12-20 16:02:27.481][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:27.482][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.484][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.485][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:27.485][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:27.485][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:27.485][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-12-20 16:02:27.485][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-12-20 16:02:27.486][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:27.487][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:27.491][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.492][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.493][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.494][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.496][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:27.497][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:27.498][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.499][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.501][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-12-20 16:02:27.503][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.504][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-12-20 16:02:27.506][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.507][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:27.508][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.509][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.511][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.512][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.513][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-12-20 16:02:27.514][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:27.516][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.517][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-12-20 16:02:27.518][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:27.519][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.521][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.522][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.523][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:27.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.527][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:27.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.530][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.531][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.533][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:27.534][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:27.535][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.536][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.538][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-12-20 16:02:27.540][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.541][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-12-20 16:02:27.542][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.544][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:27.545][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.546][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.547][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.549][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.550][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-12-20 16:02:27.551][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:27.553][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.554][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-12-20 16:02:27.555][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:27.556][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.558][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:27.559][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.561][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-12-20 16:02:27.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.565][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:27.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:27.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:27.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:27.571][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.572][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:27.573][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:27.575][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:27.576][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:27.578][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:27.580][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.689][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-12-20 16:02:27.691][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-12-20 16:02:27.693][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-12-20 16:02:27.696][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-12-20 16:02:27.698][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-12-20 16:02:27.700][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-12-20 16:02:27.702][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:27.704][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:27.706][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-12-20 16:02:27.708][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-12-20 16:02:27.710][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-12-20 16:02:27.713][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-12-20 16:02:27.715][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-12-20 16:02:27.717][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-12-20 16:02:27.719][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:27.721][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:27.724][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-12-20 16:02:27.726][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-12-20 16:02:27.728][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-12-20 16:02:27.730][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-12-20 16:02:27.732][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-12-20 16:02:27.734][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-12-20 16:02:27.736][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-12-20 16:02:27.739][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-12-20 16:02:27.741][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-12-20 16:02:27.743][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-12-20 16:02:27.745][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-12-20 16:02:27.747][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-12-20 16:02:27.749][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-12-20 16:02:27.751][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-12-20 16:02:27.753][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-12-20 16:02:27.756][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-12-20 16:02:27.758][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-12-20 16:02:27.760][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-12-20 16:02:27.762][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-12-20 16:02:27.764][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-12-20 16:02:27.767][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-12-20 16:02:27.769][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-12-20 16:02:27.771][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-12-20 16:02:27.773][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-12-20 16:02:27.775][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-12-20 16:02:27.778][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-12-20 16:02:27.780][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-12-20 16:02:27.782][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-12-20 16:02:27.784][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-12-20 16:02:27.786][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:27.789][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-12-20 16:02:27.791][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-12-20 16:02:27.793][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-12-20 16:02:27.795][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-12-20 16:02:27.797][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-12-20 16:02:27.798][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-12-20 16:02:27.800][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-12-20 16:02:27.802][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-12-20 16:02:27.805][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-12-20 16:02:27.807][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-12-20 16:02:27.809][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-12-20 16:02:27.812][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-12-20 16:02:27.814][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-12-20 16:02:27.816][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-12-20 16:02:27.818][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-12-20 16:02:27.820][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-12-20 16:02:27.822][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-12-20 16:02:27.825][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-12-20 16:02:27.827][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-12-20 16:02:27.829][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-12-20 16:02:27.831][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-12-20 16:02:27.833][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-12-20 16:02:27.835][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-12-20 16:02:27.837][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-12-20 16:02:27.839][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-12-20 16:02:27.841][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-12-20 16:02:27.843][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-12-20 16:02:27.846][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-12-20 16:02:27.848][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-12-20 16:02:27.850][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-12-20 16:02:27.852][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-12-20 16:02:27.854][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-12-20 16:02:27.856][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-12-20 16:02:27.858][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-12-20 16:02:27.860][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-12-20 16:02:27.862][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-12-20 16:02:27.864][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-12-20 16:02:27.866][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-12-20 16:02:27.868][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2025-12-20 16:02:27.870][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-12-20 16:02:27.871][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.874][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.926][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[2025-12-20 16:02:27.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.934][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[2025-12-20 16:02:27.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.957][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[2025-12-20 16:02:27.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.991][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:27.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:27.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:27.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:27.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:27.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-12-20 16:02:27.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:27.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:28.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:28.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:28.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:28.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-12-20 16:02:28.006][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/definitions.yml".
biodb.DEBUG[2025-12-20 16:02:28.008][self$getDbsInfo()$define] Define connector ncbi.ccds.
biodb.DEBUG[2025-12-20 16:02:28.010][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.012][self$setPropertyValue] Setting property "description" to "NCBI CCDS database.".
biodb.DEBUG[2025-12-20 16:02:28.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:28.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.018][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.019][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.021][self$setPropertyValue] Setting property "entry.content.type" to "html".
biodb.DEBUG[2025-12-20 16:02:28.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:28.023][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.025][self$setPropertyValue] Setting property "name" to "NCBI CCDS".
biodb.DEBUG[2025-12-20 16:02:28.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:28.027][self$setPropertyValue] Setting property "parsing.expr" to "list(attr = "value", path = "//input[@id='DATA']")".
biodb.DEBUG[2025-12-20 16:02:28.027][self$setPropertyValue] Setting property "parsing.expr" to "//b[starts-with(.,'Nucleotide Sequence')]/../tt".
biodb.DEBUG[2025-12-20 16:02:28.028][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:28.030][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:28.031][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:28.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:28.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.039][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/CCDS/".
biodb.DEBUG[2025-12-20 16:02:28.039][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils".
biodb.DEBUG[2025-12-20 16:02:28.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:28.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:28.043][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.044][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:28.046][self$getDbsInfo()$define] Define connector ncbi.gene.
biodb.DEBUG[2025-12-20 16:02:28.048][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.050][self$setPropertyValue] Setting property "description" to "NCBI Gene database.".
biodb.DEBUG[2025-12-20 16:02:28.051][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.052][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:28.053][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.056][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.057][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.059][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:28.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:28.061][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.062][self$setPropertyValue] Setting property "name" to "NCBI Gene".
biodb.DEBUG[2025-12-20 16:02:28.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:28.065][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-track_geneid".
biodb.DEBUG[2025-12-20 16:02:28.065][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_desc".
biodb.DEBUG[2025-12-20 16:02:28.065][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_maploc".
biodb.DEBUG[2025-12-20 16:02:28.065][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_locus".
biodb.DEBUG[2025-12-20 16:02:28.065][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-ref_syn_E".
biodb.DEBUG[2025-12-20 16:02:28.065][self$setPropertyValue] Setting property "parsing.expr" to "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str".
biodb.DEBUG[2025-12-20 16:02:28.066][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:28.068][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:28.069][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-12-20 16:02:28.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:28.074][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.076][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.077][self$setPropertyValue] Setting property "urls" to "https://www.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:28.077][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:28.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:28.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:28.081][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.082][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:28.084][self$getDbsInfo()$define] Define connector ncbi.pubchem.comp.
biodb.DEBUG[2025-12-20 16:02:28.086][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:28.087][self$setPropertyValue] Setting property "description" to "PubChem Compound database.".
biodb.DEBUG[2025-12-20 16:02:28.089][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.090][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:28.091][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.094][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.096][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:28.098][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:28.099][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.100][self$setPropertyValue] Setting property "name" to "PubChem Compound".
biodb.DEBUG[2025-12-20 16:02:28.101][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Allowed']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='CAS-like Style']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Preferred']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Systematic']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='IUPAC Name']/../PC-Urn_name[text()='Traditional']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Mass']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Formula']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChI']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='InChIKey']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Log P']/../../..//PC-InfoData_value_fval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='Molecular Weight']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Canonical']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.103][self$setPropertyValue] Setting property "parsing.expr" to "//PC-Urn_label[text()='SMILES']/../PC-Urn_name[text()='Isomeric']/../../..//PC-InfoData_value_sval".
biodb.DEBUG[2025-12-20 16:02:28.104][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:28.106][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-12-20 16:02:28.106][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-12-20 16:02:28.106][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-12-20 16:02:28.107][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:28.108][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.109][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.111][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:28.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.114][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.115][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:28.115][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:28.115][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:28.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:28.118][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:28.119][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.120][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:28.122][self$getDbsInfo()$define] Define connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-20 16:02:28.124][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.126][self$setPropertyValue] Setting property "description" to "PubChem Substance database.".
biodb.DEBUG[2025-12-20 16:02:28.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-12-20 16:02:28.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.131][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.132][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.133][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.135][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-12-20 16:02:28.136][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-12-20 16:02:28.137][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.138][self$setPropertyValue] Setting property "name" to "PubChem Substance".
biodb.DEBUG[2025-12-20 16:02:28.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-12-20 16:02:28.141][self$setPropertyValue] Setting property "parsing.expr" to "//PC-ID_id".
biodb.DEBUG[2025-12-20 16:02:28.141][self$setPropertyValue] Setting property "parsing.expr" to "//PC-CompoundType_id_cid".
biodb.DEBUG[2025-12-20 16:02:28.142][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-12-20 16:02:28.144][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-12-20 16:02:28.145][self$setPropertyValue] Setting property "scheduler.n" to "5".
biodb.DEBUG[2025-12-20 16:02:28.146][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.149][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-12-20 16:02:28.150][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-12-20 16:02:28.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-12-20 16:02:28.152][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-12-20 16:02:28.154][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:28.154][self$setPropertyValue] Setting property "urls" to "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/".
biodb.DEBUG[2025-12-20 16:02:28.154][self$setPropertyValue] Setting property "urls" to "https://pubchem.ncbi.nlm.nih.gov/rest/pug/".
biodb.DEBUG[2025-12-20 16:02:28.155][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-12-20 16:02:28.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-12-20 16:02:28.157][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-12-20 16:02:28.159][self$setPropertyValue] Setting property "xml.ns" to "http://www.ncbi.nlm.nih.gov".
biodb.DEBUG[2025-12-20 16:02:28.160][self$getEntryFields()$define] Define field ncbi.ccds.id.
biodb.DEBUG[2025-12-20 16:02:28.162][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-12-20 16:02:28.164][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-12-20 16:02:28.166][self$getEntryFields()$define] Define field ncbi.pubchem.subst.id.
biodb.DEBUG[2025-12-20 16:02:28.168][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-12-20 16:02:28.170][self$getEntryFields()$define] Define field uniprot.id.
biodb.DEBUG[2025-12-20 16:02:28.176][super$initialize] Initialize connector ncbi.pubchem.subst.
biodb.DEBUG[2025-12-20 16:02:28.186][biodb$getFactory()$createConn] Creating new connector ncbi.pubchem.subst for database class ncbi.pubchem.subst .
biodb.INFO [2025-12-20 16:02:28.191][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.192][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-12-20 16:02:28.194][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.195][biodb::testThat]
biodb.TRACE[2025-12-20 16:02:28.198][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/biodbNcbi/testref/entry-ncbi.pubchem.subst-3-content.xml".
biodb.DEBUG[2025-12-20 16:02:28.200][biodb$getFactory()$createEntryFromCo ...] Creating PubChem Substance entries from 1 content(s).
biodb.DEBUG[2025-12-20 16:02:28.204][biodb$getFactory()$createEntryFromCo ...] Parsing 1 PubChem Substance entries.
biodb.DEBUG[2025-12-20 16:02:28.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-12-20 16:02:28.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:28.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:28.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:28.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:28.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:28.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-12-20 16:02:28.221][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.223][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.225][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.232][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.233][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.235][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.236][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.249][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.259][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-12-20 16:02:28.297][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 3.
biodb.TRACE[2025-12-20 16:02:28.299][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:28.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:28.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: aa.seq.
biodb.TRACE[2025-12-20 16:02:28.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: aa.seq.
biodb.TRACE[2025-12-20 16:02:28.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.315][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:28.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.ccds.id.
biodb.TRACE[2025-12-20 16:02:28.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:28.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:28.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-12-20 16:02:28.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-12-20 16:02:28.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.330][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:28.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-12-20 16:02:28.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.335][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:28.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-12-20 16:02:28.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.351][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.394][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.399][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.404][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.subst.id.
biodb.TRACE[2025-12-20 16:02:28.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.432][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.433][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.436][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.452][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.458][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.463][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.468][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.469][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.472][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.473][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.488][ef$get] Asked field names are: accession.
biodb.TRACE[2025-12-20 16:02:28.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-12-20 16:02:28.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.492][ef$get] fields variable is a list.
biodb.TRACE[2025-12-20 16:02:28.499][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.500][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-12-20 16:02:28.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-12-20 16:02:28.503][ef$get] fields variable is a list.
biodb.INFO [2025-12-20 16:02:28.513][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.514][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-12-20 16:02:28.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.517][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:28.520][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-12-20 16:02:28.523][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:28.525][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:28.526][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:28.527][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:28.529][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:28.530][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:28.531][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-20 16:02:28.589][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.590][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-12-20 16:02:28.591][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.592][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.601][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.602][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-12-20 16:02:28.603][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.604][biodb::testThat]
biodb.WARN [2025-12-20 16:02:28.609][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-12-20 16:02:28.614][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-12-20 16:02:28.626][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.627][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-12-20 16:02:28.628][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.629][biodb::testThat]
biodb.DEBUG[2025-12-20 16:02:28.634][private$loadEntries] Creating entries from ids [1]: "3".
biodb.DEBUG[2025-12-20 16:02:28.636][conn$getEntryContent] Get PubChem Substance entry content(s) for 1 id(s)...
fscache.INFO [2025-12-20 16:02:28.638][cch$loadContents] Load 1 contents, from /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/ncbi.pubchem.subst-e80afa72f6aa7425ca0c72f99f7b9d75.
biodb.DEBUG[2025-12-20 16:02:28.639][conn$getEntryContent] 0 PubChem Substance entry content(s) loaded from cache.
biodb.DEBUG[2025-12-20 16:02:28.640][conn$getEntryContent] 1 entry content(s) need to be fetched from PubChem Substance database "https://pubchem.ncbi.nlm.nih.gov/".
biodb.DEBUG[2025-12-20 16:02:28.642][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-12-20 16:02:28.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.INFO [2025-12-20 16:02:28.644][private$retrieveContents] Get entry content(s) for 1 id(s)...
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-20 16:02:28.704][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.705][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-12-20 16:02:28.707][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.708][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-20 16:02:28.772][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.774][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-12-20 16:02:28.775][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.776][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-20 16:02:28.835][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.836][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:28.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.839][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-20 16:02:28.898][biodb::testThat]
biodb.INFO [2025-12-20 16:02:28.900][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-12-20 16:02:28.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-12-20 16:02:28.902][biodb::testThat]
Saving _problems/test_long_400_pubchem.subst-38.R
biodb.INFO [2025-12-20 16:02:28.961][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-12-20 16:02:28.963][self$deleteConn] Connector "ncbi.pubchem.subst" deleted.
biodb.DEBUG[2025-12-20 16:02:28.964][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-12-20 16:02:28.965][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-12-20 16:02:28.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-12-20 16:02:28.967][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-12-20 16:02:28.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-12-20 16:02:28.970][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-12-20 16:02:28.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_ccds.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$getEntryPageUrl(id)
 12.                     └─private$doGetEntryPageUrl(entry.id)
 13.                       └─base::vapply(id, fct, FUN.VALUE = "")
 14.                         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$getEntryPageUrl(id)
 14.                         └─private$doGetEntryPageUrl(entry.id)
 15.                           └─base::vapply(id, fct, FUN.VALUE = "")
 16.                             └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_100_ccds.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbCcdsC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): Entry fields have a correct value ──────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$saveEntriesAsJson(id, list(e))
  4.     └─private$bdb$saveEntriesAsJson(entries, json.files)
  5.       └─entries[[i]]$getFieldsAsJson(compute = compute)
  6.         └─self$computeFields()
  7.           └─private$computeField(f)
  8.             └─self$getBiodb()$getFactory()$getEntry(db, id = db.id)
  9.               └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 10.                 └─conn$getEntryContent(ids)
 11.                   └─self$getEntryContentFromDb(ch.missing.ids)
 12.                     └─private$doGetEntryContentFromDb(entry.id)
 13.                       └─private$doGetEntryContentOneByOne(id)
 14.                         └─self$getEntryContentRequest(entry.id, concatenate = FALSE)
 15.                           └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 16.                             └─self$getEntryPageUrl(id)
 17.                               └─private$doGetEntryPageUrl(entry.id)
 18.                                 └─base::vapply(id, fct, FUN.VALUE = "")
 19.                                   └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 11.                   └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can search for an entry by name. ────
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 12.                     └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
 13.                       └─self$wsEfetch(id, retmode = "xml", retfmt = "request")
── Error ('test_long_200_gene.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_200_gene.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbGnCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by searchable field ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for an entry by name. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_300_pubchem.comp.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_300_pubchem.comp.R:37:1'): We can search for a compound ───
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() accepts a single vector. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): ppm tolerance works in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Input data frame is not modified by annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): annotateMzValues() works correctly with real values. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_300_pubchem.comp.R:37:1'): Additional fields are accepted in annotateMzValues() ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcCC>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$retrieveContents(...)
 10.                 └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 11.                   └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): RT unit is defined when there is an RT value. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$retrieveContents(...)
  9.               └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 10.                 └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can load an entry from the database. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$retrieveContents(...)
 11.                   └─self$getEntryContentRequest(id, concatenate = concatenate, max.length = URL.MAX.LENGTH)
 12.                     └─private$doGetEntryContentRequest(entry.id, concatenate = concatenate)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry page. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): We can get a URL pointing to the entry image. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids)
 4.     └─private$doGetEntryImageUrl(entry.id)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry page URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, fct, FUN.VALUE = "")
 6.         └─biodbNcbi (local) FUN(X[[i]], ...)
── Error ('test_long_400_pubchem.subst.R:37:1'): The entry image URL can be downloaded. ──
Error: 'BiodbUrl' is not an exported object from 'namespace:biodb'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
 3.   └─conn$getEntryImageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryImageUrl(entry.id)

[ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
Error:
! Test failures.
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNcbi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNcbi/DESCRIPTION’ ... OK
* this is package ‘biodbNcbi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNcbi’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    testref   7.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NcbiCcdsConn.Rd: BiodbFactory, BiodbConn
  NcbiCcdsEntry.Rd: BiodbHtmlEntry
  NcbiEntrezConn.Rd: BiodbConn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcbPbcSC>`, opt = `<named list>`)
   3.   └─conn$getEntryImageUrl(ref.ids[[1]])
   4.     └─private$doGetEntryImageUrl(entry.id)
  
  [ FAIL 31 | WARN 1 | SKIP 1 | PASS 247 ]
  Error:
  ! Test failures.
  Warning message:
  In fun(libname, pkgname) :
    Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
    version 3.23
  Execution halted
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNcbi.Rcheck/00check.log’
for details.

Installation output

biodbNcbi.Rcheck/00install.out

* installing *source* package ‘biodbNcbi’ ...
** this is package ‘biodbNcbi’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNcbi' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNcbi)