Back to Long Tests report for BioC 3.22

This page was generated on 2026-03-28 23:55 -0400 (Sat, 28 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4893
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4687
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 8/31HostnameOS / ArchCHECK
biodbNci 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2026-03-28 09:55 -0400 (Sat, 28 Mar 2026)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_22
git_last_commit: 4ce22d8
git_last_commit_date: 2025-10-29 11:15:34 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbNci on merida1

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: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
StartedAt: 2026-03-28 16:01:22 -0400 (Sat, 28 Mar 2026)
EndedAt: 2026-03-28 16:02:43 -0400 (Sat, 28 Mar 2026)
EllapsedTime: 80.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbNci.Rcheck
Warnings: NA

Tests output

biodbNci.Rcheck/tests/testthat.Rout.fail


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2026-03-28 16:02:39.168][biodb::testContext]
biodb.INFO [2026-03-28 16:02:39.172][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:39.173][biodb::testContext] Test context - Generic long tests
biodb.INFO [2026-03-28 16:02:39.175][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:39.176][biodb::testContext]
biodb.INFO [2026-03-28 16:02:39.183][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:39.185][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:39.193][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:39.194][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:39.195][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:39.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.200][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:39.224][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:39.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.229][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:39.230][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:39.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.235][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:39.236][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:39.237][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:39.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.242][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:39.243][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:39.244][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:39.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.249][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:39.250][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:39.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.253][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[2026-03-28 16:02:39.255][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:39.256][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:39.257][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:39.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.262][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:39.263][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:39.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.268][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:39.269][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:39.270][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:39.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.275][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:39.276][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:39.277][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:39.279][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:39.280][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:39.281][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:39.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.286][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:39.287][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:39.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.292][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:39.293][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:39.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.296][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[2026-03-28 16:02:39.298][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:39.299][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:39.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.304][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:39.305][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:39.306][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:39.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.311][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:39.312][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:39.323][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:39.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.328][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:39.329][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:39.331][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:39.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.337][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:39.381][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.408][self$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[2026-03-28 16:02:39.410][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.411][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:39.412][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.413][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.415][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.417][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:39.418][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:39.419][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.421][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:39.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:39.423][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.424][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.425][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:39.425][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:39.425][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:39.425][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:39.425][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:39.427][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:39.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.429][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.430][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:39.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.433][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.434][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.435][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.436][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:39.437][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:39.438][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.440][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.441][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:39.443][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.444][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:39.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:39.448][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.449][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.451][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.452][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.453][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:39.454][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:39.455][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.457][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:39.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:39.459][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.460][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.462][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:39.462][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:39.462][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:39.462][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:39.462][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:39.463][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:39.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.466][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:39.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.469][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.470][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.471][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.472][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:39.473][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:39.474][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.476][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.477][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:39.479][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.480][self$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[2026-03-28 16:02:39.482][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.483][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:39.484][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.485][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.487][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.489][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:39.490][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:39.491][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.493][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:39.494][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:39.495][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.496][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.497][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.499][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:39.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.502][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:39.503][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.504][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.505][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.507][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.508][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:39.509][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:39.510][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.511][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.513][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:39.515][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.516][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:39.517][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:39.520][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.525][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:39.526][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:39.527][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.528][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:39.529][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:39.531][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.532][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.533][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.534][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:39.535][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.538][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:39.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.542][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:39.545][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:39.546][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.547][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.551][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:39.552][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.576][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[2026-03-28 16:02:39.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.593][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[2026-03-28 16:02:39.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.598][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[2026-03-28 16:02:39.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.621][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[2026-03-28 16:02:39.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.644][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:39.649][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:39.651][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:39.656][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:39.658][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:39.660][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:39.661][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:39.663][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:39.664][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:39.666][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:39.668][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:39.669][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:39.671][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:39.673][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:39.674][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:39.676][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:39.677][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:39.679][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:39.681][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:39.682][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:39.684][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:39.686][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:39.687][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:39.689][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:39.691][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:39.692][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:39.694][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:39.696][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:39.697][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:39.699][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:39.701][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:39.702][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:39.704][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:39.706][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:39.707][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:39.709][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:39.711][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:39.712][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:39.714][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:39.716][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:39.717][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:39.719][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:39.721][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:39.722][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:39.724][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:39.726][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:39.728][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:39.729][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:39.731][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:39.733][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:39.734][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:39.736][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:39.738][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:39.739][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:39.741][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:39.743][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:39.744][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:39.746][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:39.748][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:39.750][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:39.751][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:39.753][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:39.755][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:39.757][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:39.758][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:39.760][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:39.762][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:39.763][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:39.765][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:39.767][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:39.768][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:39.770][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:39.772][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:39.773][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:39.775][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:39.777][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:39.778][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:39.780][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:39.782][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:39.783][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:39.785][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:39.787][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:39.788][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:39.795][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:39.798][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:39.801][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:39.802][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.804][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.864][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[2026-03-28 16:02:39.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.871][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[2026-03-28 16:02:39.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:39.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:39.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:39.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:39.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:39.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:39.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:39.940][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:39.953][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-28 16:02:39.955][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.957][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-28 16:02:39.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:39.960][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.961][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-28 16:02:39.963][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.965][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-28 16:02:39.966][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:39.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.969][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-28 16:02:39.970][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-28 16:02:39.972][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-28 16:02:39.973][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:39.974][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.976][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:39.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.979][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:39.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:39.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:39.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:39.984][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:39.984][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:39.984][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-28 16:02:39.984][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-28 16:02:39.985][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:39.986][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:39.988][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:39.989][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:39.997][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-28 16:02:40.018][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-28 16:02:40.035][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-28 16:02:40.045][biodb::testThat]
biodb.INFO [2026-03-28 16:02:40.046][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2026-03-28 16:02:40.047][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:40.048][biodb::testThat]
biodb.TRACE[2026-03-28 16:02:40.052][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2026-03-28 16:02:40.054][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:40.058][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-28 16:02:40.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:40.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:40.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:40.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:40.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:40.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:40.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:40.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.204][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.230][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.240][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:40.319][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2026-03-28 16:02:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:40.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:40.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:40.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:40.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:40.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:40.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:40.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.364][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.415][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.420][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.448][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.450][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.451][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.483][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.484][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.485][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.486][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.518][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.520][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.521][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.522][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.553][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.555][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.556][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.557][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.588][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.591][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.592][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.614][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.616][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.617][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.618][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.624][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.626][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.627][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.628][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.634][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.636][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.637][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.638][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.645][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.646][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.647][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.648][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.655][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.656][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.657][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.659][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.681][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2026-03-28 16:02:40.728][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2026-03-28 16:02:40.730][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2026-03-28 16:02:40.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2026-03-28 16:02:40.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:40.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:40.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:40.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:40.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:40.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2026-03-28 16:02:40.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.793][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:40.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:40.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.798][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:40.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:40.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.809][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:40.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:40.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:40.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.861][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.866][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.891][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:40.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:40.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:40.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:40.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.919][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.925][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.935][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:40.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:40.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:40.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:40.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2026-03-28 16:02:40.971][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2026-03-28 16:02:40.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:41.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:41.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2026-03-28 16:02:41.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2026-03-28 16:02:41.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.008][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2026-03-28 16:02:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.013][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:41.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2026-03-28 16:02:41.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.030][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.077][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.082][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.087][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2026-03-28 16:02:41.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.128][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.130][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.131][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.132][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.149][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.159][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.164][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.165][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.166][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.168][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.184][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:41.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:41.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:41.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:41.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.199][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:41.201][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:41.202][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.203][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:41.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:41.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.220][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:41.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:41.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:41.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:41.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:41.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.235][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:41.237][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:41.238][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.239][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.240][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:41.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.271][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.272][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.273][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.274][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:41.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.300][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:41.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:41.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:41.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.310][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:41.312][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:41.313][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.314][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:41.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.345][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.346][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.348][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.349][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.365][ef$get] Asked field names are: accession.
biodb.TRACE[2026-03-28 16:02:41.367][ef$get] Realnames of fields are: accession.
biodb.TRACE[2026-03-28 16:02:41.368][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.369][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.375][ef$get] Asked field names are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.376][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2026-03-28 16:02:41.378][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.379][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.385][ef$get] Asked field names are: formula.
biodb.TRACE[2026-03-28 16:02:41.386][ef$get] Realnames of fields are: formula.
biodb.TRACE[2026-03-28 16:02:41.388][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.389][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.395][ef$get] Asked field names are: inchi.
biodb.TRACE[2026-03-28 16:02:41.396][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2026-03-28 16:02:41.397][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.399][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2026-03-28 16:02:41.407][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.408][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.415][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.416][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2026-03-28 16:02:41.417][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.418][ef$get] fields variable is a list.
biodb.TRACE[2026-03-28 16:02:41.425][ef$get] Asked field names are: name.
biodb.TRACE[2026-03-28 16:02:41.426][ef$get] Realnames of fields are: name.
biodb.TRACE[2026-03-28 16:02:41.427][ef$get] 1 fields were returned.
biodb.TRACE[2026-03-28 16:02:41.428][ef$get] fields variable is a list.
biodb.INFO [2026-03-28 16:02:41.438][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.440][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2026-03-28 16:02:41.441][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.442][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:41.445][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2026-03-28 16:02:41.450][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2026-03-28 16:02:41.452][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-28 16:02:41.491][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-28 16:02:41.493][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-28 16:02:41.494][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-28 16:02:41.666][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.667][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2026-03-28 16:02:41.668][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.669][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.678][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.679][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2026-03-28 16:02:41.680][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.681][biodb::testThat]
biodb.WARN [2026-03-28 16:02:41.709][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2026-03-28 16:02:41.733][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2026-03-28 16:02:41.744][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.745][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2026-03-28 16:02:41.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.747][biodb::testThat]
biodb.DEBUG[2026-03-28 16:02:41.770][private$loadEntries] Creating entries from ids [1]: "749674".
biodb.DEBUG[2026-03-28 16:02:41.834][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)...
biodb.DEBUG[2026-03-28 16:02:41.836][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2026-03-28 16:02:41.837][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2026-03-28 16:02:41.839][self$download] Extract whole database of nci.cactus.
biodb.INFO [2026-03-28 16:02:41.856][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
Saving _problems/test_long_100_generic-38.R
biodb.INFO [2026-03-28 16:02:41.931][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.933][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2026-03-28 16:02:41.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.935][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.945][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.947][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2026-03-28 16:02:41.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.949][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.959][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.961][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:41.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.963][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.972][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.973][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2026-03-28 16:02:41.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2026-03-28 16:02:41.976][biodb::testThat]
biodb.INFO [2026-03-28 16:02:41.984][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:41.986][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-28 16:02:41.987][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:41.988][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:41.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:41.991][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:41.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:41.993][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:41.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2026-03-28 16:02:42.007][biodb::testContext]
biodb.INFO [2026-03-28 16:02:42.009][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:42.010][biodb::testContext] Test context - Example long tests
biodb.INFO [2026-03-28 16:02:42.011][biodb::testContext] ********************************************************************************
biodb.INFO [2026-03-28 16:02:42.012][biodb::testContext]
biodb.INFO [2026-03-28 16:02:42.015][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:42.017][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:42.022][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:42.023][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2026-03-28 16:02:42.024][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2026-03-28 16:02:42.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.029][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2026-03-28 16:02:42.030][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2026-03-28 16:02:42.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.035][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2026-03-28 16:02:42.036][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2026-03-28 16:02:42.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.041][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2026-03-28 16:02:42.042][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2026-03-28 16:02:42.043][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2026-03-28 16:02:42.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.048][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2026-03-28 16:02:42.049][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2026-03-28 16:02:42.050][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2026-03-28 16:02:42.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.055][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2026-03-28 16:02:42.056][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2026-03-28 16:02:42.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.061][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2026-03-28 16:02:42.062][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2026-03-28 16:02:42.063][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2026-03-28 16:02:42.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.068][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2026-03-28 16:02:42.069][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2026-03-28 16:02:42.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.073][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2026-03-28 16:02:42.075][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2026-03-28 16:02:42.076][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2026-03-28 16:02:42.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.085][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:42.087][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2026-03-28 16:02:42.088][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2026-03-28 16:02:42.089][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2026-03-28 16:02:42.090][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2026-03-28 16:02:42.092][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2026-03-28 16:02:42.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.096][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2026-03-28 16:02:42.098][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2026-03-28 16:02:42.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.102][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2026-03-28 16:02:42.103][self$set] Set key entries.sep to "|".
biodb.DEBUG[2026-03-28 16:02:42.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.108][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2026-03-28 16:02:42.109][self$set] Set key offline to FALSE.
biodb.DEBUG[2026-03-28 16:02:42.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.114][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2026-03-28 16:02:42.115][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2026-03-28 16:02:42.116][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2026-03-28 16:02:42.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.121][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2026-03-28 16:02:42.122][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2026-03-28 16:02:42.133][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2026-03-28 16:02:42.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.137][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[2026-03-28 16:02:42.138][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2026-03-28 16:02:42.139][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2026-03-28 16:02:42.141][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2026-03-28 16:02:42.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.146][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2026-03-28 16:02:42.148][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.149][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2026-03-28 16:02:42.151][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.152][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:42.153][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.155][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.156][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.157][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.158][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:42.160][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:42.161][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.162][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2026-03-28 16:02:42.163][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:42.165][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.166][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.167][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:42.167][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:42.167][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:42.167][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:42.167][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:42.168][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:42.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.172][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:42.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.174][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.176][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.177][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:42.179][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:42.180][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.182][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.183][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2026-03-28 16:02:42.185][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.187][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:42.188][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.190][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:42.191][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.192][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.193][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.195][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.196][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:42.197][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:42.199][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.200][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2026-03-28 16:02:42.202][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:42.203][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.205][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.206][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2026-03-28 16:02:42.206][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2026-03-28 16:02:42.206][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2026-03-28 16:02:42.206][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2026-03-28 16:02:42.206][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2026-03-28 16:02:42.208][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:42.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:42.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.216][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.217][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:42.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:42.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.222][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.223][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2026-03-28 16:02:42.225][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.227][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2026-03-28 16:02:42.228][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.229][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:42.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.232][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.233][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.234][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.235][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2026-03-28 16:02:42.236][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:42.238][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.239][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2026-03-28 16:02:42.240][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:42.241][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.243][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.244][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.245][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:42.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.249][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:42.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.252][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.253][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.254][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:42.255][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:42.257][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.258][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.259][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2026-03-28 16:02:42.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.263][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2026-03-28 16:02:42.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:42.266][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.268][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.269][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.270][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.271][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2026-03-28 16:02:42.272][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:42.274][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.275][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2026-03-28 16:02:42.276][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:42.277][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.280][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.281][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2026-03-28 16:02:42.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.285][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:42.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.288][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.289][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.294][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:42.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:42.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.298][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.300][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:42.301][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.346][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[2026-03-28 16:02:42.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.351][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[2026-03-28 16:02:42.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.391][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2026-03-28 16:02:42.393][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2026-03-28 16:02:42.394][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2026-03-28 16:02:42.396][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2026-03-28 16:02:42.398][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2026-03-28 16:02:42.399][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2026-03-28 16:02:42.401][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:42.403][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:42.404][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2026-03-28 16:02:42.406][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2026-03-28 16:02:42.408][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2026-03-28 16:02:42.409][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2026-03-28 16:02:42.411][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2026-03-28 16:02:42.413][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2026-03-28 16:02:42.414][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2026-03-28 16:02:42.416][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2026-03-28 16:02:42.418][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2026-03-28 16:02:42.419][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2026-03-28 16:02:42.421][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2026-03-28 16:02:42.423][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2026-03-28 16:02:42.425][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2026-03-28 16:02:42.426][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2026-03-28 16:02:42.428][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2026-03-28 16:02:42.430][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2026-03-28 16:02:42.431][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2026-03-28 16:02:42.433][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2026-03-28 16:02:42.435][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2026-03-28 16:02:42.436][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2026-03-28 16:02:42.438][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2026-03-28 16:02:42.440][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2026-03-28 16:02:42.441][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2026-03-28 16:02:42.443][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2026-03-28 16:02:42.445][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2026-03-28 16:02:42.446][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2026-03-28 16:02:42.448][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2026-03-28 16:02:42.450][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2026-03-28 16:02:42.452][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2026-03-28 16:02:42.453][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2026-03-28 16:02:42.455][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2026-03-28 16:02:42.457][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2026-03-28 16:02:42.458][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2026-03-28 16:02:42.460][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2026-03-28 16:02:42.462][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2026-03-28 16:02:42.463][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2026-03-28 16:02:42.465][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2026-03-28 16:02:42.467][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2026-03-28 16:02:42.469][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2026-03-28 16:02:42.470][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2026-03-28 16:02:42.472][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2026-03-28 16:02:42.474][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2026-03-28 16:02:42.475][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2026-03-28 16:02:42.477][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2026-03-28 16:02:42.483][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2026-03-28 16:02:42.485][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2026-03-28 16:02:42.486][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2026-03-28 16:02:42.488][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2026-03-28 16:02:42.490][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2026-03-28 16:02:42.491][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2026-03-28 16:02:42.493][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2026-03-28 16:02:42.495][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2026-03-28 16:02:42.496][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2026-03-28 16:02:42.498][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2026-03-28 16:02:42.499][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2026-03-28 16:02:42.501][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2026-03-28 16:02:42.503][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2026-03-28 16:02:42.505][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2026-03-28 16:02:42.506][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2026-03-28 16:02:42.508][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2026-03-28 16:02:42.510][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2026-03-28 16:02:42.511][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2026-03-28 16:02:42.513][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2026-03-28 16:02:42.515][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2026-03-28 16:02:42.516][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2026-03-28 16:02:42.518][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2026-03-28 16:02:42.520][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2026-03-28 16:02:42.521][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2026-03-28 16:02:42.523][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2026-03-28 16:02:42.525][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2026-03-28 16:02:42.527][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2026-03-28 16:02:42.528][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2026-03-28 16:02:42.530][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2026-03-28 16:02:42.532][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2026-03-28 16:02:42.533][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2026-03-28 16:02:42.535][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2026-03-28 16:02:42.537][initialize] This is biodb version 1.18.0.
biodb.DEBUG[2026-03-28 16:02:42.538][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2026-03-28 16:02:42.539][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.542][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2026-03-28 16:02:42.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2026-03-28 16:02:42.674][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2026-03-28 16:02:42.676][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2026-03-28 16:02:42.679][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.680][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2026-03-28 16:02:42.682][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.683][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2026-03-28 16:02:42.684][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.686][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2026-03-28 16:02:42.687][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.688][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.689][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2026-03-28 16:02:42.691][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2026-03-28 16:02:42.692][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.693][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2026-03-28 16:02:42.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2026-03-28 16:02:42.696][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2026-03-28 16:02:42.697][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2026-03-28 16:02:42.699][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.700][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2026-03-28 16:02:42.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.703][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.704][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2026-03-28 16:02:42.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2026-03-28 16:02:42.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2026-03-28 16:02:42.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2026-03-28 16:02:42.709][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:42.709][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2026-03-28 16:02:42.709][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2026-03-28 16:02:42.709][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2026-03-28 16:02:42.710][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2026-03-28 16:02:42.711][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2026-03-28 16:02:42.713][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2026-03-28 16:02:42.714][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2026-03-28 16:02:42.716][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2026-03-28 16:02:42.719][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2026-03-28 16:02:42.724][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2026-03-28 16:02:42.725][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2026-03-28 16:02:42.727][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2026-03-28 16:02:42.728][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2026-03-28 16:02:42.729][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2026-03-28 16:02:42.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2026-03-28 16:02:42.731][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2026-03-28 16:02:42.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2026-03-28 16:02:42.733][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2026-03-28 16:02:42.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): ,

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ──
Error in `private$doExtractDownload()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doExtractDownload()
── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ──
Error in `cch$getTmpFolderPath()`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─private$bdb$getFactory()$getEntry(...)
 6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 7.           └─conn$getEntryContent(ids)
 8.             └─self$download()
 9.               └─private$doExtractDownload()

[ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  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’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─private$doExtractDownload()
  
  [ FAIL 2 | WARN 0 | SKIP 2 | PASS 85 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR, 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 ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.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
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbNci' is deprecated and will be removed from Bioconductor
  version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)