| Back to Long Tests report for BioC 3.21 |
This page was generated on 2025-04-12 23:55 -0400 (Sat, 12 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4634 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4572 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 9/30 | Hostname | OS / Arch | CHECK | |||||||
| biodbNci 1.11.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | |||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
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. |
| Package: biodbNci |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.11.0.tar.gz |
| StartedAt: 2025-04-12 16:04:38 -0400 (Sat, 12 Apr 2025) |
| EndedAt: 2025-04-12 16:05:39 -0400 (Sat, 12 Apr 2025) |
| EllapsedTime: 61.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbNci.Rcheck |
| Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2025-04-12 16:05:35.778][biodb::testContext]
biodb.INFO [2025-04-12 16:05:35.780][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-12 16:05:35.780][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-12 16:05:35.781][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-12 16:05:35.782][biodb::testContext]
biodb.INFO [2025-04-12 16:05:35.788][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-04-12 16:05:35.790][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-12 16:05:35.796][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-12 16:05:35.797][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-12 16:05:35.798][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-12 16:05:35.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.802][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-12 16:05:35.818][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-12 16:05:35.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.821][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-12 16:05:35.822][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-12 16:05:35.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.826][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-12 16:05:35.827][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-12 16:05:35.828][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-12 16:05:35.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.831][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-12 16:05:35.832][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-12 16:05:35.833][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-12 16:05:35.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.836][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-12 16:05:35.837][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-12 16:05:35.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.840][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-12 16:05:35.841][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-12 16:05:35.842][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-12 16:05:35.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.846][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-12 16:05:35.847][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-12 16:05:35.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.850][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-12 16:05:35.851][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-12 16:05:35.852][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-12 16:05:35.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.855][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-12 16:05:35.856][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-12 16:05:35.857][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-12 16:05:35.858][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-12 16:05:35.859][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-12 16:05:35.860][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-12 16:05:35.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.863][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-12 16:05:35.864][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-12 16:05:35.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.867][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-12 16:05:35.868][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-12 16:05:35.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.872][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-12 16:05:35.873][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-12 16:05:35.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.876][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-12 16:05:35.877][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-12 16:05:35.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.880][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-12 16:05:35.881][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-12 16:05:35.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.885][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-12 16:05:35.885][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-12 16:05:35.890][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-12 16:05:35.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.893][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-12 16:05:35.894][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-12 16:05:35.895][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-12 16:05:35.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:35.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:35.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:35.901][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-12 16:05:35.931][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:35.950][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-12 16:05:35.951][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.952][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:35.953][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.954][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:35.955][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:35.956][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:35.957][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-12 16:05:35.958][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:35.959][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.960][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-12 16:05:35.961][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:35.961][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:35.962][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.963][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-12 16:05:35.963][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-12 16:05:35.963][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-12 16:05:35.963][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-12 16:05:35.963][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-12 16:05:35.964][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:35.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:35.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:35.967][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:35.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:35.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:35.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:35.970][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:35.971][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:35.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:35.973][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:35.974][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:35.975][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-12 16:05:35.977][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:35.978][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-12 16:05:35.978][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.979][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:35.980][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.981][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:35.982][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:35.983][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:35.984][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-12 16:05:35.985][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:35.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.987][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-12 16:05:35.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:35.989][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:35.989][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:35.990][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-12 16:05:35.990][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-12 16:05:35.990][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-12 16:05:35.990][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-12 16:05:35.990][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-12 16:05:35.991][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:35.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:35.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:35.994][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:35.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:35.996][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:35.997][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:35.997][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:35.998][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:35.999][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:36.000][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.001][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.002][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-12 16:05:36.004][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.005][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-12 16:05:36.005][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.006][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:36.007][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.009][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.010][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.011][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-12 16:05:36.012][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:36.013][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.014][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-12 16:05:36.015][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:36.016][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.016][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.017][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.018][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:36.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:36.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:36.021][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:36.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:36.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:36.023][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.024][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.025][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:36.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:36.027][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.028][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.029][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-12 16:05:36.030][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.031][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-12 16:05:36.032][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:36.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.037][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.038][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-12 16:05:36.039][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:36.040][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.041][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-12 16:05:36.042][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:36.042][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.043][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.044][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.045][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:36.046][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:36.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:36.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:36.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:36.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:36.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.051][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.052][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:36.054][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:36.055][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.056][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.061][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-12 16:05:36.062][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.079][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[2025-04-12 16:05:36.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.112][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[2025-04-12 16:05:36.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.120][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[2025-04-12 16:05:36.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.137][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-12 16:05:36.142][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-12 16:05:36.143][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-12 16:05:36.144][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-12 16:05:36.145][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-12 16:05:36.147][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-12 16:05:36.148][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-12 16:05:36.149][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-12 16:05:36.151][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-12 16:05:36.152][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-12 16:05:36.153][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-12 16:05:36.154][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-12 16:05:36.156][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-12 16:05:36.157][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-12 16:05:36.158][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-12 16:05:36.160][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-12 16:05:36.161][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-12 16:05:36.162][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-12 16:05:36.163][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-12 16:05:36.165][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-12 16:05:36.166][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-12 16:05:36.167][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-12 16:05:36.169][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-12 16:05:36.170][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-12 16:05:36.171][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-12 16:05:36.172][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-12 16:05:36.174][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-12 16:05:36.175][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-12 16:05:36.176][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-12 16:05:36.178][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-12 16:05:36.179][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-12 16:05:36.180][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-12 16:05:36.181][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-12 16:05:36.183][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-12 16:05:36.184][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-12 16:05:36.185][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-12 16:05:36.187][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-12 16:05:36.188][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-12 16:05:36.190][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-12 16:05:36.191][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-12 16:05:36.192][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-12 16:05:36.193][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-12 16:05:36.195][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-12 16:05:36.196][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-12 16:05:36.197][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-12 16:05:36.199][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-12 16:05:36.200][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-12 16:05:36.201][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-12 16:05:36.203][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-12 16:05:36.204][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-12 16:05:36.210][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-12 16:05:36.212][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-12 16:05:36.214][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-12 16:05:36.215][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-12 16:05:36.217][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-12 16:05:36.218][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-12 16:05:36.220][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-12 16:05:36.221][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-12 16:05:36.222][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-12 16:05:36.224][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-12 16:05:36.225][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-12 16:05:36.227][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-12 16:05:36.228][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-12 16:05:36.230][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-12 16:05:36.231][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-12 16:05:36.233][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-12 16:05:36.234][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-12 16:05:36.236][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-12 16:05:36.237][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-12 16:05:36.239][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-12 16:05:36.240][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-12 16:05:36.241][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-12 16:05:36.243][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-12 16:05:36.244][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-12 16:05:36.246][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-12 16:05:36.247][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-12 16:05:36.249][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-12 16:05:36.250][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-12 16:05:36.251][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-12 16:05:36.253][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-12 16:05:36.254][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-12 16:05:36.256][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-12 16:05:36.257][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-12 16:05:36.264][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-12 16:05:36.266][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-04-12 16:05:36.269][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-12 16:05:36.270][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.272][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.390][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[2025-04-12 16:05:36.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:36.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:36.398][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-12 16:05:36.407][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-12 16:05:36.409][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.410][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-12 16:05:36.411][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.412][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:36.413][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.414][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-12 16:05:36.415][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.416][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.417][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-12 16:05:36.418][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:36.418][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.419][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-12 16:05:36.420][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-12 16:05:36.421][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-12 16:05:36.422][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:36.423][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.424][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-12 16:05:36.425][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:36.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:36.427][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:36.428][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:36.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:36.429][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:36.430][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-12 16:05:36.430][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-12 16:05:36.430][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-12 16:05:36.430][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-12 16:05:36.431][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:36.432][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:36.433][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:36.434][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:36.439][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-12 16:05:36.460][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-12 16:05:36.461][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-12 16:05:36.465][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-12 16:05:36.468][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-12 16:05:36.472][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-12 16:05:36.473][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-12 16:05:36.474][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-12 16:05:36.476][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-12 16:05:36.477][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-12 16:05:36.504][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-12 16:05:36.512][biodb::testThat]
biodb.INFO [2025-04-12 16:05:36.513][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-04-12 16:05:36.514][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:36.514][biodb::testThat]
biodb.TRACE[2025-04-12 16:05:36.517][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-04-12 16:05:36.519][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-12 16:05:36.522][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-12 16:05:36.529][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-12 16:05:36.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:36.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:36.541][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:36.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:36.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:36.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-12 16:05:36.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.579][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.605][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.634][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.637][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.645][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-12 16:05:36.706][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-04-12 16:05:36.708][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:36.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:36.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.712][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:36.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:36.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.716][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:36.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:36.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.719][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:36.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:36.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.750][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.770][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.781][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.784][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.788][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:36.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.812][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.813][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.814][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.815][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.830][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.837][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.838][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.840][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.841][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.861][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.862][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.864][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.886][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.887][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.889][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.910][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.911][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.913][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.927][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:36.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:36.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.930][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.934][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:36.935][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:36.936][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.936][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.940][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:36.941][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:36.942][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.943][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.946][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.947][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:36.948][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.949][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.953][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.954][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:36.955][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:36.956][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:36.971][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-04-12 16:05:37.003][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-04-12 16:05:37.004][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-04-12 16:05:37.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-12 16:05:37.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:37.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:37.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:37.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:37.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-12 16:05:37.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.049][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.053][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.057][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.061][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.103][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.115][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.118][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.126][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-12 16:05:37.152][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-04-12 16:05:37.171][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:37.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:37.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:37.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:37.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.197][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.229][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.232][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.236][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.265][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.268][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.279][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.282][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.286][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.290][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.291][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.292][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.293][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.318][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.319][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.320][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.320][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.339][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.342][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.345][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.367][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.368][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.370][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.393][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.394][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.405][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.417][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.418][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.419][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.420][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.430][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.431][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.432][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.436][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.437][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.438][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.439][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.446][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.449][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.452][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.453][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.454][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.455][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.459][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.460][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.461][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.462][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.465][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.466][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.467][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.468][ef$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.472][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.473][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.474][ef$get] fields variable is a list.
biodb.INFO [2025-04-12 16:05:37.481][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.482][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-12 16:05:37.482][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.483][biodb::testThat]
biodb.DEBUG[2025-04-12 16:05:37.485][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-04-12 16:05:37.492][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-04-12 16:05:37.495][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-04-12 16:05:37.497][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-04-12 16:05:37.499][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-04-12 16:05:37.500][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-04-12 16:05:37.502][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-04-12 16:05:37.503][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-04-12 16:05:37.504][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-04-12 16:05:37.505][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-04-12 16:05:37.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-12 16:05:37.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:37.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:37.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:37.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:37.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-12 16:05:37.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.561][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.565][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.572][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-12 16:05:37.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-12 16:05:37.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:37.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:37.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:37.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:37.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-04-12 16:05:37.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.616][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.620][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-12 16:05:37.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-12 16:05:37.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-12 16:05:37.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-04-12 16:05:37.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.643][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-12 16:05:37.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-12 16:05:37.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-12 16:05:37.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-12 16:05:37.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.678][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-12 16:05:37.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.682][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.685][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.693][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-04-12 16:05:37.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-12 16:05:37.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-12 16:05:37.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-12 16:05:37.733][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-04-12 16:05:37.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-12 16:05:37.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-12 16:05:37.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-12 16:05:37.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-12 16:05:37.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-12 16:05:37.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-12 16:05:37.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-04-12 16:05:37.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-04-12 16:05:37.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-04-12 16:05:37.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-04-12 16:05:37.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-04-12 16:05:37.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-04-12 16:05:37.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-12 16:05:37.765][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.766][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-12 16:05:37.767][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.768][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.773][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.773][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-04-12 16:05:37.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.775][biodb::testThat]
biodb.WARN [2025-04-12 16:05:37.793][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-04-12 16:05:37.810][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-04-12 16:05:37.817][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.818][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-04-12 16:05:37.819][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.820][biodb::testThat]
biodb.TRACE[2025-04-12 16:05:37.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.851][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:37.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:37.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.855][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:37.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:37.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.891][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-12 16:05:37.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.895][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:37.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-12 16:05:37.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-12 16:05:37.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:37.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-12 16:05:37.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-12 16:05:37.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-04-12 16:05:37.906][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.907][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-12 16:05:37.908][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.909][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.915][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.916][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-12 16:05:37.917][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.918][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.924][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.925][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-12 16:05:37.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.926][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.931][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.932][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-12 16:05:37.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-12 16:05:37.934][biodb::testThat]
biodb.INFO [2025-04-12 16:05:37.939][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-12 16:05:37.940][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-12 16:05:37.941][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-12 16:05:37.942][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-12 16:05:37.942][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:37.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:37.944][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:37.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:37.946][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-04-12 16:05:37.959][biodb::testContext]
biodb.INFO [2025-04-12 16:05:37.960][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-12 16:05:37.960][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-04-12 16:05:37.961][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-12 16:05:37.962][biodb::testContext]
biodb.INFO [2025-04-12 16:05:37.964][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-04-12 16:05:37.966][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-04-12 16:05:37.969][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-12 16:05:37.970][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-12 16:05:37.971][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-12 16:05:37.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:37.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:37.974][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-12 16:05:37.975][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-12 16:05:37.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:37.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:37.978][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-12 16:05:37.979][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-12 16:05:37.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:37.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:37.983][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-12 16:05:37.984][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-12 16:05:37.985][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-12 16:05:37.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:37.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:37.988][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-12 16:05:37.989][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-12 16:05:37.990][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-12 16:05:37.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:37.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:37.993][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-12 16:05:37.994][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-12 16:05:37.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:37.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:37.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:37.998][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-12 16:05:37.999][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-12 16:05:37.999][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-12 16:05:38.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.003][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-12 16:05:38.004][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-12 16:05:38.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.007][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-12 16:05:38.008][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-12 16:05:38.009][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-12 16:05:38.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.012][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-12 16:05:38.013][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-12 16:05:38.014][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-12 16:05:38.015][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-12 16:05:38.016][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-12 16:05:38.017][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-12 16:05:38.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.020][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-12 16:05:38.021][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-12 16:05:38.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.025][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-12 16:05:38.026][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-12 16:05:38.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.028][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[2025-04-12 16:05:38.029][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-12 16:05:38.030][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-12 16:05:38.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.033][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-12 16:05:38.034][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-12 16:05:38.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.038][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-12 16:05:38.039][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-12 16:05:38.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.042][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-12 16:05:38.043][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-12 16:05:38.046][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-12 16:05:38.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.050][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-12 16:05:38.051][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-12 16:05:38.052][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-12 16:05:38.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.055][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-12 16:05:38.057][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.058][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-12 16:05:38.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.060][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:38.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.061][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.064][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-12 16:05:38.065][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:38.066][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.067][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-12 16:05:38.068][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:38.069][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.070][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.071][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-12 16:05:38.071][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-12 16:05:38.071][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-12 16:05:38.071][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-12 16:05:38.071][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-12 16:05:38.072][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:38.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:38.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.078][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.079][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:38.080][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:38.081][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.082][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.083][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-12 16:05:38.088][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.089][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-12 16:05:38.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.091][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:38.092][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.094][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.095][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-12 16:05:38.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:38.097][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.098][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-12 16:05:38.099][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:38.100][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.101][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.102][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-12 16:05:38.102][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-12 16:05:38.102][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-12 16:05:38.102][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-12 16:05:38.102][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-12 16:05:38.103][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:38.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.104][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.105][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:38.106][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.107][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.108][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.109][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.110][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:38.111][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:38.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.112][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.114][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-12 16:05:38.115][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.116][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-12 16:05:38.117][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.118][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:38.119][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.120][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.121][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.122][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.122][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-12 16:05:38.123][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:38.124][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.125][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-12 16:05:38.126][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:38.127][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.128][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.129][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.130][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:38.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:38.133][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.134][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.135][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.136][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.137][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:38.138][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:38.139][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.140][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.141][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-12 16:05:38.142][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.143][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-12 16:05:38.144][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.145][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:38.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.148][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.149][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.150][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-12 16:05:38.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:38.152][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.153][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-12 16:05:38.153][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:38.154][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.155][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.156][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-12 16:05:38.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.160][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:38.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.163][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:38.165][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:38.166][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.167][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.168][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-12 16:05:38.169][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.199][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[2025-04-12 16:05:38.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.227][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[2025-04-12 16:05:38.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.245][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-12 16:05:38.246][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-12 16:05:38.247][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-12 16:05:38.248][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-12 16:05:38.250][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-12 16:05:38.251][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-12 16:05:38.252][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-12 16:05:38.254][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-12 16:05:38.255][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-12 16:05:38.256][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-12 16:05:38.258][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-12 16:05:38.259][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-12 16:05:38.260][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-12 16:05:38.261][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-12 16:05:38.263][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-12 16:05:38.264][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-12 16:05:38.265][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-12 16:05:38.267][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-12 16:05:38.268][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-12 16:05:38.269][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-12 16:05:38.270][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-12 16:05:38.272][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-12 16:05:38.273][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-12 16:05:38.274][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-12 16:05:38.276][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-12 16:05:38.277][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-12 16:05:38.278][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-12 16:05:38.279][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-12 16:05:38.281][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-12 16:05:38.282][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-12 16:05:38.283][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-12 16:05:38.284][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-12 16:05:38.286][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-12 16:05:38.287][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-12 16:05:38.288][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-12 16:05:38.290][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-12 16:05:38.291][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-12 16:05:38.292][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-12 16:05:38.293][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-12 16:05:38.295][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-12 16:05:38.296][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-12 16:05:38.297][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-12 16:05:38.299][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-12 16:05:38.300][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-12 16:05:38.301][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-12 16:05:38.302][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-12 16:05:38.304][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-12 16:05:38.305][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-12 16:05:38.306][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-12 16:05:38.308][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-12 16:05:38.309][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-12 16:05:38.310][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-12 16:05:38.311][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-12 16:05:38.313][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-12 16:05:38.314][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-12 16:05:38.315][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-12 16:05:38.317][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-12 16:05:38.318][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-12 16:05:38.319][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-12 16:05:38.320][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-12 16:05:38.322][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-12 16:05:38.323][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-12 16:05:38.324][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-12 16:05:38.326][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-12 16:05:38.327][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-12 16:05:38.328][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-12 16:05:38.329][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-12 16:05:38.331][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-12 16:05:38.332][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-12 16:05:38.333][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-12 16:05:38.338][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-12 16:05:38.340][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-12 16:05:38.341][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-12 16:05:38.342][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-12 16:05:38.343][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-12 16:05:38.345][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-12 16:05:38.346][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-12 16:05:38.347][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-12 16:05:38.348][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-12 16:05:38.350][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-12 16:05:38.351][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-12 16:05:38.352][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-12 16:05:38.353][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-12 16:05:38.355][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-12 16:05:38.356][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-04-12 16:05:38.357][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-12 16:05:38.358][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.360][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-12 16:05:38.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-12 16:05:38.464][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-04-12 16:05:38.465][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-04-12 16:05:38.467][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.468][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-04-12 16:05:38.469][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.470][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-12 16:05:38.471][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.472][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-04-12 16:05:38.473][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.474][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.475][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-04-12 16:05:38.476][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-12 16:05:38.477][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.478][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-04-12 16:05:38.479][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-04-12 16:05:38.480][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-04-12 16:05:38.481][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-12 16:05:38.481][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.482][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-12 16:05:38.483][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.485][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-12 16:05:38.486][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-12 16:05:38.487][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-12 16:05:38.488][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-12 16:05:38.489][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-12 16:05:38.489][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-04-12 16:05:38.489][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-04-12 16:05:38.489][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-04-12 16:05:38.490][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-12 16:05:38.490][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-12 16:05:38.491][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-12 16:05:38.492][self$setPropertyValue]
biodb.DEBUG[2025-04-12 16:05:38.493][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-04-12 16:05:38.496][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-04-12 16:05:38.497][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-04-12 16:05:38.498][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-04-12 16:05:38.500][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-04-12 16:05:38.501][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-12 16:05:38.502][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-12 16:05:38.503][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-12 16:05:38.504][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-12 16:05:38.505][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-04-12 16:05:38.506][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-04-12 16:05:38.507][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-12 16:05:38.508][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-04-12 16:05:38.509][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-04-12 16:05:38.510][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-12 16:05:38.511][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-12 16:05:38.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-12 16:05:38.512][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-12 16:05:38.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-12 16:05:38.514][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-12 16:05:38.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
>
> proc.time()
user system elapsed
4.111 0.233 4.335
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* 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 ‘1.11.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
NciCactusConn.Rd: BiodbConn
NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** this is package ‘biodbNci’ version ‘1.11.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)