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 10/33 | Hostname | OS / Arch | CHECK | |||||||
Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | ERROR | ||||||||
To the developers/maintainers of the biodbLipidmaps 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: biodbLipidmaps |
Version: 1.10.0 |
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 biodbLipidmaps_1.10.0.tar.gz |
StartedAt: 2024-06-22 16:04:12 -0400 (Sat, 22 Jun 2024) |
EndedAt: 2024-06-22 16:04:58 -0400 (Sat, 22 Jun 2024) |
EllapsedTime: 45.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbLipidmaps.Rcheck |
Warnings: NA |
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
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(biodbLipidmaps) Warning message: In fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbLipidmaps") biodb.INFO [2024-06-22 16:04:50.161][biodb::testContext] biodb.INFO [2024-06-22 16:04:50.164][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-22 16:04:50.165][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-06-22 16:04:50.166][biodb::testContext] ******************************************************************************** biodb.INFO [2024-06-22 16:04:50.167][biodb::testContext] biodb.INFO [2024-06-22 16:04:50.174][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-06-22 16:04:50.176][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-06-22 16:04:50.184][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:04:50.185][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-06-22 16:04:50.186][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-06-22 16:04:50.187][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.190][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-06-22 16:04:50.210][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-06-22 16:04:50.211][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.213][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.214][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-06-22 16:04:50.215][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-06-22 16:04:50.216][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.218][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-06-22 16:04:50.219][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-06-22 16:04:50.221][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-06-22 16:04:50.221][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.224][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-06-22 16:04:50.225][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-06-22 16:04:50.226][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-06-22 16:04:50.227][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.230][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-06-22 16:04:50.231][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-06-22 16:04:50.232][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.234][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.235][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-06-22 16:04:50.236][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-06-22 16:04:50.237][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-06-22 16:04:50.238][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.241][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-06-22 16:04:50.242][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-06-22 16:04:50.243][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.246][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-06-22 16:04:50.247][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-06-22 16:04:50.248][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-06-22 16:04:50.249][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.251][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-06-22 16:04:50.252][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-06-22 16:04:50.253][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-06-22 16:04:50.254][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-06-22 16:04:50.255][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-06-22 16:04:50.257][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-06-22 16:04:50.257][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.259][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.260][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-06-22 16:04:50.261][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-06-22 16:04:50.262][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.265][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-06-22 16:04:50.266][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-06-22 16:04:50.267][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.269][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.270][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-06-22 16:04:50.271][self$set] Set key offline to FALSE. biodb.DEBUG[2024-06-22 16:04:50.272][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.275][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-06-22 16:04:50.276][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-06-22 16:04:50.277][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.279][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.280][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-06-22 16:04:50.281][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-06-22 16:04:50.282][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.284][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-06-22 16:04:50.285][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-06-22 16:04:50.289][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-06-22 16:04:50.290][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.292][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.293][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-06-22 16:04:50.294][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-06-22 16:04:50.295][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-06-22 16:04:50.296][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.302][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-06-22 16:04:50.338][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.361][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-06-22 16:04:50.362][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.363][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:04:50.364][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.365][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:04:50.366][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.366][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:04:50.367][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:04:50.368][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:04:50.369][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.370][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-06-22 16:04:50.371][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:04:50.372][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.373][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.374][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:04:50.374][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:04:50.374][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-22 16:04:50.374][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-22 16:04:50.374][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-22 16:04:50.375][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:04:50.375][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.377][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:04:50.378][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.380][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:04:50.381][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.381][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:04:50.382][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:04:50.383][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.384][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.385][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-06-22 16:04:50.387][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.388][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-06-22 16:04:50.389][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.389][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:04:50.390][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.391][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:04:50.392][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.393][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:04:50.394][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-22 16:04:50.395][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:04:50.396][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.397][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-06-22 16:04:50.398][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:04:50.399][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.399][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.400][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:04:50.400][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:04:50.400][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-06-22 16:04:50.400][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-06-22 16:04:50.400][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-06-22 16:04:50.401][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:04:50.402][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.404][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:04:50.405][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.406][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:04:50.407][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.408][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:04:50.409][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:04:50.410][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.411][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.412][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-06-22 16:04:50.413][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.414][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-06-22 16:04:50.415][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.416][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:04:50.417][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.418][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:04:50.419][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:04:50.421][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:04:50.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:04:50.423][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.423][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-06-22 16:04:50.424][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:04:50.425][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.426][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.427][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.428][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:04:50.429][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.431][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:04:50.431][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.433][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:04:50.434][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.435][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:04:50.436][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:04:50.436][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.437][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.438][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-06-22 16:04:50.440][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.441][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-06-22 16:04:50.442][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.443][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:04:50.444][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:04:50.446][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:04:50.447][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-06-22 16:04:50.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:04:50.449][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.450][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-06-22 16:04:50.451][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:04:50.452][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.453][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.454][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.455][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:04:50.455][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.457][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:04:50.458][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.460][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:04:50.461][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.462][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:04:50.462][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:04:50.463][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.464][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.468][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:04:50.469][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.470][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.474][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.477][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 16:04:50.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.479][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.479][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.481][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 16:04:50.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.483][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.484][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.486][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 16:04:50.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.488][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.489][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.495][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 16:04:50.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.497][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 16:04:50.497][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.499][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 16:04:50.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.501][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 16:04:50.502][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.504][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 16:04:50.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.506][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.506][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.508][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 16:04:50.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.510][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.511][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.515][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.517][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 16:04:50.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.519][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.520][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.521][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 16:04:50.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.523][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.524][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.526][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 16:04:50.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.528][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.529][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.530][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 16:04:50.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.532][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.533][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.535][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 16:04:50.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.536][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.537][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.539][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 16:04:50.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.541][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 16:04:50.542][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.544][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 16:04:50.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.545][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 16:04:50.546][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.548][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 16:04:50.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.550][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.551][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-06-22 16:04:50.557][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-06-22 16:04:50.558][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-06-22 16:04:50.559][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-06-22 16:04:50.561][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-06-22 16:04:50.562][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-06-22 16:04:50.564][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-06-22 16:04:50.565][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-06-22 16:04:50.566][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-06-22 16:04:50.568][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-06-22 16:04:50.569][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-06-22 16:04:50.571][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-06-22 16:04:50.572][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-06-22 16:04:50.573][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-06-22 16:04:50.575][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-06-22 16:04:50.576][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-06-22 16:04:50.577][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-06-22 16:04:50.579][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-06-22 16:04:50.580][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-06-22 16:04:50.581][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-06-22 16:04:50.583][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-06-22 16:04:50.584][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-06-22 16:04:50.586][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-06-22 16:04:50.587][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-06-22 16:04:50.588][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-06-22 16:04:50.590][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-06-22 16:04:50.591][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-06-22 16:04:50.592][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-06-22 16:04:50.594][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-06-22 16:04:50.595][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-06-22 16:04:50.597][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-06-22 16:04:50.598][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-06-22 16:04:50.599][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-06-22 16:04:50.601][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-06-22 16:04:50.602][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-06-22 16:04:50.603][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-06-22 16:04:50.605][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-06-22 16:04:50.606][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-06-22 16:04:50.620][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-06-22 16:04:50.621][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-06-22 16:04:50.623][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-06-22 16:04:50.624][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-06-22 16:04:50.625][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-06-22 16:04:50.627][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-06-22 16:04:50.628][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-06-22 16:04:50.630][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-06-22 16:04:50.631][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-06-22 16:04:50.632][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-06-22 16:04:50.634][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-06-22 16:04:50.635][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-06-22 16:04:50.637][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-06-22 16:04:50.638][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-06-22 16:04:50.639][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-06-22 16:04:50.641][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-06-22 16:04:50.642][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-06-22 16:04:50.644][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-06-22 16:04:50.645][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-06-22 16:04:50.646][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-06-22 16:04:50.648][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-06-22 16:04:50.649][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-06-22 16:04:50.651][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-06-22 16:04:50.652][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-06-22 16:04:50.653][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-06-22 16:04:50.655][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-06-22 16:04:50.656][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-06-22 16:04:50.657][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-06-22 16:04:50.659][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-06-22 16:04:50.660][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-06-22 16:04:50.662][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-06-22 16:04:50.663][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-06-22 16:04:50.664][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-06-22 16:04:50.666][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-06-22 16:04:50.667][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-06-22 16:04:50.668][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-06-22 16:04:50.670][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-06-22 16:04:50.671][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-06-22 16:04:50.672][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-06-22 16:04:50.674][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-06-22 16:04:50.675][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-06-22 16:04:50.677][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-06-22 16:04:50.678][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-06-22 16:04:50.679][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-06-22 16:04:50.681][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-06-22 16:04:50.687][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-06-22 16:04:50.688][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-06-22 16:04:50.692][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-06-22 16:04:50.692][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.693][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 16:04:50.694][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.695][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.700][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.703][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 16:04:50.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.705][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 16:04:50.706][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.709][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 16:04:50.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.711][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.712][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.715][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 16:04:50.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.717][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.718][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.721][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 16:04:50.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.723][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.724][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.727][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 16:04:50.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.729][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.730][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.733][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 16:04:50.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.736][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.741][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.742][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.748][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.753][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.756][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 16:04:50.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.758][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.759][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.762][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 16:04:50.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.764][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.768][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 16:04:50.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.769][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.770][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.773][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 16:04:50.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.775][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.776][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.779][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 16:04:50.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.781][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:50.781][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.785][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 16:04:50.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.787][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.793][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-06-22 16:04:50.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.796][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 16:04:50.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-06-22 16:04:50.799][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/definitions.yml". biodb.DEBUG[2024-06-22 16:04:50.808][self$getDbsInfo()$define] Define connector lipidmaps.structure. biodb.DEBUG[2024-06-22 16:04:50.810][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.810][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-06-22 16:04:50.811][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.812][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-06-22 16:04:50.813][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-06-22 16:04:50.815][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.816][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-06-22 16:04:50.817][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-06-22 16:04:50.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-06-22 16:04:50.819][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.820][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure". biodb.DEBUG[2024-06-22 16:04:50.820][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "MASS". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA". biodb.DEBUG[2024-06-22 16:04:50.821][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME". biodb.DEBUG[2024-06-22 16:04:50.822][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-06-22 16:04:50.823][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-06-22 16:04:50.823][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-06-22 16:04:50.824][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-06-22 16:04:50.825][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.827][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-06-22 16:04:50.828][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-06-22 16:04:50.829][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-06-22 16:04:50.829][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-06-22 16:04:50.830][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/". biodb.DEBUG[2024-06-22 16:04:50.830][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/". biodb.DEBUG[2024-06-22 16:04:50.831][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-06-22 16:04:50.832][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-06-22 16:04:50.833][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-06-22 16:04:50.834][self$setPropertyValue] biodb.DEBUG[2024-06-22 16:04:50.839][self$getEntryFields()$define] Define field lipidmaps.structure.id. biodb.DEBUG[2024-06-22 16:04:50.841][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-06-22 16:04:50.868][initialize] Initialize connector lipidmaps.structure. biodb.DEBUG[2024-06-22 16:04:50.869][initialize] Register connector lipidmaps.structure with the request scheduler biodb.DEBUG[2024-06-22 16:04:50.873][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure. biodb.DEBUG[2024-06-22 16:04:50.877][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure". biodb.DEBUG[2024-06-22 16:04:50.882][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-06-22 16:04:50.882][self$setFrequency] t=1.000000, n=1.000000 biodb.DEBUG[2024-06-22 16:04:50.884][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org". biodb.DEBUG[2024-06-22 16:04:50.885][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure . biodb.INFO [2024-06-22 16:04:50.894][biodb::testThat] biodb.INFO [2024-06-22 16:04:50.895][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-06-22 16:04:50.895][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:50.896][biodb::testThat] biodb.TRACE[2024-06-22 16:04:50.900][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv". biodb.DEBUG[2024-06-22 16:04:50.901][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-06-22 16:04:50.905][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-06-22 16:04:50.913][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:04:50.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:50.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:50.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:50.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:50.928][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:50.929][FUN] Functions in observer BiodbConfig: [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 16:04:50.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:50.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:50.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:50.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:50.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:50.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:50.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.962][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:50.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:50.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.966][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:50.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.969][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:50.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:50.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.995][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:50.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:50.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:50.999][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.003][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.007][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:51.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.011][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.014][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.029][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:51.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.033][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-06-22 16:04:51.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.044][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:51.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.110][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.114][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.118][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.129][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:51.154][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001. biodb.TRACE[2024-06-22 16:04:51.157][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.160][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.164][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:51.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:51.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:51.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:51.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.199][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.233][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.237][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.257][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.258][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.259][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.260][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.279][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.283][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.284][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.284][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.285][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.296][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.323][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.327][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.331][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.332][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.333][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.333][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.337][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.345][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.348][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.352][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.355][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.356][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.357][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.358][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.380][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.381][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.382][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.383][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.394][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.397][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.401][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.405][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.406][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.407][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.408][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.418][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.419][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.420][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.421][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.425][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.426][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.427][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.428][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.431][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.432][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.433][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.434][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.438][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.439][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.440][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.440][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.444][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.445][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.446][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.447][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.450][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.451][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.452][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.453][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.468][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000002-content.tsv". biodb.DEBUG[2024-06-22 16:04:51.500][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-06-22 16:04:51.501][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-06-22 16:04:51.503][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:04:51.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:51.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:51.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:51.509][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 16:04:51.510][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:51.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:04:51.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:51.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:51.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:51.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:51.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.541][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.549][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.553][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.556][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:51.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.560][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:51.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.571][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.575][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.579][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:51.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.582][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-06-22 16:04:51.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.593][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:51.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.597][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.600][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.608][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:51.633][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000002. biodb.TRACE[2024-06-22 16:04:51.651][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.655][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:51.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.659][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:51.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:51.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:51.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:51.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.673][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.703][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.706][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.710][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:51.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.742][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.743][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.744][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.745][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.759][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.766][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.767][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.768][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.769][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.780][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.783][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.787][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.791][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.792][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.792][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.793][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.794][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.808][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.815][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.816][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.817][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.817][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.818][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.839][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.840][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.841][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.842][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.863][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.864][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.865][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.866][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.877][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.880][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.884][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.888][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.888][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.889][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.890][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.901][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.902][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.903][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.904][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.907][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.908][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.913][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.914][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.918][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.919][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:51.919][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.920][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.924][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:51.925][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:51.926][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.927][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.930][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.931][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:51.932][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.933][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.936][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:51.937][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:51.938][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.939][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.943][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.944][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:51.945][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.945][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.949][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA08040013-content.tsv". biodb.DEBUG[2024-06-22 16:04:51.950][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s). biodb.DEBUG[2024-06-22 16:04:51.952][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries. biodb.DEBUG[2024-06-22 16:04:51.953][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:04:51.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:51.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:51.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:51.959][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 16:04:51.960][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:51.961][FUN] Functions in observer BiodbConfig: [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 16:04:51.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:51.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:51.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:51.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:51.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.001][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.005][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.009][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.012][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.016][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.020][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.027][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.031][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:52.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.035][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:52.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.053][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:52.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.057][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-06-22 16:04:52.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.067][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.071][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.079][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.082][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.093][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.100][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:52.130][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA08040013. biodb.TRACE[2024-06-22 16:04:52.132][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:52.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:52.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.135][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:52.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:52.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.139][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:52.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:52.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.142][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:52.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:52.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.183][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.190][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.210][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.211][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.212][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.212][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.234][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.235][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.236][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.237][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.252][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.259][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.260][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.261][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.262][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.263][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.273][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.280][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.284][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.285][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.286][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.286][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.298][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.301][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.305][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.309][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.313][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.315][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.315][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.316][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.337][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.338][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.339][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.340][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.350][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.354][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.361][ef$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.362][ef$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.363][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.364][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.365][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.374][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.382][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.385][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.386][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.387][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.388][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.389][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.411][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.412][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.423][ef$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.424][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.424][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.425][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.429][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.430][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.431][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.432][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.435][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.436][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.437][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.438][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.441][ef$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.442][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.443][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.444][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.448][ef$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.449][ef$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.449][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.450][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.454][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.455][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.456][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.457][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.460][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.461][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.462][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.463][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.466][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.467][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.468][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.469][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.473][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.474][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.474][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.475][ef$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:52.481][biodb::testThat] biodb.INFO [2024-06-22 16:04:52.482][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-06-22 16:04:52.483][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:52.484][biodb::testThat] biodb.DEBUG[2024-06-22 16:04:52.486][private$loadEntries] Creating entries from ids [3]: "LMFA00000001, LMFA00000002, LMFA08040013". biodb.DEBUG[2024-06-22 16:04:52.493][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 3 id(s)... biodb.TRACE[2024-06-22 16:04:52.497][cch$loadFileContent] Trying to load 3 files from cache: [3]: "LMFA00000001, LMFA00000002, LMFA08040013". biodb.TRACE[2024-06-22 16:04:52.498][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE". biodb.TRACE[2024-06-22 16:04:52.500][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv". biodb.DEBUG[2024-06-22 16:04:52.501][conn$getEntryContent] 3 LIPID MAPS Structure entry content(s) loaded from cache. biodb.DEBUG[2024-06-22 16:04:52.502][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 3 content(s). biodb.DEBUG[2024-06-22 16:04:52.503][self$createEntryFromContent] Parsing 3 LIPID MAPS Structure entries. biodb.DEBUG[2024-06-22 16:04:52.505][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:04:52.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:52.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:52.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:52.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:52.512][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:52.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:04:52.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.536][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.539][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.551][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.558][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:52.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.562][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:52.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.580][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:52.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.584][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-06-22 16:04:52.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.595][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:52.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.599][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.617][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.620][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.628][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:52.642][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:04:52.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:52.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:52.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:52.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:52.650][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:52.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:04:52.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-06-22 16:04:52.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.669][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-06-22 16:04:52.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.672][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-06-22 16:04:52.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.680][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-06-22 16:04:52.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.683][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.687][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-06-22 16:04:52.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.691][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:52.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.695][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass. biodb.TRACE[2024-06-22 16:04:52.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.698][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-06-22 16:04:52.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-06-22 16:04:52.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.713][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:52.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.720][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms. biodb.TRACE[2024-06-22 16:04:52.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.731][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS. biodb.TRACE[2024-06-22 16:04:52.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.735][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:52.761][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-06-22 16:04:52.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:52.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:52.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:52.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:52.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:52.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-06-22 16:04:52.771][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.775][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id. biodb.TRACE[2024-06-22 16:04:52.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-06-22 16:04:52.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-06-22 16:04:52.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:52.822][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002, NA. biodb.DEBUG[2024-06-22 16:04:52.823][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL. biodb.TRACE[2024-06-22 16:04:52.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-22 16:04:52.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-22 16:04:52.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-22 16:04:52.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-22 16:04:52.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-22 16:04:52.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-22 16:04:52.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-06-22 16:04:52.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-06-22 16:04:52.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-06-22 16:04:52.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-06-22 16:04:52.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-06-22 16:04:52.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-06-22 16:04:52.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:52.869][biodb::testThat] biodb.INFO [2024-06-22 16:04:52.870][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-06-22 16:04:52.871][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:52.872][biodb::testThat] biodb.TRACE[2024-06-22 16:04:52.875][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.876][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.877][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.877][ef$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:52.879][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name". biodb.TRACE[2024-06-22 16:04:52.900][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.904][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:52.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:52.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:52.913][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-06-22 16:04:52.923][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-06-22 16:04:52.942][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:52.956][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-06-22 16:04:52.957][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:52.958][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.DEBUG[2024-06-22 16:04:52.960][function(conn, opt)] With found IDs [1]: "LMFA00000001". biodb.TRACE[2024-06-22 16:04:52.969][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.970][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:52.971][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:52.972][ef$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:52.975][biodb::testThat] biodb.INFO [2024-06-22 16:04:52.976][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-06-22 16:04:52.977][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:52.978][biodb::testThat] biodb.TRACE[2024-06-22 16:04:52.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:52.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:53.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:53.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:53.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:53.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:53.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:53.104][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-06-22 16:04:53.107][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:53.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-06-22 16:04:53.109][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:53.110][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.INFO [2024-06-22 16:04:53.123][biodb::testThat] biodb.INFO [2024-06-22 16:04:53.125][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-06-22 16:04:53.126][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:53.126][biodb::testThat] biodb.TRACE[2024-06-22 16:04:53.136][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.144][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:53.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:53.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.148][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:53.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:53.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.187][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-06-22 16:04:53.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:53.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-06-22 16:04:53.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:53.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:53.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-06-22 16:04:53.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:53.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:53.203][biodb::testThat] biodb.INFO [2024-06-22 16:04:53.204][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-06-22 16:04:53.205][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:53.205][biodb::testThat] biodb.INFO [2024-06-22 16:04:53.213][biodb::testThat] biodb.INFO [2024-06-22 16:04:53.214][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-06-22 16:04:53.215][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:53.216][biodb::testThat] biodb.INFO [2024-06-22 16:04:53.222][biodb::testThat] biodb.INFO [2024-06-22 16:04:53.223][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-06-22 16:04:53.224][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:53.225][biodb::testThat] biodb.DEBUG[2024-06-22 16:04:53.228][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001". biodb.DEBUG[2024-06-22 16:04:54.907][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001. biodb.INFO [2024-06-22 16:04:55.336][biodb::testThat] biodb.INFO [2024-06-22 16:04:55.337][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-06-22 16:04:55.338][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:55.339][biodb::testThat] biodb.TRACE[2024-06-22 16:04:55.346][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:55.347][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:55.348][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.349][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.350][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.351][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.352][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.353][ef$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:55.355][biodb::testThat] biodb.INFO [2024-06-22 16:04:55.357][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-06-22 16:04:55.358][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:55.359][biodb::testThat] biodb.TRACE[2024-06-22 16:04:55.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:55.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:55.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:55.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:55.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:55.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:55.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:55.479][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-06-22 16:04:55.483][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:55.484][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-06-22 16:04:55.485][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:55.487][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.DEBUG[2024-06-22 16:04:55.545][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride". biodb.DEBUG[2024-06-22 16:04:55.548][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:55.550][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a". biodb.TRACE[2024-06-22 16:04:55.551][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:55.552][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content". biodb.TRACE[2024-06-22 16:04:55.563][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:55.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:55.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-06-22 16:04:55.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-06-22 16:04:55.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.589][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:55.593][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:55.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:55.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-06-22 16:04:55.603][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06". biodb.DEBUG[2024-06-22 16:04:55.606][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:55.607][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359". biodb.TRACE[2024-06-22 16:04:55.608][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:55.662][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content". biodb.DEBUG[2024-06-22 16:04:56.749][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06". biodb.DEBUG[2024-06-22 16:04:56.753][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:56.754][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3". biodb.TRACE[2024-06-22 16:04:56.756][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:56.757][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content". biodb.DEBUG[2024-06-22 16:04:56.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06". biodb.DEBUG[2024-06-22 16:04:56.778][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-06-22 16:04:56.779][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54". biodb.TRACE[2024-06-22 16:04:56.781][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-06-22 16:04:56.782][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content". biodb.TRACE[2024-06-22 16:04:56.795][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-06-22 16:04:56.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-06-22 16:04:56.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:56.805][biodb::testThat] biodb.INFO [2024-06-22 16:04:56.806][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-06-22 16:04:56.807][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:56.808][biodb::testThat] biodb.TRACE[2024-06-22 16:04:56.811][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.815][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:56.843][biodb::testThat] biodb.INFO [2024-06-22 16:04:56.844][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-06-22 16:04:56.845][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:56.846][biodb::testThat] biodb.TRACE[2024-06-22 16:04:56.849][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.853][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:56.871][biodb::testThat] biodb.INFO [2024-06-22 16:04:56.872][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-06-22 16:04:56.873][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:56.874][biodb::testThat] biodb.TRACE[2024-06-22 16:04:56.887][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.891][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.907][ef$get] Asked field names are: name. biodb.TRACE[2024-06-22 16:04:56.908][ef$get] Realnames of fields are: name. biodb.TRACE[2024-06-22 16:04:56.909][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.910][ef$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.911][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:56.912][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-06-22 16:04:56.913][ef$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.913][ef$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:56.915][biodb::testThat] biodb.INFO [2024-06-22 16:04:56.916][biodb::testThat] Running test function test.annotateMzValues_real_values (" annotateMzValues() works correctly with real values. "). biodb.INFO [2024-06-22 16:04:56.917][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:56.918][biodb::testThat] biodb.TRACE[2024-06-22 16:04:56.920][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.924][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:56.940][biodb::testThat] biodb.INFO [2024-06-22 16:04:56.941][biodb::testThat] Running test function test_annotateMzValues_additional_fields (" Additional fields are accepted in annotateMzValues() "). biodb.INFO [2024-06-22 16:04:56.942][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-06-22 16:04:56.943][biodb::testThat] biodb.TRACE[2024-06-22 16:04:56.945][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-06-22 16:04:56.949][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-06-22 16:04:56.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-06-22 16:04:56.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-06-22 16:04:56.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-06-22 16:04:56.964][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-06-22 16:04:56.965][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler biodb.INFO [2024-06-22 16:04:56.966][self$deleteConn] Connector "lipidmaps.structure" deleted. biodb.DEBUG[2024-06-22 16:04:56.967][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-06-22 16:04:56.968][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-06-22 16:04:56.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-06-22 16:04:56.970][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-06-22 16:04:56.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-06-22 16:04:56.971][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-06-22 16:04:56.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 6 | WARN 0 | SKIP 0 | PASS 190 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ── Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─testthat::expect_true(...) 4. └─testthat::quasi_label(enquo(object), label, arg = "object") 5. └─rlang::eval_bare(expr, quo_get_env(quo)) ── Error ('test_long_100_generic.R:37:1'): annotateMzValues() accepts a single vector. ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): ppm tolerance works in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): Input data frame is not modified by annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): annotateMzValues() works correctly with real values. ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): Additional fields are accepted in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) [ FAIL 6 | WARN 0 | SKIP 0 | PASS 190 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### 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 biodbLipidmaps_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.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 ‘biodbLipidmaps/DESCRIPTION’ ... OK * this is package ‘biodbLipidmaps’ version ‘1.10.0’ * 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 ‘biodbLipidmaps’ can be installed ... OK * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... 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 files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ ERROR Running the tests in ‘longtests/testthat.R’ failed. Last 13 lines of output: 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) ── Error ('test_long_100_generic.R:37:1'): Additional fields are accepted in annotateMzValues() ── Error in `e$hasField(mf)`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`) 3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE) 4. └─biodb (local) FUN(X[[i]], ...) [ FAIL 6 | WARN 0 | SKIP 0 | PASS 190 ] Error: Test failures Execution halted * DONE Status: 1 ERROR See ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbLipidmaps.Rcheck/00check.log’ for details.
biodbLipidmaps.Rcheck/00install.out
* installing *source* package ‘biodbLipidmaps’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)