Back to Long Tests report for BioC 3.21 |
This page was generated on 2025-08-09 23:55 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
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 1.12.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | |||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
merida1 | macOS 12.7.5 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: 1.12.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz |
StartedAt: 2025-08-09 16:04:43 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 16:07:57 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 194.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbNci.Rcheck |
Warnings: NA |
biodbNci.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 [2025-08-09 16:06:00.741][biodb::testContext] biodb.INFO [2025-08-09 16:06:00.745][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:06:00.746][biodb::testContext] Test context - Generic long tests biodb.INFO [2025-08-09 16:06:00.747][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:06:00.748][biodb::testContext] biodb.INFO [2025-08-09 16:06:00.755][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0. biodb.DEBUG[2025-08-09 16:06:00.758][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2025-08-09 16:06:00.766][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:06:00.767][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-09 16:06:00.768][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-09 16:06:00.769][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.773][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-09 16:06:00.789][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-09 16:06:00.791][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.794][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-09 16:06:00.795][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-09 16:06:00.796][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.800][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-09 16:06:00.801][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-09 16:06:00.802][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-09 16:06:00.803][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.807][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-09 16:06:00.808][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-09 16:06:00.809][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-09 16:06:00.810][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.814][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-09 16:06:00.815][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-09 16:06:00.816][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.819][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-09 16:06:00.820][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-09 16:06:00.822][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-09 16:06:00.823][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.826][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-09 16:06:00.827][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-09 16:06:00.828][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.832][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-09 16:06:00.833][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-09 16:06:00.834][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-09 16:06:00.835][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.839][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:06:00.840][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-09 16:06:00.841][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-09 16:06:00.842][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-09 16:06:00.844][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-09 16:06:00.845][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-09 16:06:00.846][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.849][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-09 16:06:00.851][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-09 16:06:00.852][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.855][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-09 16:06:00.856][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-09 16:06:00.858][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.861][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-09 16:06:00.862][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-09 16:06:00.863][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.867][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-09 16:06:00.868][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-08-09 16:06:00.869][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.871][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[2025-08-09 16:06:00.872][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-09 16:06:00.874][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-09 16:06:00.875][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.878][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:06:00.879][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-09 16:06:00.883][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-09 16:06:00.884][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.887][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-09 16:06:00.888][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-09 16:06:00.890][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-09 16:06:00.891][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:00.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:00.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:00.896][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-09 16:06:00.924][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:06:00.945][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-08-09 16:06:00.946][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.948][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:06:00.949][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.951][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:06:00.952][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:00.953][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:06:00.954][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:06:00.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:06:00.957][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.958][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-09 16:06:00.959][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:06:00.960][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:00.961][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.963][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:06:00.963][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:06:00.963][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:06:00.963][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:06:00.963][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:06:00.964][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:06:00.965][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:00.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:00.967][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:06:00.968][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:00.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:00.971][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:06:00.972][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:00.973][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:06:00.974][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:06:00.975][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:00.976][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:00.978][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-09 16:06:00.980][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:06:00.981][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:06:00.982][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.983][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:06:00.984][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:06:00.987][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:00.988][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:06:00.989][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:06:00.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:06:00.992][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.993][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-09 16:06:00.994][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:06:00.995][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:00.997][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:06:00.998][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:06:00.998][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:06:00.998][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:06:00.998][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:06:00.998][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:06:00.999][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:06:01.001][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.003][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:06:01.004][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.006][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:06:01.007][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.009][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:06:01.010][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:06:01.011][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.012][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.013][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-09 16:06:01.015][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.017][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-08-09 16:06:01.018][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.019][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:06:01.020][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:06:01.023][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.024][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:06:01.025][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:06:01.026][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:06:01.027][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.029][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-09 16:06:01.030][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:06:01.031][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.032][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.033][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.034][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:06:01.036][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.038][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:06:01.039][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.041][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:06:01.042][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.043][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:06:01.045][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:06:01.046][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.047][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.048][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-09 16:06:01.050][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.051][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:06:01.053][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.054][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:06:01.055][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:06:01.057][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.058][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:06:01.060][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:06:01.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:06:01.062][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.063][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-09 16:06:01.064][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:06:01.066][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.067][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.068][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.069][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:06:01.070][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.073][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:06:01.074][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.076][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:06:01.077][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.078][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:06:01.079][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:06:01.081][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.082][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.085][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:06:01.086][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.089][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.094][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.099][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.104][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[2025-08-09 16:06:01.105][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.116][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.120][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[2025-08-09 16:06:01.121][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.126][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.132][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.136][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[2025-08-09 16:06:01.137][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.143][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.148][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.158][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.164][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.169][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.174][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.180][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.185][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-09 16:06:01.190][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-09 16:06:01.191][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-09 16:06:01.193][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-09 16:06:01.194][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-09 16:06:01.196][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-09 16:06:01.198][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-09 16:06:01.200][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-09 16:06:01.201][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-09 16:06:01.203][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-09 16:06:01.204][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-09 16:06:01.206][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-09 16:06:01.207][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-09 16:06:01.209][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-09 16:06:01.210][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-09 16:06:01.212][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-09 16:06:01.213][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-09 16:06:01.215][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-09 16:06:01.216][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-09 16:06:01.218][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-09 16:06:01.220][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-09 16:06:01.221][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-09 16:06:01.223][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-09 16:06:01.224][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-09 16:06:01.226][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-09 16:06:01.227][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-09 16:06:01.229][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-09 16:06:01.230][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-09 16:06:01.232][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-09 16:06:01.233][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-09 16:06:01.235][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-09 16:06:01.237][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-09 16:06:01.238][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-09 16:06:01.240][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-09 16:06:01.241][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-09 16:06:01.243][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-09 16:06:01.244][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-09 16:06:01.246][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-09 16:06:01.247][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-09 16:06:01.249][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-09 16:06:01.250][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-09 16:06:01.252][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-09 16:06:01.254][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-09 16:06:01.255][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-09 16:06:01.257][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-09 16:06:01.258][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-09 16:06:01.260][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-09 16:06:01.261][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-09 16:06:01.263][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-09 16:06:01.264][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-09 16:06:01.266][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-09 16:06:01.268][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-09 16:06:01.269][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-09 16:06:01.271][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-09 16:06:01.272][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-09 16:06:01.274][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-09 16:06:01.275][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-09 16:06:01.277][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-09 16:06:01.278][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-09 16:06:01.280][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-09 16:06:01.282][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-09 16:06:01.283][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-09 16:06:01.285][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-09 16:06:01.286][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-09 16:06:01.288][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-09 16:06:01.289][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-09 16:06:01.291][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-09 16:06:01.292][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-09 16:06:01.294][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-09 16:06:01.296][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-09 16:06:01.297][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-09 16:06:01.299][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-09 16:06:01.300][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-09 16:06:01.302][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-09 16:06:01.303][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-09 16:06:01.305][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-09 16:06:01.306][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-09 16:06:01.308][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-09 16:06:01.310][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-09 16:06:01.311][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-09 16:06:01.313][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-09 16:06:01.314][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-09 16:06:01.316][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-09 16:06:01.338][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-09 16:06:01.341][initialize] This is biodb version 1.16.0. biodb.DEBUG[2025-08-09 16:06:01.344][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:06:01.345][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.347][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.353][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.360][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.368][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.403][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.410][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.418][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.424][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[2025-08-09 16:06:01.425][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.433][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.440][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.447][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[2025-08-09 16:06:01.448][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.455][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.462][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[2025-08-09 16:06:01.463][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.470][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.478][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.485][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.500][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:06:01.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:06:01.510][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-09 16:06:01.519][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-09 16:06:01.521][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.522][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-09 16:06:01.523][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.524][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:06:01.526][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.527][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-09 16:06:01.528][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:06:01.530][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-09 16:06:01.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:06:01.533][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.534][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-09 16:06:01.535][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-09 16:06:01.536][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-09 16:06:01.538][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-09 16:06:01.539][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.540][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-09 16:06:01.541][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.542][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.543][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:06:01.544][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:06:01.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:06:01.547][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:06:01.548][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:06:01.548][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:06:01.548][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-09 16:06:01.548][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-09 16:06:01.549][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:06:01.550][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:06:01.551][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-09 16:06:01.552][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:06:01.558][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-09 16:06:01.578][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-09 16:06:01.580][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2025-08-09 16:06:01.584][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2025-08-09 16:06:01.587][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2025-08-09 16:06:01.591][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-08-09 16:06:01.592][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-08-09 16:06:01.594][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2025-08-09 16:06:01.596][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2025-08-09 16:06:01.597][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2025-08-09 16:06:01.598][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-09 16:06:01.615][biodb::testThat] biodb.INFO [2025-08-09 16:06:01.616][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-08-09 16:06:01.618][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:06:01.619][biodb::testThat] biodb.TRACE[2025-08-09 16:06:01.624][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2025-08-09 16:06:01.626][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-09 16:06:01.629][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-09 16:06:01.636][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-09 16:06:01.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:01.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:01.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:01.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:01.657][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:01.658][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:06:01.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:01.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:01.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:01.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:01.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:01.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:01.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:01.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:01.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:01.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:01.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:01.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:01.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:01.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:01.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:01.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:01.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.756][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.761][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.770][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-09 16:06:01.841][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2025-08-09 16:06:01.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:06:01.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:06:01.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.849][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:06:01.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:06:01.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.857][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-09 16:06:01.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-09 16:06:01.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-09 16:06:01.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-09 16:06:01.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.905][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.948][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.953][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.963][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:01.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.992][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.993][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.995][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:01.996][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:01.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:01.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:01.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.012][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.027][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.028][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.029][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.031][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.061][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.063][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.064][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.065][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.091][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.096][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.097][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.098][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.099][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.131][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.132][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.133][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.134][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.155][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.157][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.158][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.159][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.166][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.167][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.169][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.170][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.177][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.178][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.180][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.181][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.189][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.190][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.191][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.192][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.199][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.201][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.202][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.203][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.222][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2025-08-09 16:06:02.252][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-09 16:06:02.253][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-09 16:06:02.255][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-09 16:06:02.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:06:02.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:06:02.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:06:02.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:06:02.267][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:06:02.268][FUN] Functions in observer BiodbConfig: [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[2025-08-09 16:06:02.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.308][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.314][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.319][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.359][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.379][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.395][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.399][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.409][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-09 16:06:02.443][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2025-08-09 16:06:02.465][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:06:02.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:06:02.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.470][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:06:02.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:06:02.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.475][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-09 16:06:02.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-09 16:06:02.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-09 16:06:02.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-09 16:06:02.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.497][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.543][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.548][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:06:02.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.585][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.586][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.587][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.588][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.609][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.614][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.618][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.620][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.621][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.622][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.623][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.657][ef$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.659][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.660][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.661][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.682][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.691][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.693][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.694][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.695][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.715][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.725][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.726][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.727][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.728][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.758][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.760][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.761][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.762][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.792][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.794][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.795][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.796][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.811][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:06:02.813][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:06:02.819][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.820][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.827][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:06:02.828][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:06:02.829][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.830][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.838][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:06:02.840][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:06:02.841][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.843][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.850][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:06:02.851][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:06:02.852][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.853][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.860][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:06:02.862][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:06:02.863][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.864][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.871][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.872][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:06:02.873][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.874][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:06:02.881][ef$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:06:02.883][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:06:02.884][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:06:02.885][ef$get] fields variable is a list. biodb.INFO [2025-08-09 16:06:02.897][biodb::testThat] biodb.INFO [2025-08-09 16:06:02.898][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-08-09 16:06:02.900][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:06:02.901][biodb::testThat] biodb.DEBUG[2025-08-09 16:06:02.904][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2025-08-09 16:06:02.910][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.INFO [2025-08-09 16:06:02.916][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427". biodb.DEBUG[2025-08-09 16:06:02.918][self$isDownloaded] Database nci.cactus has not yet been downloaded. biodb.INFO [2025-08-09 16:06:02.920][self$download] Downloading whole database of nci.cactus. biodb.INFO [2025-08-09 16:06:02.921][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ... biodb.DEBUG[2025-08-09 16:06:03.061][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz' Content type 'application/x-gzip' length 206737123 bytes (197.2 MB) ================================================== downloaded 197.2 MB biodb.TRACE[2025-08-09 16:06:05.435][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\nci.cactus1320014702d92gz". biodb.TRACE[2025-08-09 16:06:05.436][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.DEBUG[2025-08-09 16:06:05.750][cch$addFilesToCache] Done adding files. biodb.DEBUG[2025-08-09 16:06:05.755][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.DEBUG[2025-08-09 16:06:05.756][self$download] Downloading of nci.cactus completed. biodb.TRACE[2025-08-09 16:06:05.760][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker132005ac63f0fmarker". biodb.TRACE[2025-08-09 16:06:05.761][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker". biodb.DEBUG[2025-08-09 16:06:05.843][self$addFilesToCache] Done adding files. biodb.DEBUG[2025-08-09 16:06:05.845][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-09 16:06:05.847][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-09 16:06:05.849][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.DEBUG[2025-08-09 16:06:05.851][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.INFO [2025-08-09 16:07:18.730][biodb::testThat] biodb.INFO [2025-08-09 16:07:18.731][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-08-09 16:07:18.733][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:18.734][biodb::testThat] biodb.INFO [2025-08-09 16:07:18.743][biodb::testThat] biodb.INFO [2025-08-09 16:07:18.744][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-08-09 16:07:18.746][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:18.747][biodb::testThat] biodb.WARN [2025-08-09 16:07:18.765][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2025-08-09 16:07:18.783][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2025-08-09 16:07:18.796][biodb::testThat] biodb.INFO [2025-08-09 16:07:18.797][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-08-09 16:07:18.798][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:18.799][biodb::testThat] biodb.DEBUG[2025-08-09 16:07:18.816][private$loadEntries] Creating entries from ids [1]: "749674". biodb.DEBUG[2025-08-09 16:07:18.860][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)... biodb.DEBUG[2025-08-09 16:07:18.863][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-09 16:07:18.865][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-09 16:07:18.867][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-09 16:07:18.881][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.DEBUG[2025-08-09 16:07:18.883][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.INFO [2025-08-09 16:07:52.330][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.331][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-08-09 16:07:52.332][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:52.334][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.344][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.345][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-08-09 16:07:52.347][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:52.348][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.358][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.360][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-08-09 16:07:52.361][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:52.362][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.371][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.373][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-08-09 16:07:52.374][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:07:52.375][biodb::testThat] biodb.INFO [2025-08-09 16:07:52.384][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-08-09 16:07:52.385][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2025-08-09 16:07:52.386][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-09 16:07:52.387][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-09 16:07:52.389][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:52.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:52.391][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.393][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.394][FUN] Functions in observer BiodbConfig: [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 [2025-08-09 16:07:52.404][biodb::testContext] biodb.INFO [2025-08-09 16:07:52.405][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:07:52.406][biodb::testContext] Test context - Example long tests biodb.INFO [2025-08-09 16:07:52.408][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:07:52.409][biodb::testContext] biodb.INFO [2025-08-09 16:07:52.412][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0. biodb.DEBUG[2025-08-09 16:07:52.414][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2025-08-09 16:07:52.420][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:07:52.421][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-09 16:07:52.422][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-09 16:07:52.423][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.426][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-09 16:07:52.428][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-09 16:07:52.429][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.432][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-09 16:07:52.433][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-09 16:07:52.434][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.438][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-09 16:07:52.439][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-09 16:07:52.440][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-09 16:07:52.441][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.444][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-09 16:07:52.445][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-09 16:07:52.447][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-09 16:07:52.448][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.453][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-09 16:07:52.455][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-09 16:07:52.456][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.459][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-09 16:07:52.460][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-09 16:07:52.462][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-09 16:07:52.463][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.466][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-09 16:07:52.467][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-09 16:07:52.468][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.472][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-09 16:07:52.473][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-09 16:07:52.474][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-09 16:07:52.475][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.479][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:07:52.480][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-09 16:07:52.481][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-09 16:07:52.483][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-09 16:07:52.485][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-09 16:07:52.487][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-09 16:07:52.489][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.494][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-09 16:07:52.496][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-09 16:07:52.498][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.504][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-09 16:07:52.506][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-09 16:07:52.508][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.513][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-09 16:07:52.515][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-09 16:07:52.517][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.523][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-09 16:07:52.525][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2025-08-09 16:07:52.526][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.532][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-09 16:07:52.534][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-09 16:07:52.536][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.541][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:07:52.543][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-09 16:07:52.548][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-09 16:07:52.550][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.556][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-09 16:07:52.558][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-09 16:07:52.560][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-09 16:07:52.562][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.568][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-09 16:07:52.572][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.574][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-08-09 16:07:52.576][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.578][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:07:52.580][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:07:52.583][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.584][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:07:52.585][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:07:52.587][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:07:52.588][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.589][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-09 16:07:52.591][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:07:52.592][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.594][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.595][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:07:52.595][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:07:52.595][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:07:52.595][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:07:52.595][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:07:52.596][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:07:52.598][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.600][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:07:52.602][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.604][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:07:52.606][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.607][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:07:52.608][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:07:52.609][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.611][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.612][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-09 16:07:52.615][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.616][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:07:52.617][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.619][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:07:52.620][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.621][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:07:52.623][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.624][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:07:52.625][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:07:52.627][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:07:52.628][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.629][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-09 16:07:52.631][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:07:52.632][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.633][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.635][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:07:52.635][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:07:52.635][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:07:52.635][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:07:52.635][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:07:52.636][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:07:52.638][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.640][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:07:52.641][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.644][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:07:52.645][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.647][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:07:52.648][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:07:52.649][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.651][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.652][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-09 16:07:52.654][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.656][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-08-09 16:07:52.657][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.658][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:07:52.660][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.661][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:07:52.663][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.664][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:07:52.665][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:07:52.667][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:07:52.668][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.669][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-09 16:07:52.671][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:07:52.672][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.673][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.675][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.676][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:07:52.678][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.680][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:07:52.681][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.684][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:07:52.685][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.687][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:07:52.688][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:07:52.689][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.691][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.692][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-09 16:07:52.694][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.696][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:07:52.697][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.699][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:07:52.700][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.701][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:07:52.703][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.704][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:07:52.705][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:07:52.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:07:52.708][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.710][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-09 16:07:52.711][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:07:52.713][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.714][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:07:52.715][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.717][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:07:52.718][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.721][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:07:52.722][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:52.723][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:52.724][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:07:52.726][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.727][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:07:52.728][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:07:52.730][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:52.731][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:52.733][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:07:52.734][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.737][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.743][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.749][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.755][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.761][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.768][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.774][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.780][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.786][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.792][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.798][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.805][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.811][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.817][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.823][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.830][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.836][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:52.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.842][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-09 16:07:52.844][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-09 16:07:52.846][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-09 16:07:52.847][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-09 16:07:52.849][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-09 16:07:52.851][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-09 16:07:52.853][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-09 16:07:52.855][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-09 16:07:52.856][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-09 16:07:52.858][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-09 16:07:52.860][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-09 16:07:52.862][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-09 16:07:52.863][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-09 16:07:52.865][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-09 16:07:52.867][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-09 16:07:52.869][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-09 16:07:52.870][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-09 16:07:52.872][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-09 16:07:52.874][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-09 16:07:52.876][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-09 16:07:52.877][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-09 16:07:52.879][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-09 16:07:52.881][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-09 16:07:52.883][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-09 16:07:52.885][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-09 16:07:52.886][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-09 16:07:52.888][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-09 16:07:52.890][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-09 16:07:52.892][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-09 16:07:52.893][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-09 16:07:52.895][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-09 16:07:52.897][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-09 16:07:52.899][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-09 16:07:52.900][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-09 16:07:52.902][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-09 16:07:52.904][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-09 16:07:52.906][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-09 16:07:52.907][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-09 16:07:52.909][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-09 16:07:52.911][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-09 16:07:52.913][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-09 16:07:52.915][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-09 16:07:52.916][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-09 16:07:52.918][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-09 16:07:52.920][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-09 16:07:52.922][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-09 16:07:52.923][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-09 16:07:52.925][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-09 16:07:52.927][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-09 16:07:52.929][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-09 16:07:52.931][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-09 16:07:52.932][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-09 16:07:52.934][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-09 16:07:52.936][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-09 16:07:52.938][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-09 16:07:52.939][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-09 16:07:52.941][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-09 16:07:52.943][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-09 16:07:52.945][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-09 16:07:52.946][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-09 16:07:52.948][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-09 16:07:52.950][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-09 16:07:52.952][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-09 16:07:52.953][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-09 16:07:52.955][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-09 16:07:52.957][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-09 16:07:52.959][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-09 16:07:52.960][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-09 16:07:52.962][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-09 16:07:52.964][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-09 16:07:52.966][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-09 16:07:52.968][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-09 16:07:52.969][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-09 16:07:52.971][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-09 16:07:52.973][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-09 16:07:52.975][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-09 16:07:52.976][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-09 16:07:52.978][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-09 16:07:52.980][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-09 16:07:52.982][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-09 16:07:52.983][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-09 16:07:52.985][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-09 16:07:52.987][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-09 16:07:52.989][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-09 16:07:52.991][initialize] This is biodb version 1.16.0. biodb.DEBUG[2025-08-09 16:07:52.993][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:07:52.994][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:52.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:52.996][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:52.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:52.999][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.006][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[2025-08-09 16:07:53.008][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.016][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.025][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.032][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[2025-08-09 16:07:53.033][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.042][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.049][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[2025-08-09 16:07:53.050][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.059][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.067][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.075][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[2025-08-09 16:07:53.076][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.083][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[2025-08-09 16:07:53.084][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.093][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.100][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[2025-08-09 16:07:53.101][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.118][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.127][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.135][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:07:53.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:07:53.146][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-09 16:07:53.148][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-09 16:07:53.151][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:07:53.152][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-09 16:07:53.153][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:07:53.155][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:07:53.156][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-09 16:07:53.157][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-09 16:07:53.159][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-09 16:07:53.160][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:07:53.161][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-09 16:07:53.163][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:07:53.164][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:07:53.165][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-09 16:07:53.167][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-09 16:07:53.168][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-09 16:07:53.169][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-09 16:07:53.171][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:53.172][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-09 16:07:53.173][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:53.175][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:53.176][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:07:53.177][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:07:53.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:07:53.180][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:07:53.181][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:07:53.181][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:07:53.181][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-09 16:07:53.181][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-09 16:07:53.183][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:07:53.184][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:07:53.185][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-09 16:07:53.186][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:07:53.188][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-09 16:07:53.192][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-09 16:07:53.193][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2025-08-09 16:07:53.195][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2025-08-09 16:07:53.197][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2025-08-09 16:07:53.199][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-08-09 16:07:53.200][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2025-08-09 16:07:53.202][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2025-08-09 16:07:53.203][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2025-08-09 16:07:53.205][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2025-08-09 16:07:53.207][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-09 16:07:53.208][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2025-08-09 16:07:53.209][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2025-08-09 16:07:53.211][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-09 16:07:53.212][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-09 16:07:53.213][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:07:53.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:07:53.216][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:07:53.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:07:53.218][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:07:53.219][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". [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ── Error in `writeLines(readLines(fd), txtfile)`: Error writing to connection: No space left on device Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`) 3. └─conn$getBiodb()$getFactory()$getEntry(...) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doExtractDownload() 8. └─base::writeLines(readLines(fd), txtfile) ── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ── Error in `writeLines(readLines(fd), txtfile)`: Error writing to connection: No space left on device Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`) 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doExtractDownload() 10. └─base::writeLines(readLines(fd), txtfile) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ] Error: Test failures In addition: Warning message: In for (i in .rlang_purrr_index(.x, .right)) { : closing unused connection 4 (C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz) Execution halted
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'biodbNci/DESCRIPTION' ... OK * this is package 'biodbNci' version '1.12.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'biodbNci' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 14.2.0' * 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: NciCactusConn.Rd: BiodbConn NciCactusEntry.Rd: BiodbSdfEntry Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking files in 'vignettes' ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... OK * checking tests in 'longtests' ... Running 'testthat.R' ERROR Running the tests in 'longtests/testthat.R' failed. Last 13 lines of output: 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doExtractDownload() 10. └─base::writeLines(readLines(fd), txtfile) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ] Error: Test failures In addition: Warning message: In for (i in .rlang_purrr_index(.x, .right)) { : closing unused connection 4 (C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz) Execution halted * DONE Status: 1 ERROR, 1 NOTE See 'E:/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 '1.12.0' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -s -static-libgcc -o biodbNci.dll tmp.def RcppExports.o extractEntries.o test-100-example.o test-runner.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)