Back to Long Tests report for BioC 3.22

This page was generated on 2025-04-26 23:55 -0400 (Sat, 26 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4722
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4494
lconwaymacOS 12.7.1 Montereyx86_644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4523
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 9/30HostnameOS / ArchCHECK
biodbNci 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-26 09:55 -0400 (Sat, 26 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 536802f
git_last_commit_date: 2025-04-15 12:47:37 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on lconway

To the developers/maintainers of the biodbNci 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: biodbNci
Version: 1.13.0
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 biodbNci_1.13.0.tar.gz
StartedAt: 2025-04-26 16:01:05 -0400 (Sat, 26 Apr 2025)
EndedAt: 2025-04-26 16:27:06 -0400 (Sat, 26 Apr 2025)
EllapsedTime: 1561.6 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-04-26 16:02:05.780][biodb::testContext]
biodb.INFO [2025-04-26 16:02:05.783][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:02:05.784][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-26 16:02:05.785][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:02:05.786][biodb::testContext]
biodb.INFO [2025-04-26 16:02:05.791][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:02:05.792][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:02:05.798][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:02:05.799][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:02:05.800][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:02:05.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.803][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:02:05.816][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:02:05.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.820][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:02:05.820][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:02:05.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.823][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:02:05.824][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:02:05.825][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:02:05.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.827][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:02:05.828][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:02:05.829][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:02:05.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.832][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:02:05.833][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:02:05.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.835][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:02:05.836][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:02:05.837][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:02:05.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.839][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:02:05.840][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:02:05.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.843][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:02:05.844][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:02:05.844][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:02:05.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.847][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:02:05.848][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:02:05.849][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:02:05.850][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:02:05.850][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:02:05.851][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:02:05.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.854][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:02:05.855][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:02:05.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.858][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:02:05.858][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:02:05.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.861][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:02:05.862][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:02:05.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.864][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:02:05.865][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:02:05.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.868][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:02:05.869][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:02:05.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.872][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:02:05.873][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:02:05.891][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:02:05.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.894][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:02:05.895][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:02:05.896][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:02:05.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:05.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:05.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:05.901][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:02:05.928][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.946][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-26 16:02:05.947][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.948][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:05.949][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.949][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.950][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.951][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.952][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:02:05.953][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:05.954][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.954][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:02:05.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:05.956][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:05.957][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.958][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:02:05.958][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:02:05.958][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:02:05.958][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:02:05.958][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:02:05.959][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:05.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:05.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:05.961][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:05.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:05.963][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:05.963][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.964][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:05.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:05.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:05.967][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.967][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:05.968][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:02:05.970][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.971][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:02:05.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:05.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.976][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:02:05.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:05.978][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.979][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:02:05.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:05.981][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:05.981][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.982][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:02:05.982][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:02:05.982][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:02:05.982][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:02:05.982][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:02:05.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:05.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:05.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:05.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:05.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:05.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:05.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.988][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:05.989][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:05.990][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:05.990][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.991][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:05.992][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:02:05.994][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.995][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-26 16:02:05.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.996][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:05.997][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:05.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:05.998][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:05.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.000][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:02:06.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:06.002][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.002][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:02:06.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:06.004][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.005][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.005][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.006][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:06.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:06.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:06.008][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:06.009][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:06.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:06.010][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.011][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.012][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:06.013][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:06.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.014][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.015][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:02:06.017][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.018][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:02:06.019][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:06.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.023][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:02:06.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:06.025][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.025][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:02:06.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:06.027][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.028][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.028][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.029][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:02:06.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:06.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:06.031][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:06.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:06.033][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:06.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.034][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:06.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:06.037][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.037][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.040][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:02:06.041][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.046][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[2025-04-26 16:02:06.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.107][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:02:06.110][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:02:06.111][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:02:06.112][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:02:06.113][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:02:06.114][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:02:06.115][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:02:06.116][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:02:06.117][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:02:06.118][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:02:06.120][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:02:06.121][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:02:06.122][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:02:06.123][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:02:06.124][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:02:06.125][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:02:06.126][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:02:06.127][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:02:06.128][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:02:06.129][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:02:06.130][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:02:06.131][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:02:06.132][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:02:06.133][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:02:06.134][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:02:06.136][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:02:06.137][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:02:06.138][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:02:06.139][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:02:06.140][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:02:06.141][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:02:06.142][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:02:06.143][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:02:06.144][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:02:06.145][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:02:06.146][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:02:06.148][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:02:06.149][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:02:06.150][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:02:06.151][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:02:06.152][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:02:06.153][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:02:06.155][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:02:06.156][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:02:06.157][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:02:06.158][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:02:06.159][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:02:06.160][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:02:06.161][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:02:06.162][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:02:06.163][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:02:06.164][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:02:06.165][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:02:06.166][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:02:06.167][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:02:06.168][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:02:06.169][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:02:06.170][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:02:06.171][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:02:06.172][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:02:06.173][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:02:06.174][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:02:06.175][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:02:06.176][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:02:06.177][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:02:06.178][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:02:06.179][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:02:06.180][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:02:06.181][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:02:06.182][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:02:06.183][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:02:06.184][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:02:06.185][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:02:06.186][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:02:06.187][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:02:06.188][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:02:06.189][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:02:06.190][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:02:06.192][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:02:06.193][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:02:06.194][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:02:06.195][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:02:06.196][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:02:06.201][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:02:06.202][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:02:06.205][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:02:06.205][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.207][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.207][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[2025-04-26 16:02:06.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.234][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[2025-04-26 16:02:06.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.243][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[2025-04-26 16:02:06.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.262][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[2025-04-26 16:02:06.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.272][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[2025-04-26 16:02:06.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:02:06.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:02:06.297][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-26 16:02:06.304][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-26 16:02:06.306][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.307][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-26 16:02:06.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.308][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:02:06.309][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.310][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-26 16:02:06.311][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.311][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.312][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-26 16:02:06.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:02:06.313][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.314][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-26 16:02:06.315][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-26 16:02:06.316][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-26 16:02:06.317][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:02:06.317][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.318][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:02:06.319][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:06.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:06.320][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:02:06.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:02:06.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:02:06.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:02:06.323][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:02:06.323][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:02:06.323][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-26 16:02:06.323][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-26 16:02:06.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:02:06.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:02:06.325][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:02:06.326][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:02:06.330][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-26 16:02:06.347][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-26 16:02:06.348][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-26 16:02:06.351][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-26 16:02:06.354][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-26 16:02:06.356][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:02:06.357][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:02:06.358][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:02:06.359][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:02:06.360][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:02:06.361][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-26 16:02:06.367][biodb::testThat]
biodb.INFO [2025-04-26 16:02:06.368][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-26 16:02:06.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:02:06.369][biodb::testThat]
biodb.TRACE[2025-04-26 16:02:06.400][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-04-26 16:02:06.402][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:02:06.404][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:02:06.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:02:06.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-26 16:02:06.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.498][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.501][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.508][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:02:06.562][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-04-26 16:02:06.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.567][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.570][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:06.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:06.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.573][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:06.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:06.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.601][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.629][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.633][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.636][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.659][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.660][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.661][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.675][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.678][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.681][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.682][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.684][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.684][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.704][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.705][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.706][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.726][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.727][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.728][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.752][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.762][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.763][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.765][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.769][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.771][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.780][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.783][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.787][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.788][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.789][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.794][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.795][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.796][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.797][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.812][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-04-26 16:02:06.839][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-26 16:02:06.840][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:02:06.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:02:06.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:02:06.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:02:06.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:02:06.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:02:06.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:02:06.849][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[2025-04-26 16:02:06.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.876][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:06.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:06.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.879][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:06.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:06.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:06.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:06.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.912][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.918][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:06.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:06.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.922][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:06.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:06.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:06.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.935][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.939][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.945][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:06.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:02:06.968][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-04-26 16:02:06.983][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.987][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:02:06.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.990][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:06.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:02:06.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:06.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:02:06.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:06.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:06.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:06.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:06.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.008][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.034][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.037][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.041][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:02:07.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.067][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.068][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.070][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.081][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.087][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.090][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.091][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.093][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.094][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:07.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:07.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:07.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:07.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:07.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:07.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.113][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:07.114][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:07.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.116][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.117][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:07.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:07.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.131][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:07.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:07.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:07.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.137][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:07.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:07.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.140][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:07.141][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:07.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.142][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:07.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:07.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.162][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.163][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.164][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.176][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:07.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:07.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:07.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:07.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:07.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.185][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:07.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:07.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.187][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:07.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:07.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.207][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.207][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.209][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.219][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:02:07.220][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:02:07.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.221][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.227][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.228][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:02:07.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.229][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.234][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:02:07.235][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:02:07.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.237][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:02:07.243][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:02:07.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.244][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.249][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.250][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:02:07.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.252][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.260][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.261][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:02:07.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.263][ef$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:02:07.267][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:02:07.268][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:02:07.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:02:07.269][ef$get] fields variable is a list.
biodb.INFO [2025-04-26 16:02:07.276][biodb::testThat]
biodb.INFO [2025-04-26 16:02:07.277][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-26 16:02:07.278][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:02:07.279][biodb::testThat]
biodb.DEBUG[2025-04-26 16:02:07.281][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-04-26 16:02:07.286][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2025-04-26 16:02:07.288][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2025-04-26 16:02:07.289][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-04-26 16:02:07.290][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-04-26 16:02:07.291][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-04-26 16:02:07.292][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2025-04-26 16:02:40.819][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus170be37981242gz".
biodb.TRACE[2025-04-26 16:02:40.820][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:02:40.821][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:02:40.822][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:02:40.823][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-04-26 16:02:40.825][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker170be60d6c791marker".
biodb.TRACE[2025-04-26 16:02:40.826][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-04-26 16:02:40.827][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:02:40.828][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-04-26 16:02:40.829][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-04-26 16:02:40.830][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-04-26 16:02:40.831][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-04-26 16:03:39.507][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-04-26 16:03:39.509][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2025-04-26 16:25:07.274][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2025-04-26 16:25:07.611][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-04-26 16:27:02.374][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-26 16:27:02.398][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-04-26 16:27:02.422][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker170be34c83242marker".
biodb.TRACE[2025-04-26 16:27:02.424][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-04-26 16:27:02.426][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-04-26 16:27:02.428][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-04-26 16:27:02.429][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-26 16:27:02.487][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-04-26 16:27:02.570][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-26 16:27:02.608][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-04-26 16:27:02.610][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-04-26 16:27:02.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:27:02.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:02.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:02.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:02.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:02.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:02.670][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:27:02.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.692][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:27:02.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:27:02.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:27:02.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:27:02.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:27:02.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:27:02.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:27:02.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:27:02.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.718][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.722][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.725][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.732][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:27:02.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-26 16:27:02.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:02.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:02.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:02.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:02.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:02.756][FUN] Functions in observer BiodbConfig: [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[2025-04-26 16:27:02.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.772][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:27:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:27:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.775][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-26 16:27:02.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-26 16:27:02.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:27:02.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:27:02.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-26 16:27:02.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-26 16:27:02.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-26 16:27:02.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.800][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-26 16:27:02.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-26 16:27:02.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:27:02.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:27:02.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-26 16:27:02.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-26 16:27:02.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-26 16:27:02.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.831][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.835][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.843][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-26 16:27:02.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-26 16:27:02.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-26 16:27:02.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-26 16:27:02.876][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-04-26 16:27:02.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:27:02.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:27:02.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:27:02.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:27:02.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:27:02.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:27:02.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-26 16:27:02.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-26 16:27:02.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:27:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-26 16:27:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:27:02.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-26 16:27:02.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:27:02.910][biodb::testThat]
biodb.INFO [2025-04-26 16:27:02.911][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-26 16:27:02.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:02.912][biodb::testThat]
biodb.INFO [2025-04-26 16:27:02.919][biodb::testThat]
biodb.INFO [2025-04-26 16:27:02.919][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-26 16:27:02.920][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:02.921][biodb::testThat]
biodb.WARN [2025-04-26 16:27:02.942][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-26 16:27:02.958][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-26 16:27:02.967][biodb::testThat]
biodb.INFO [2025-04-26 16:27:02.968][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-26 16:27:02.968][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:02.969][biodb::testThat]
biodb.TRACE[2025-04-26 16:27:02.993][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:27:02.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:27:02.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:02.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:02.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:27:02.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:27:03.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:03.002][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:27:03.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:27:03.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:27:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:27:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:03.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:27:03.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:27:03.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:03.064][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-26 16:27:03.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-26 16:27:03.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:03.067][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-26 16:27:03.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-26 16:27:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-26 16:27:03.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-26 16:27:03.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-26 16:27:03.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-26 16:27:03.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-26 16:27:03.165][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.166][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-26 16:27:03.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:03.168][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.175][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.176][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-26 16:27:03.177][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:03.178][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.185][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.185][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-26 16:27:03.186][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:03.187][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.193][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.194][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-26 16:27:03.195][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-26 16:27:03.197][biodb::testThat]
biodb.INFO [2025-04-26 16:27:03.204][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:27:03.205][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-26 16:27:03.206][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-26 16:27:03.207][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:27:03.207][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:03.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:03.209][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:03.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:03.210][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-26 16:27:03.241][biodb::testContext]
biodb.INFO [2025-04-26 16:27:03.242][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:27:03.243][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-04-26 16:27:03.244][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-26 16:27:03.245][biodb::testContext]
biodb.INFO [2025-04-26 16:27:03.395][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:27:03.484][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-26 16:27:03.552][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:27:03.553][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-26 16:27:03.554][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-26 16:27:03.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.558][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-26 16:27:03.574][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-26 16:27:03.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.577][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-26 16:27:03.578][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-26 16:27:03.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.581][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-26 16:27:03.582][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-26 16:27:03.583][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-26 16:27:03.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.586][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-26 16:27:03.586][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-26 16:27:03.587][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-26 16:27:03.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.590][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-26 16:27:03.591][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-26 16:27:03.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.594][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-26 16:27:03.595][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-26 16:27:03.596][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-26 16:27:03.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.599][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-26 16:27:03.600][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-26 16:27:03.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.603][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-26 16:27:03.603][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-26 16:27:03.604][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-26 16:27:03.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.607][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:27:03.608][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-26 16:27:03.609][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-26 16:27:03.610][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-26 16:27:03.610][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-26 16:27:03.611][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-26 16:27:03.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.614][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-26 16:27:03.615][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-26 16:27:03.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.618][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-26 16:27:03.619][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-26 16:27:03.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.622][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-26 16:27:03.623][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-26 16:27:03.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.625][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[2025-04-26 16:27:03.626][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-26 16:27:03.627][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-26 16:27:03.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:03.630][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-26 16:27:03.631][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-26 16:27:03.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:03.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:03.633][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[2025-04-26 16:27:03.634][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-26 16:27:03.635][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-26 16:27:05.014][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-26 16:27:05.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.017][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-26 16:27:05.018][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-26 16:27:05.019][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-26 16:27:05.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.022][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-26 16:27:05.024][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.025][self$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[2025-04-26 16:27:05.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.026][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:27:05.027][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.028][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.029][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.029][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.030][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:27:05.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:27:05.032][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.033][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-26 16:27:05.034][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:27:05.034][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.036][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:27:05.036][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:27:05.036][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:27:05.036][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:27:05.036][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:27:05.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:27:05.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.039][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:27:05.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.042][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:27:05.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:27:05.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.045][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.046][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-26 16:27:05.048][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.049][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:27:05.049][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.050][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:27:05.051][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.052][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.053][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.053][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.054][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:27:05.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:27:05.056][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.057][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-26 16:27:05.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:27:05.058][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.060][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-26 16:27:05.060][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-26 16:27:05.060][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-26 16:27:05.060][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-26 16:27:05.060][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-26 16:27:05.061][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:27:05.062][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:27:05.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.065][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.066][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.067][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:27:05.068][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:27:05.068][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.069][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.070][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-26 16:27:05.072][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.072][self$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[2025-04-26 16:27:05.073][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.074][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:27:05.075][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.076][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.076][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.077][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.078][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-26 16:27:05.079][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:27:05.080][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.080][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-26 16:27:05.081][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:27:05.082][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.083][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.084][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.084][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:27:05.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:27:05.087][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.090][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:27:05.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:27:05.092][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.093][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.094][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-26 16:27:05.095][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.096][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-26 16:27:05.097][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.098][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:27:05.098][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.099][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.100][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.101][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.102][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-26 16:27:05.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:27:05.103][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.104][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-26 16:27:05.105][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:27:05.106][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.106][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.107][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-26 16:27:05.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.110][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.110][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:27:05.111][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.112][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.113][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.113][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.114][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:27:05.115][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:27:05.116][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.116][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.118][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:27:05.118][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.137][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[2025-04-26 16:27:05.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.141][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[2025-04-26 16:27:05.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.155][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.DEBUG[2025-04-26 16:27:05.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.166][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[2025-04-26 16:27:05.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.170][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[2025-04-26 16:27:05.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.174][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[2025-04-26 16:27:05.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.177][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[2025-04-26 16:27:05.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.181][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[2025-04-26 16:27:05.182][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-26 16:27:05.183][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-26 16:27:05.184][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-26 16:27:05.185][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-26 16:27:05.187][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-26 16:27:05.188][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-26 16:27:05.189][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-26 16:27:05.190][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-26 16:27:05.191][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-26 16:27:05.192][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-26 16:27:05.193][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-26 16:27:05.194][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-26 16:27:05.196][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-26 16:27:05.197][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-26 16:27:05.198][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-26 16:27:05.199][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-26 16:27:05.200][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-26 16:27:05.201][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-26 16:27:05.202][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-26 16:27:05.204][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-26 16:27:05.205][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-26 16:27:05.206][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-26 16:27:05.207][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-26 16:27:05.208][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-26 16:27:05.209][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-26 16:27:05.210][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-26 16:27:05.212][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-26 16:27:05.213][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-26 16:27:05.214][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-26 16:27:05.215][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-26 16:27:05.216][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-26 16:27:05.217][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-26 16:27:05.218][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-26 16:27:05.219][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-26 16:27:05.221][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-26 16:27:05.222][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-26 16:27:05.223][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-26 16:27:05.224][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-26 16:27:05.225][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-26 16:27:05.226][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-26 16:27:05.227][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-26 16:27:05.229][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-26 16:27:05.230][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-26 16:27:05.231][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-26 16:27:05.232][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-26 16:27:05.233][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-26 16:27:05.234][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-26 16:27:05.235][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-26 16:27:05.237][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-26 16:27:05.238][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-26 16:27:05.239][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-26 16:27:05.240][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-26 16:27:05.241][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-26 16:27:05.242][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-26 16:27:05.243][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-26 16:27:05.244][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-26 16:27:05.245][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-26 16:27:05.247][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-26 16:27:05.248][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-26 16:27:05.249][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-26 16:27:05.250][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-26 16:27:05.251][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-26 16:27:05.252][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-26 16:27:05.253][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-26 16:27:05.254][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-26 16:27:05.255][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-26 16:27:05.256][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-26 16:27:05.258][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-26 16:27:05.259][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-26 16:27:05.260][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-26 16:27:05.261][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-26 16:27:05.262][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-26 16:27:05.263][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-26 16:27:05.264][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-26 16:27:05.265][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-26 16:27:05.267][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-26 16:27:05.268][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-26 16:27:05.269][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-26 16:27:05.270][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-26 16:27:05.271][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-26 16:27:05.272][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-26 16:27:05.273][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-26 16:27:05.274][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-26 16:27:05.275][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-26 16:27:05.277][initialize] This is biodb version 1.17.0.
biodb.DEBUG[2025-04-26 16:27:05.278][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-26 16:27:05.278][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.280][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.311][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[2025-04-26 16:27:05.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.316][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[2025-04-26 16:27:05.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.356][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[2025-04-26 16:27:05.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-26 16:27:05.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-26 16:27:05.369][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-26 16:27:05.371][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-26 16:27:05.373][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.373][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-26 16:27:05.374][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.375][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-26 16:27:05.376][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.377][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-26 16:27:05.378][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.378][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.379][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-26 16:27:05.380][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-26 16:27:05.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.382][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-26 16:27:05.383][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-26 16:27:05.384][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-26 16:27:05.385][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.386][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-26 16:27:05.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.388][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-26 16:27:05.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-26 16:27:05.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-26 16:27:05.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-26 16:27:05.391][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:27:05.391][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-26 16:27:05.391][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-26 16:27:05.391][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-26 16:27:05.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-26 16:27:05.393][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-26 16:27:05.394][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-26 16:27:05.394][self$setPropertyValue]
biodb.DEBUG[2025-04-26 16:27:05.395][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-26 16:27:05.399][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-26 16:27:05.400][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-26 16:27:05.401][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-26 16:27:05.402][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-26 16:27:05.403][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:27:05.404][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-26 16:27:05.405][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:27:05.406][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:27:05.407][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-26 16:27:05.408][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-26 16:27:05.409][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-26 16:27:05.410][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-26 16:27:05.410][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-26 16:27:05.411][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-26 16:27:05.412][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-26 16:27:05.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-26 16:27:05.413][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-26 16:27:05.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-26 16:27:05.415][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-26 16:27:05.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
    user   system  elapsed 
1069.276  249.022 1501.171

'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 biodbNci_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* 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 ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.13.0’
* 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 ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)