Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
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 12/33 | Hostname | OS / Arch | CHECK | |||||||
biodbNci 1.8.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the biodbNci package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: biodbNci |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz |
StartedAt: 2024-05-04 16:00:52 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:27:12 -0400 (Sat, 04 May 2024) |
EllapsedTime: 1579.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbNci.Rcheck |
Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 [2024-05-04 16:01:48.706][biodb::testContext] biodb.INFO [2024-05-04 16:01:48.709][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:01:48.710][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-05-04 16:01:48.711][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:01:48.711][biodb::testContext] biodb.INFO [2024-05-04 16:01:48.716][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:01:48.718][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:01:48.723][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:48.724][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:01:48.725][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:01:48.726][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.728][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:01:48.741][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:01:48.742][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.744][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:01:48.745][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:01:48.746][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.748][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:01:48.749][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:01:48.750][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:01:48.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.752][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:01:48.753][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:01:48.754][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:01:48.755][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.757][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:01:48.757][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:01:48.758][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.760][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:01:48.761][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:01:48.762][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:01:48.762][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.764][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:01:48.765][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:01:48.766][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.768][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:01:48.769][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:01:48.770][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:01:48.771][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.773][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:01:48.774][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:01:48.774][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:01:48.775][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:01:48.776][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:01:48.777][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:01:48.777][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.779][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[2024-05-04 16:01:48.780][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:01:48.781][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:01:48.781][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.783][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:01:48.784][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:01:48.785][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.787][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:01:48.788][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:01:48.789][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.791][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:01:48.792][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:01:48.792][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.795][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:01:48.795][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:01:48.796][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.799][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:01:48.799][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:01:48.819][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:01:48.820][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.822][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:01:48.823][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:01:48.824][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:01:48.824][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.829][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:01:48.855][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.873][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:01:48.874][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.875][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:48.876][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.877][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:48.878][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.879][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:48.880][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:01:48.881][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:48.882][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.882][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:01:48.883][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:48.884][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.885][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.886][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:48.886][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:01:48.886][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:01:48.886][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:01:48.886][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:01:48.887][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:48.887][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.889][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:48.890][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.891][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:48.892][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.893][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:48.893][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:48.894][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.895][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.896][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:01:48.897][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.898][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:01:48.899][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.899][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:48.900][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.901][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:48.902][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:48.903][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:01:48.904][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:48.905][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.906][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:01:48.907][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:48.908][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.909][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.909][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:48.909][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:01:48.909][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:01:48.909][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:01:48.909][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:01:48.910][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:48.911][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.912][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:48.913][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.914][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.915][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:48.916][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.916][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:48.917][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:48.918][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.919][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.920][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:01:48.921][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.922][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:01:48.922][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.923][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:48.924][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.925][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:48.925][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:48.927][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:01:48.928][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:48.929][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.929][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:01:48.930][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:48.931][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.932][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.932][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.933][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:48.934][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.935][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:48.936][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.937][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:48.938][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.939][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:48.940][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:48.940][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.941][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.942][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:01:48.944][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.944][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:01:48.945][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.946][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:48.947][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.948][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:48.948][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:48.950][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:01:48.951][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:48.952][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.953][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:01:48.954][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:48.955][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.955][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:48.956][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.957][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:48.958][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.959][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:48.960][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:48.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:48.962][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:48.962][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.963][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:48.964][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:48.965][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:48.966][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:48.969][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:48.970][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.971][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.975][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.978][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.982][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.985][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.989][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.992][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:48.996][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:48.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:48.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:48.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:48.998][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[2024-05-04 16:01:48.999][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.003][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.006][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[2024-05-04 16:01:49.007][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.014][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.017][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.020][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.023][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[2024-05-04 16:01:49.023][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.027][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.030][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.034][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:01:49.038][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:01:49.039][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:01:49.040][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:01:49.041][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:01:49.042][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:01:49.043][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:01:49.044][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:01:49.045][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:01:49.046][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:01:49.047][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:01:49.048][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:01:49.049][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:01:49.050][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:01:49.051][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:01:49.053][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:01:49.054][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:01:49.055][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:01:49.056][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:01:49.057][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:01:49.058][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:01:49.059][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:01:49.060][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:01:49.061][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:01:49.062][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:01:49.063][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:01:49.065][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:01:49.066][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:01:49.067][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:01:49.068][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:01:49.069][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:01:49.070][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:01:49.071][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:01:49.072][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:01:49.074][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:01:49.075][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:01:49.076][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:01:49.077][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:01:49.078][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:01:49.079][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:01:49.080][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:01:49.081][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:01:49.082][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:01:49.084][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:01:49.085][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:01:49.086][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:01:49.087][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:01:49.088][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:01:49.089][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:01:49.090][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:01:49.092][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:01:49.093][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:01:49.094][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:01:49.095][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:01:49.096][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:01:49.097][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:01:49.098][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:01:49.099][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:01:49.101][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:01:49.102][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:01:49.103][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:01:49.104][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:01:49.105][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:01:49.106][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:01:49.107][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:01:49.108][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:01:49.110][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:01:49.111][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:01:49.112][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:01:49.113][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:01:49.114][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:01:49.115][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:01:49.116][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:01:49.117][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:01:49.118][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:01:49.119][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:01:49.120][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:01:49.122][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:01:49.123][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:01:49.124][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:01:49.125][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:01:49.126][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:01:49.127][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:01:49.131][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:01:49.133][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:01:49.135][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:49.136][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.137][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.142][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.147][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.157][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.162][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.167][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.171][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.176][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.181][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.186][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.190][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.195][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.201][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.206][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.211][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.216][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.221][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.226][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:49.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:49.232][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2024-05-04 16:01:49.240][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2024-05-04 16:01:49.242][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:49.243][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2024-05-04 16:01:49.243][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:49.244][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:49.245][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:49.246][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2024-05-04 16:01:49.246][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:49.247][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:49.248][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2024-05-04 16:01:49.249][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:49.250][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:49.251][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2024-05-04 16:01:49.251][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2024-05-04 16:01:49.252][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2024-05-04 16:01:49.253][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:01:49.254][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:49.255][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:01:49.256][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:49.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:49.257][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:49.258][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:49.259][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:49.259][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:49.260][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:01:49.260][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:01:49.260][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2024-05-04 16:01:49.260][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2024-05-04 16:01:49.261][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:49.262][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:49.263][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:49.263][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:49.268][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2024-05-04 16:01:49.288][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2024-05-04 16:01:49.290][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2024-05-04 16:01:49.293][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2024-05-04 16:01:49.297][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2024-05-04 16:01:49.300][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:01:49.301][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:01:49.302][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:01:49.303][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:01:49.304][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:01:49.305][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2024-05-04 16:01:49.342][biodb::testThat] biodb.INFO [2024-05-04 16:01:49.343][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 16:01:49.343][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:49.344][biodb::testThat] biodb.TRACE[2024-05-04 16:01:49.347][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2024-05-04 16:01:49.349][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2024-05-04 16:01:49.352][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2024-05-04 16:01:49.359][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:49.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.374][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.375][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:01:49.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.429][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.486][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.554][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.560][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:49.611][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2024-05-04 16:01:49.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:49.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:49.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.617][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:49.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:49.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:49.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:49.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.623][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:49.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:49.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.654][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.683][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.686][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.714][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.715][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.715][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.716][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.728][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.731][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.738][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.739][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.740][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.740][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.761][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.762][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.763][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.764][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.784][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.784][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.785][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.786][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.806][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.807][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.808][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.808][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.819][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.820][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.821][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.822][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.831][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.832][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.832][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.833][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.838][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.838][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.839][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.840][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.844][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.845][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.846][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.847][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.851][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.852][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.853][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.854][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.868][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2024-05-04 16:01:49.895][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2024-05-04 16:01:49.896][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2024-05-04 16:01:49.897][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:49.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:49.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:49.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:49.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:49.905][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:49.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:01:49.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:49.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:49.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.934][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:49.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:49.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.937][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:49.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:49.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.945][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.948][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:49.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:49.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:49.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:49.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:49.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:49.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:49.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.995][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:49.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:49.998][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:49.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.004][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:50.026][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2024-05-04 16:01:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:50.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:50.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.045][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:50.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.048][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:50.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:50.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:50.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:50.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.066][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.095][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.099][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.102][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:01:50.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.129][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.130][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.131][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.132][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.143][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:50.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.146][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:50.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:50.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.149][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:50.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.153][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:50.154][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:50.154][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.155][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:50.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:50.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:50.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:50.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:50.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:50.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:50.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.177][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:50.177][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:50.178][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.179][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:50.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:50.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.194][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:50.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:50.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:50.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:50.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:50.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:50.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.204][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:50.205][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:50.206][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.207][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:50.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:50.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.225][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.228][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.229][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.230][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.230][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:50.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:50.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:50.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:50.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:50.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.251][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:50.252][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:50.253][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.253][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:50.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:50.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:50.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:50.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.268][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:50.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:50.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:50.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.274][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:50.275][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:50.275][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.276][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:50.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:50.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.287][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:50.288][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:50.289][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.290][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.294][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:01:50.295][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:01:50.296][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.296][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.301][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:01:50.301][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:01:50.302][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.303][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.307][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:01:50.308][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:01:50.309][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.310][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.318][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:01:50.319][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:01:50.320][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.320][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.325][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.326][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:01:50.326][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.327][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:50.331][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:50.332][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:50.333][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:50.334][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:01:50.341][biodb::testThat] biodb.INFO [2024-05-04 16:01:50.342][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 16:01:50.343][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:50.344][biodb::testThat] biodb.DEBUG[2024-05-04 16:01:50.346][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2024-05-04 16:01:50.352][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.INFO [2024-05-04 16:01:50.355][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427". biodb.DEBUG[2024-05-04 16:01:50.356][self$isDownloaded] Database nci.cactus has not yet been downloaded. biodb.INFO [2024-05-04 16:01:50.357][self$download] Downloading whole database of nci.cactus. biodb.INFO [2024-05-04 16:01:50.358][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ... biodb.DEBUG[2024-05-04 16:01:50.360][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz' Content type 'application/x-gzip' length 206737123 bytes (197.2 MB) ================================================== downloaded 197.2 MB biodb.TRACE[2024-05-04 16:02:29.572][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus158861f908ba3gz". biodb.TRACE[2024-05-04 16:02:29.573][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.DEBUG[2024-05-04 16:02:29.574][cch$addFilesToCache] Done adding files. biodb.DEBUG[2024-05-04 16:02:29.575][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.DEBUG[2024-05-04 16:02:29.576][self$download] Downloading of nci.cactus completed. biodb.TRACE[2024-05-04 16:02:29.578][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker158864abf8a85marker". biodb.TRACE[2024-05-04 16:02:29.579][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker". biodb.DEBUG[2024-05-04 16:02:29.579][self$addFilesToCache] Done adding files. biodb.DEBUG[2024-05-04 16:02:29.581][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2024-05-04 16:02:29.582][self$download] Extract whole database of nci.cactus. biodb.INFO [2024-05-04 16:02:29.582][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.DEBUG[2024-05-04 16:02:29.583][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz". biodb.DEBUG[2024-05-04 16:03:29.652][private$doExtractDownload] Delete existing entry files in cache system. biodb.DEBUG[2024-05-04 16:03:29.653][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp". biodb.TRACE[2024-05-04 16:25:06.132][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...". biodb.TRACE[2024-05-04 16:25:06.446][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...". biodb.DEBUG[2024-05-04 16:27:07.221][self$addFilesToCache] Done adding files. biodb.DEBUG[2024-05-04 16:27:07.264][private$doExtractDownload] Delete extracted database. biodb.TRACE[2024-05-04 16:27:07.275][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker15886651f4819marker". biodb.TRACE[2024-05-04 16:27:07.276][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker". biodb.DEBUG[2024-05-04 16:27:07.277][self$addFilesToCache] Done adding files. biodb.TRACE[2024-05-04 16:27:07.278][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690". biodb.TRACE[2024-05-04 16:27:07.279][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-05-04 16:27:07.304][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf". biodb.DEBUG[2024-05-04 16:27:07.435][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 16:27:07.436][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s). biodb.DEBUG[2024-05-04 16:27:07.437][self$createEntryFromContent] Parsing 2 NCI CACTUS entries. biodb.DEBUG[2024-05-04 16:27:07.438][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:27:07.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:07.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:07.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:07.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:07.698][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:07.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:27:07.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:27:07.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:27:07.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.784][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:27:07.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:27:07.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:27:07.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:27:07.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:27:07.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:27:07.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.800][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:27:07.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:27:07.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:27:07.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:27:07.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.809][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.815][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:27:07.827][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:27:07.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:07.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:07.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:07.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:07.834][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:07.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:27:07.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.849][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:27:07.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:27:07.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:27:07.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:27:07.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.856][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:27:07.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:27:07.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.859][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:27:07.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:27:07.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:27:07.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.883][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.886][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:27:07.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:27:07.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:27:07.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:27:07.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:27:07.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:27:07.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:27:07.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:27:07.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:27:07.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:27:07.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.902][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.905][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.911][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:27:07.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:27:07.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:27:07.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:27:07.942][self$createEntryFromContent] Accession numbers: 749674, 750690. biodb.TRACE[2024-05-04 16:27:07.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:27:07.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:27:07.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:27:07.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:27:07.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:27:07.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:27:07.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:27:07.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:27:07.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:27:07.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:27:07.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:07.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:27:07.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:27:07.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:07.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:27:07.972][biodb::testThat] biodb.INFO [2024-05-04 16:27:07.973][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 16:27:07.974][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:07.974][biodb::testThat] biodb.INFO [2024-05-04 16:27:07.980][biodb::testThat] biodb.INFO [2024-05-04 16:27:07.981][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 16:27:07.982][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:07.983][biodb::testThat] biodb.WARN [2024-05-04 16:27:07.999][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2024-05-04 16:27:08.013][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2024-05-04 16:27:08.021][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.022][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 16:27:08.023][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:08.024][biodb::testThat] biodb.TRACE[2024-05-04 16:27:08.205][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.211][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:27:08.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:27:08.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:27:08.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:27:08.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.241][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.245][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:27:08.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.248][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:27:08.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:27:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:27:08.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:27:08.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:27:08.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:27:08.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:27:08.341][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.342][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 16:27:08.343][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:08.344][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.351][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.352][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 16:27:08.353][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:08.354][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.361][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.362][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 16:27:08.363][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:08.363][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.369][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.370][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 16:27:08.370][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:27:08.371][biodb::testThat] biodb.INFO [2024-05-04 16:27:08.377][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:27:08.378][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2024-05-04 16:27:08.378][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2024-05-04 16:27:08.379][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:27:08.380][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:08.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:08.381][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:08.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:08.383][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:08.383][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 16:27:08.402][biodb::testContext] biodb.INFO [2024-05-04 16:27:08.403][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:27:08.404][biodb::testContext] Test context - Example long tests biodb.INFO [2024-05-04 16:27:08.405][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:27:08.406][biodb::testContext] biodb.INFO [2024-05-04 16:27:08.407][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:27:08.517][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:27:08.819][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:27:10.290][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:27:10.291][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:27:10.292][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.294][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:27:10.295][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:27:10.296][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.298][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:27:10.299][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:27:10.300][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.324][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:27:10.324][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:27:10.325][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:27:10.327][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.329][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:27:10.330][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:27:10.331][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:27:10.332][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.334][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:27:10.335][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:27:10.336][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.338][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:27:10.339][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:27:10.340][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:27:10.340][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.343][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:27:10.344][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:27:10.345][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.347][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:27:10.349][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:27:10.351][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:27:10.352][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.354][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:27:10.355][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:27:10.355][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:27:10.356][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:27:10.357][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:27:10.358][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:27:10.359][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.361][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:27:10.362][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:27:10.362][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.364][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:27:10.365][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:27:10.366][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.367][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[2024-05-04 16:27:10.368][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:27:10.369][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:27:10.370][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.372][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:27:10.373][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:27:10.373][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.375][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:27:10.376][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:27:10.377][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.379][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:27:10.380][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:27:10.442][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:27:10.443][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.445][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:27:10.446][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:27:10.447][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:27:10.448][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.450][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:27:10.451][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.452][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:27:10.453][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.466][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:27:10.466][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.467][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:27:10.468][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.469][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:27:10.470][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:27:10.470][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:27:10.471][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.472][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:27:10.473][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:27:10.473][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.474][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.475][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:27:10.475][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:27:10.475][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:27:10.475][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:27:10.475][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:27:10.476][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:27:10.477][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.477][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.478][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:27:10.479][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.480][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.480][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:27:10.482][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.482][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:27:10.484][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:27:10.486][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.486][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.487][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:27:10.488][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.489][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:27:10.490][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.491][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:27:10.491][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.492][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:27:10.493][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.493][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:27:10.494][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:27:10.495][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:27:10.496][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.496][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:27:10.497][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:27:10.498][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.498][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.499][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:27:10.499][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:27:10.499][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:27:10.499][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:27:10.499][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:27:10.512][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:27:10.513][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.515][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:27:10.516][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.516][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.517][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:27:10.518][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.519][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:27:10.519][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:27:10.520][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.521][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.522][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:27:10.523][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.524][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:27:10.525][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.526][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:27:10.527][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:27:10.530][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:27:10.543][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:27:10.544][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:27:10.545][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.546][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:27:10.547][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:27:10.547][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.548][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.549][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.550][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:27:10.550][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.551][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.552][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:27:10.552][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.553][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.554][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:27:10.554][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.556][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:27:10.556][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:27:10.558][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.558][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.559][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:27:10.561][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.562][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:27:10.563][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.563][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:27:10.564][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.565][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:27:10.565][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:27:10.567][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:27:10.568][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:27:10.568][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.569][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:27:10.570][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:27:10.570][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.571][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.572][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.573][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:27:10.573][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.575][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:27:10.575][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.577][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:27:10.577][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.578][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:27:10.579][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:27:10.579][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.580][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.581][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:27:10.582][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.583][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.586][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.590][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.594][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.597][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.601][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.604][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.608][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.611][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.614][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.617][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.621][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.624][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.627][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.630][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.634][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.637][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.648][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:27:10.649][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:27:10.651][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:27:10.652][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:27:10.662][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:27:10.676][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:27:10.683][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:27:10.712][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:27:10.714][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:27:10.715][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:27:10.716][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:27:10.717][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:27:10.718][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:27:10.719][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:27:10.720][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:27:10.721][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:27:10.722][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:27:10.723][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:27:10.724][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:27:10.725][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:27:10.726][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:27:10.727][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:27:10.728][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:27:10.729][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:27:10.730][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:27:10.731][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:27:10.732][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:27:10.733][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:27:10.734][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:27:10.735][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:27:10.736][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:27:10.737][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:27:10.738][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:27:10.739][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:27:10.740][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:27:10.741][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:27:10.742][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:27:10.743][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:27:10.744][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:27:10.745][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:27:10.745][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:27:10.746][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:27:10.747][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:27:10.748][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:27:10.749][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:27:10.750][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:27:10.751][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:27:10.752][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:27:10.753][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:27:10.754][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:27:10.755][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:27:10.756][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:27:10.757][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:27:10.758][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:27:10.759][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:27:10.760][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:27:10.761][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:27:10.762][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:27:10.763][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:27:10.764][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:27:10.765][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:27:10.766][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:27:10.767][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:27:10.768][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:27:10.769][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:27:10.770][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:27:10.771][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:27:10.772][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:27:10.773][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:27:10.773][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:27:10.774][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:27:10.775][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:27:10.776][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:27:10.777][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:27:10.778][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:27:10.779][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:27:10.780][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:27:10.781][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:27:10.782][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:27:10.783][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:27:10.784][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:27:10.785][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:27:10.786][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:27:10.787][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:27:10.788][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:27:10.789][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:27:10.790][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.791][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.792][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.797][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.801][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.805][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[2024-05-04 16:27:10.806][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.810][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.814][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.818][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[2024-05-04 16:27:10.819][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.823][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.828][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[2024-05-04 16:27:10.828][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.833][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.837][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[2024-05-04 16:27:10.838][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.843][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.847][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.852][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.857][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:27:10.862][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.866][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[2024-05-04 16:27:10.866][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:27:10.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.871][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[2024-05-04 16:27:10.873][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2024-05-04 16:27:10.874][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2024-05-04 16:27:10.876][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.877][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2024-05-04 16:27:10.877][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.878][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:27:10.879][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.880][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2024-05-04 16:27:10.881][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.881][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:27:10.882][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2024-05-04 16:27:10.883][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:27:10.884][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.885][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2024-05-04 16:27:10.885][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2024-05-04 16:27:10.886][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2024-05-04 16:27:10.887][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:27:10.888][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.888][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:27:10.889][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.890][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.891][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:27:10.891][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:27:10.892][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:27:10.893][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:27:10.894][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:27:10.894][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:27:10.894][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2024-05-04 16:27:10.894][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2024-05-04 16:27:10.894][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:27:10.895][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:27:10.896][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:27:10.897][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:27:10.898][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2024-05-04 16:27:10.900][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2024-05-04 16:27:10.901][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2024-05-04 16:27:10.902][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2024-05-04 16:27:10.903][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2024-05-04 16:27:10.904][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:27:10.904][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:27:10.905][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:27:10.906][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:27:10.907][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:27:10.908][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2024-05-04 16:27:10.909][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:27:10.910][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2024-05-04 16:27:10.911][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2024-05-04 16:27:10.911][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:27:10.912][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:27:10.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:27:10.913][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:27:10.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:27:10.915][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:27:10.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ] > > proc.time() user system elapsed 1099.126 240.894 1523.778
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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 ‘1.8.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbNci’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ OK * DONE Status: OK
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractEntries.cpp -o extractEntries.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-100-example.cpp -o test-100-example.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)