Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
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 | OK | ||||||||
merida1 | macOS 12.7.4 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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz |
StartedAt: 2024-06-22 16:04:50 -0400 (Sat, 22 Jun 2024) |
EndedAt: 2024-06-22 16:05:55 -0400 (Sat, 22 Jun 2024) |
EllapsedTime: 65.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbNci.Rcheck |
Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbNci) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbNci") biodb.INFO [2024-06-22 16:05:52.087][biodb::testContext] biodb.INFO [2024-06-22 16:05:52.089][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-22 16:05:52.090][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-06-22 16:05:52.091][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-22 16:05:52.092][biodb::testContext] biodb.INFO [2024-06-22 16:05:52.098][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-06-22 16:05:52.100][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-06-22 16:05:52.107][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:05:52.108][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-06-22 16:05:52.109][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-06-22 16:05:52.109][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.112][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-06-22 16:05:52.129][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-06-22 16:05:52.130][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.132][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-06-22 16:05:52.133][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-06-22 16:05:52.134][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.136][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-06-22 16:05:52.137][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-06-22 16:05:52.138][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-06-22 16:05:52.139][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.142][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-06-22 16:05:52.143][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-06-22 16:05:52.143][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-06-22 16:05:52.144][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.147][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-06-22 16:05:52.148][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-06-22 16:05:52.148][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.151][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-06-22 16:05:52.152][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-06-22 16:05:52.153][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-06-22 16:05:52.154][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.156][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-06-22 16:05:52.157][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-06-22 16:05:52.158][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.160][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-06-22 16:05:52.161][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-06-22 16:05:52.162][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-06-22 16:05:52.163][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.165][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-06-22 16:05:52.166][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-06-22 16:05:52.167][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-06-22 16:05:52.168][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-06-22 16:05:52.169][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-06-22 16:05:52.170][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-06-22 16:05:52.171][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.173][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-06-22 16:05:52.174][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-06-22 16:05:52.175][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.178][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-06-22 16:05:52.179][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-06-22 16:05:52.179][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.182][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-06-22 16:05:52.183][self$set] Set key offline to FALSE. biodb.DEBUG[2024-06-22 16:05:52.184][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.186][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-06-22 16:05:52.187][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-06-22 16:05:52.188][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.190][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-06-22 16:05:52.191][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-06-22 16:05:52.192][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.195][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-06-22 16:05:52.196][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-06-22 16:05:52.199][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-06-22 16:05:52.200][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.202][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-06-22 16:05:52.203][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-06-22 16:05:52.204][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-06-22 16:05:52.205][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.210][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-06-22 16:05:52.247][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.261][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-06-22 16:05:52.262][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.263][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:52.264][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:52.266][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:52.268][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:05:52.269][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:52.270][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.270][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-06-22 16:05:52.271][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:52.272][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.273][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.274][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:05:52.274][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:05:52.274][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-22 16:05:52.274][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-22 16:05:52.274][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-22 16:05:52.275][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:52.276][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.278][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:52.278][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.279][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.280][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:52.281][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.282][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:52.283][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:52.284][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.284][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.285][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-06-22 16:05:52.287][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.288][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-06-22 16:05:52.289][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.290][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:52.291][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:52.293][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.293][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:52.294][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-22 16:05:52.295][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:52.296][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.297][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-06-22 16:05:52.298][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:52.299][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.300][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.301][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:05:52.301][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:05:52.301][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-22 16:05:52.301][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-22 16:05:52.301][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-22 16:05:52.302][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:52.302][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.304][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:52.305][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.306][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.307][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:52.308][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.308][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:52.309][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:52.310][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.311][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.312][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-06-22 16:05:52.314][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.315][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-06-22 16:05:52.316][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.316][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:52.317][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.318][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:52.319][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.320][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:52.321][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:05:52.322][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:52.323][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.324][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-06-22 16:05:52.324][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:52.325][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.326][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.327][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.328][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:52.329][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.330][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.331][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:52.332][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.332][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.333][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:52.334][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.335][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:52.336][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:52.337][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.337][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.339][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-06-22 16:05:52.340][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.341][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-06-22 16:05:52.342][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.343][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:52.344][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.345][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:52.346][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.346][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:52.347][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-22 16:05:52.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:52.349][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.350][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-06-22 16:05:52.351][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:52.352][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.353][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.354][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.355][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:52.355][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.357][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:52.358][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.360][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:52.361][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.361][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:52.362][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:52.363][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.364][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.368][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:05:52.369][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.370][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.374][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.378][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[2024-06-22 16:05:52.378][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.382][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.386][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.394][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.399][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.419][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.423][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.428][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.432][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.436][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.441][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.445][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.449][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[2024-06-22 16:05:52.450][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.455][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.459][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.463][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-06-22 16:05:52.469][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-06-22 16:05:52.470][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-06-22 16:05:52.471][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-06-22 16:05:52.473][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-06-22 16:05:52.474][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-06-22 16:05:52.476][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-06-22 16:05:52.477][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-06-22 16:05:52.478][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-06-22 16:05:52.480][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-06-22 16:05:52.481][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-06-22 16:05:52.482][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-06-22 16:05:52.484][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-06-22 16:05:52.485][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-06-22 16:05:52.486][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-06-22 16:05:52.488][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-06-22 16:05:52.489][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-06-22 16:05:52.491][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-06-22 16:05:52.492][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-06-22 16:05:52.493][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-06-22 16:05:52.495][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-06-22 16:05:52.496][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-06-22 16:05:52.497][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-06-22 16:05:52.499][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-06-22 16:05:52.500][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-06-22 16:05:52.501][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-06-22 16:05:52.503][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-06-22 16:05:52.504][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-06-22 16:05:52.506][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-06-22 16:05:52.507][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-06-22 16:05:52.508][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-06-22 16:05:52.510][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-06-22 16:05:52.511][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-06-22 16:05:52.512][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-06-22 16:05:52.514][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-06-22 16:05:52.515][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-06-22 16:05:52.516][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-06-22 16:05:52.518][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-06-22 16:05:52.519][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-06-22 16:05:52.521][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-06-22 16:05:52.522][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-06-22 16:05:52.523][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-06-22 16:05:52.525][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-06-22 16:05:52.526][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-06-22 16:05:52.527][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-06-22 16:05:52.529][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-06-22 16:05:52.530][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-06-22 16:05:52.531][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-06-22 16:05:52.533][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-06-22 16:05:52.534][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-06-22 16:05:52.536][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-06-22 16:05:52.537][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-06-22 16:05:52.538][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-06-22 16:05:52.540][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-06-22 16:05:52.541][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-06-22 16:05:52.542][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-06-22 16:05:52.544][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-06-22 16:05:52.545][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-06-22 16:05:52.546][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-06-22 16:05:52.548][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-06-22 16:05:52.549][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-06-22 16:05:52.550][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-06-22 16:05:52.552][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-06-22 16:05:52.553][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-06-22 16:05:52.555][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-06-22 16:05:52.556][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-06-22 16:05:52.557][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-06-22 16:05:52.559][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-06-22 16:05:52.560][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-06-22 16:05:52.561][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-06-22 16:05:52.563][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-06-22 16:05:52.564][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-06-22 16:05:52.565][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-06-22 16:05:52.567][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-06-22 16:05:52.568][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-06-22 16:05:52.569][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-06-22 16:05:52.571][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-06-22 16:05:52.572][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-06-22 16:05:52.573][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-06-22 16:05:52.575][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-06-22 16:05:52.576][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-06-22 16:05:52.577][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-06-22 16:05:52.579][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-06-22 16:05:52.584][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-06-22 16:05:52.586][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-06-22 16:05:52.589][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:05:52.590][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.592][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.597][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[2024-06-22 16:05:52.602][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.607][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.613][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.617][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[2024-06-22 16:05:52.618][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.623][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[2024-06-22 16:05:52.624][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.630][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.635][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.641][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.647][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.652][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.658][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.664][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.669][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.675][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.681][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.686][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.692][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:52.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:52.699][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2024-06-22 16:05:52.707][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2024-06-22 16:05:52.709][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.710][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2024-06-22 16:05:52.711][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.712][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:52.713][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.714][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2024-06-22 16:05:52.715][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.716][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:52.717][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2024-06-22 16:05:52.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:52.718][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.719][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2024-06-22 16:05:52.720][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2024-06-22 16:05:52.721][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2024-06-22 16:05:52.722][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-06-22 16:05:52.723][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.724][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-06-22 16:05:52.725][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.726][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.727][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:52.727][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:52.728][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:52.729][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:52.730][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-06-22 16:05:52.730][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-06-22 16:05:52.730][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2024-06-22 16:05:52.730][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2024-06-22 16:05:52.731][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:52.732][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:52.733][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:52.734][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:52.739][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2024-06-22 16:05:52.762][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2024-06-22 16:05:52.767][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2024-06-22 16:05:52.771][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2024-06-22 16:05:52.775][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2024-06-22 16:05:52.780][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-06-22 16:05:52.781][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-06-22 16:05:52.782][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-06-22 16:05:52.783][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-06-22 16:05:52.784][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-06-22 16:05:52.785][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2024-06-22 16:05:52.794][biodb::testThat] biodb.INFO [2024-06-22 16:05:52.795][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-06-22 16:05:52.796][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:52.797][biodb::testThat] biodb.TRACE[2024-06-22 16:05:52.800][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2024-06-22 16:05:52.802][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2024-06-22 16:05:52.805][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2024-06-22 16:05:52.814][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:05:52.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:52.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:52.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:52.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:52.828][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:52.829][FUN] Functions in observer BiodbConfig: [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[2024-06-22 16:05:52.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:52.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:52.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:52.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:52.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:52.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:52.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:52.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:52.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:52.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:52.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:52.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:52.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:52.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:52.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:52.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:52.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:52.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:52.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:52.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:52.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.919][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:52.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:52.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:52.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:52.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.930][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:52.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:52.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:52.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:52.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:52.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:52.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:52.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:52.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:52.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:52.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:05:53.023][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2024-06-22 16:05:53.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:53.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:53.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.036][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:53.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:53.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.069][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.103][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.107][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.111][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.131][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.132][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.133][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.134][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.153][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.156][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.157][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.158][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.159][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.181][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.182][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.183][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.184][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.198][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.202][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.206][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.207][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.207][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.208][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.209][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.230][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.231][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.248][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.249][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.249][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.250][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.254][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.255][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.256][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.257][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.260][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.261][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.262][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.263][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.267][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.268][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.269][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.270][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.273][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.274][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.275][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.276][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.291][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2024-06-22 16:05:53.324][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2024-06-22 16:05:53.325][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2024-06-22 16:05:53.326][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:05:53.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:53.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:53.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:53.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:53.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:53.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:05:53.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.371][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.375][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.379][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.421][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.436][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.440][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.447][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:05:53.472][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2024-06-22 16:05:53.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:53.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:53.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:53.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.516][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.546][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.550][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.553][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.582][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.583][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.584][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.585][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.595][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.599][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.603][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.606][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.607][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.608][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.609][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.610][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.635][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.636][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.637][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.637][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.659][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.660][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.661][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.662][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.683][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.684][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.685][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.686][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.708][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.709][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.709][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.710][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.732][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.733][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.734][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.735][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.749][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.750][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.751][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.752][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.755][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.756][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.757][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.758][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.762][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.763][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.764][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.764][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.768][ef$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.769][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.770][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.771][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.774][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.775][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.776][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.777][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.781][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.782][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.783][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.783][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.787][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.788][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.789][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.790][ef$get] fields variable is a list. biodb.INFO [2024-06-22 16:05:53.796][biodb::testThat] biodb.INFO [2024-06-22 16:05:53.797][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-06-22 16:05:53.798][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:53.798][biodb::testThat] biodb.DEBUG[2024-06-22 16:05:53.800][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2024-06-22 16:05:53.807][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.DEBUG[2024-06-22 16:05:53.812][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2024-06-22 16:05:53.813][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.TRACE[2024-06-22 16:05:53.815][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690". biodb.TRACE[2024-06-22 16:05:53.816][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-06-22 16:05:53.818][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf". biodb.DEBUG[2024-06-22 16:05:53.819][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache. biodb.DEBUG[2024-06-22 16:05:53.820][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s). biodb.DEBUG[2024-06-22 16:05:53.821][self$createEntryFromContent] Parsing 2 NCI CACTUS entries. biodb.DEBUG[2024-06-22 16:05:53.822][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:05:53.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:53.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:53.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:53.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:53.829][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:53.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:05:53.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.844][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.848][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.856][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.876][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.891][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:05:53.906][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:05:53.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:53.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:53.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:53.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:53.913][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:53.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:05:53.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:53.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.930][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.934][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-06-22 16:05:53.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-06-22 16:05:53.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:05:53.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:05:53.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:05:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.953][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:05:53.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:05:53.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-06-22 16:05:53.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-06-22 16:05:53.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-06-22 16:05:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-06-22 16:05:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.995][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:53.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:53.998][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:53.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:54.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-06-22 16:05:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:05:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:05:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:05:54.045][self$createEntryFromContent] Accession numbers: 749674, 750690. biodb.TRACE[2024-06-22 16:05:54.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-22 16:05:54.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-22 16:05:54.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-22 16:05:54.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-22 16:05:54.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-22 16:05:54.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-22 16:05:54.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-22 16:05:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-22 16:05:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-22 16:05:54.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-22 16:05:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-22 16:05:54.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-22 16:05:54.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:05:54.077][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.078][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-06-22 16:05:54.078][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.079][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.084][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.085][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-06-22 16:05:54.086][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.087][biodb::testThat] biodb.WARN [2024-06-22 16:05:54.105][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2024-06-22 16:05:54.123][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2024-06-22 16:05:54.130][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.131][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-06-22 16:05:54.132][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.133][biodb::testThat] biodb.TRACE[2024-06-22 16:05:54.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.161][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:54.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:54.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:54.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:54.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.200][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:05:54.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.208][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:54.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:05:54.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:05:54.212][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:54.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:05:54.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:05:54.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:05:54.220][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.221][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-06-22 16:05:54.222][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.222][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.229][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.229][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-06-22 16:05:54.230][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.231][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.237][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.238][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-06-22 16:05:54.239][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.240][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.245][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.246][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-06-22 16:05:54.246][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:05:54.247][biodb::testThat] biodb.INFO [2024-06-22 16:05:54.252][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-06-22 16:05:54.257][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2024-06-22 16:05:54.258][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2024-06-22 16:05:54.259][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-06-22 16:05:54.260][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.261][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.263][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.264][FUN] Functions in observer BiodbConfig: [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 [2024-06-22 16:05:54.272][biodb::testContext] biodb.INFO [2024-06-22 16:05:54.273][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-22 16:05:54.274][biodb::testContext] Test context - Example long tests biodb.INFO [2024-06-22 16:05:54.275][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-22 16:05:54.275][biodb::testContext] biodb.INFO [2024-06-22 16:05:54.277][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-06-22 16:05:54.279][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-06-22 16:05:54.282][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:05:54.283][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-06-22 16:05:54.284][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-06-22 16:05:54.285][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.288][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-06-22 16:05:54.289][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-06-22 16:05:54.289][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.292][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-06-22 16:05:54.293][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-06-22 16:05:54.294][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.296][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-06-22 16:05:54.297][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-06-22 16:05:54.298][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-06-22 16:05:54.299][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.301][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-06-22 16:05:54.302][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-06-22 16:05:54.303][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-06-22 16:05:54.304][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.306][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-06-22 16:05:54.307][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-06-22 16:05:54.308][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.311][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-06-22 16:05:54.312][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-06-22 16:05:54.313][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-06-22 16:05:54.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.316][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-06-22 16:05:54.317][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-06-22 16:05:54.318][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.320][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-06-22 16:05:54.321][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-06-22 16:05:54.322][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-06-22 16:05:54.323][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.325][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-06-22 16:05:54.326][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-06-22 16:05:54.327][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-06-22 16:05:54.328][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-06-22 16:05:54.329][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-06-22 16:05:54.330][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-06-22 16:05:54.331][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.333][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-06-22 16:05:54.334][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-06-22 16:05:54.335][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.337][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-06-22 16:05:54.338][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-06-22 16:05:54.339][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.342][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-06-22 16:05:54.343][self$set] Set key offline to FALSE. biodb.DEBUG[2024-06-22 16:05:54.343][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.346][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-06-22 16:05:54.347][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-06-22 16:05:54.348][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.350][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-06-22 16:05:54.351][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-06-22 16:05:54.352][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.354][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-06-22 16:05:54.355][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-06-22 16:05:54.359][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-06-22 16:05:54.360][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.363][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-06-22 16:05:54.364][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-06-22 16:05:54.365][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-06-22 16:05:54.365][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.368][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-06-22 16:05:54.370][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.371][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-06-22 16:05:54.371][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.372][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:54.373][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:54.375][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.376][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:54.377][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:05:54.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:54.379][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.380][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-06-22 16:05:54.380][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:54.385][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.386][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.387][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:05:54.387][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:05:54.387][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-22 16:05:54.387][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-22 16:05:54.387][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-22 16:05:54.388][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:54.389][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.391][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:54.392][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.392][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.393][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:54.394][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.395][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:54.396][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:54.397][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.397][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.399][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-06-22 16:05:54.400][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.401][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-06-22 16:05:54.402][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.403][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:54.404][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.405][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:54.406][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.406][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:54.407][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-22 16:05:54.408][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:54.409][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.410][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-06-22 16:05:54.411][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:54.412][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.413][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.414][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:05:54.414][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:05:54.414][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-22 16:05:54.414][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-22 16:05:54.414][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-22 16:05:54.415][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:54.416][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.416][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.417][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:54.418][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.419][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.420][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:54.421][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.422][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:54.422][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:54.423][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.424][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.425][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-06-22 16:05:54.427][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.428][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-06-22 16:05:54.429][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.430][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:54.431][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.432][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:54.433][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:54.434][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:05:54.435][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:54.436][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.437][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-06-22 16:05:54.438][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:54.439][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.440][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.441][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.442][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:54.443][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.444][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:54.445][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.447][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:54.448][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.449][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:54.449][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:54.450][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.451][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.452][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-06-22 16:05:54.454][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.455][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-06-22 16:05:54.456][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.457][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:54.458][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.458][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:05:54.459][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.460][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:54.461][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-22 16:05:54.462][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:54.463][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.464][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-06-22 16:05:54.465][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:54.466][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.467][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.468][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.468][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:05:54.469][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.471][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:54.472][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.473][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.474][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:54.474][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.475][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:54.476][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:54.477][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.478][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.479][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:05:54.480][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.482][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.486][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.490][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.494][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.498][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.502][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.506][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.518][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.522][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.526][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.530][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.534][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.538][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.542][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.546][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.550][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.554][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-06-22 16:05:54.556][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-06-22 16:05:54.557][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-06-22 16:05:54.558][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-06-22 16:05:54.560][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-06-22 16:05:54.561][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-06-22 16:05:54.562][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-06-22 16:05:54.564][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-06-22 16:05:54.565][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-06-22 16:05:54.566][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-06-22 16:05:54.568][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-06-22 16:05:54.569][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-06-22 16:05:54.570][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-06-22 16:05:54.572][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-06-22 16:05:54.573][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-06-22 16:05:54.574][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-06-22 16:05:54.576][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-06-22 16:05:54.577][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-06-22 16:05:54.578][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-06-22 16:05:54.580][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-06-22 16:05:54.581][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-06-22 16:05:54.583][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-06-22 16:05:54.584][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-06-22 16:05:54.585][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-06-22 16:05:54.586][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-06-22 16:05:54.588][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-06-22 16:05:54.589][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-06-22 16:05:54.590][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-06-22 16:05:54.592][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-06-22 16:05:54.593][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-06-22 16:05:54.594][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-06-22 16:05:54.595][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-06-22 16:05:54.597][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-06-22 16:05:54.598][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-06-22 16:05:54.599][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-06-22 16:05:54.600][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-06-22 16:05:54.602][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-06-22 16:05:54.603][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-06-22 16:05:54.604][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-06-22 16:05:54.605][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-06-22 16:05:54.607][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-06-22 16:05:54.608][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-06-22 16:05:54.609][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-06-22 16:05:54.610][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-06-22 16:05:54.612][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-06-22 16:05:54.613][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-06-22 16:05:54.614][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-06-22 16:05:54.615][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-06-22 16:05:54.617][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-06-22 16:05:54.618][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-06-22 16:05:54.619][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-06-22 16:05:54.620][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-06-22 16:05:54.622][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-06-22 16:05:54.623][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-06-22 16:05:54.624][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-06-22 16:05:54.625][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-06-22 16:05:54.627][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-06-22 16:05:54.628][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-06-22 16:05:54.633][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-06-22 16:05:54.635][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-06-22 16:05:54.636][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-06-22 16:05:54.637][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-06-22 16:05:54.638][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-06-22 16:05:54.640][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-06-22 16:05:54.641][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-06-22 16:05:54.642][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-06-22 16:05:54.643][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-06-22 16:05:54.645][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-06-22 16:05:54.646][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-06-22 16:05:54.647][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-06-22 16:05:54.648][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-06-22 16:05:54.650][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-06-22 16:05:54.651][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-06-22 16:05:54.652][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-06-22 16:05:54.653][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-06-22 16:05:54.655][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-06-22 16:05:54.656][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-06-22 16:05:54.657][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-06-22 16:05:54.658][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-06-22 16:05:54.660][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-06-22 16:05:54.661][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-06-22 16:05:54.662][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-06-22 16:05:54.663][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-06-22 16:05:54.665][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-06-22 16:05:54.666][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-06-22 16:05:54.667][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:05:54.668][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.670][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.671][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.677][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.683][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.688][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.694][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.700][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.706][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.711][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.717][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.723][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.728][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.734][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.740][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.745][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.751][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.761][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.766][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:05:54.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:05:54.773][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2024-06-22 16:05:54.774][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2024-06-22 16:05:54.776][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.777][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2024-06-22 16:05:54.778][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.779][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:05:54.779][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.780][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2024-06-22 16:05:54.781][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.782][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:05:54.783][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2024-06-22 16:05:54.784][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:05:54.785][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.786][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2024-06-22 16:05:54.787][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2024-06-22 16:05:54.788][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2024-06-22 16:05:54.789][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-06-22 16:05:54.790][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.790][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-06-22 16:05:54.791][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.793][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:05:54.794][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:05:54.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:05:54.796][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:05:54.796][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-06-22 16:05:54.796][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-06-22 16:05:54.796][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2024-06-22 16:05:54.796][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2024-06-22 16:05:54.797][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:05:54.798][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:05:54.799][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-06-22 16:05:54.800][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:05:54.801][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2024-06-22 16:05:54.804][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2024-06-22 16:05:54.805][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2024-06-22 16:05:54.806][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2024-06-22 16:05:54.807][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2024-06-22 16:05:54.808][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-06-22 16:05:54.809][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-06-22 16:05:54.811][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-06-22 16:05:54.812][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-06-22 16:05:54.813][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-06-22 16:05:54.814][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2024-06-22 16:05:54.815][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-06-22 16:05:54.816][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2024-06-22 16:05:54.817][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2024-06-22 16:05:54.817][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-06-22 16:05:54.818][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:05:54.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:05:54.820][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:05:54.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:05:54.821][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:05:54.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ] > > proc.time() user system elapsed 4.201 0.275 4.464
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘biodbNci/DESCRIPTION’ ... OK * this is package ‘biodbNci’ version ‘1.8.0’ * 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/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)