Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 8/33 | Hostname | OS / Arch | CHECK | |||||||
biodbHmdb 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | ERROR | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | WARNINGS | ||||||||
To the developers/maintainers of the biodbHmdb 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: biodbHmdb |
Version: 1.10.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz |
StartedAt: 2024-05-04 16:04:49 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:08:00 -0400 (Sat, 04 May 2024) |
EllapsedTime: 191.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbHmdb.Rcheck |
Warnings: NA |
biodbHmdb.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbHmdb) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbHmdb") biodb.INFO [2024-05-04 16:06:32.718][biodb::testContext] biodb.INFO [2024-05-04 16:06:32.721][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:06:32.722][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-05-04 16:06:32.723][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:06:32.725][biodb::testContext] biodb.INFO [2024-05-04 16:06:32.731][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:06:32.733][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:06:32.741][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:06:32.742][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:06:32.744][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:06:32.745][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.748][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:06:32.764][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:06:32.765][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.769][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:06:32.770][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:06:32.771][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.775][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:06:32.776][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:06:32.777][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:06:32.778][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.781][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:06:32.783][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:06:32.784][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:06:32.785][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.788][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:06:32.790][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:06:32.791][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.794][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:06:32.795][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:06:32.796][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:06:32.797][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.801][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:06:32.802][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:06:32.803][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.806][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:06:32.807][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:06:32.809][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:06:32.810][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.813][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:06:32.814][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:06:32.815][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:06:32.817][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:06:32.818][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:06:32.819][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:06:32.820][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.823][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:06:32.825][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:06:32.826][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.829][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:06:32.830][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:06:32.831][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.835][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:06:32.836][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:06:32.838][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.841][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:06:32.842][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:06:32.843][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.847][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:06:32.848][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:06:32.849][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.852][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:06:32.854][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:06:32.857][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:06:32.859][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.862][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:06:32.863][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:06:32.864][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:06:32.865][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:32.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:32.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:32.871][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:06:32.906][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.920][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:06:32.921][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.923][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:32.924][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.925][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:32.926][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.927][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:32.929][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:06:32.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:32.931][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.932][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:06:32.933][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:32.935][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:32.936][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.939][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:06:32.939][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:06:32.939][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:06:32.939][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:06:32.939][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:06:32.940][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:32.941][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:32.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:32.943][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:32.944][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:32.946][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:32.947][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:32.948][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:32.949][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:32.950][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:32.951][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.952][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:32.954][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:06:32.956][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.957][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:06:32.958][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.959][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:32.961][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:32.963][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:32.965][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:06:32.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:32.968][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.969][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:06:32.970][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:32.971][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:32.972][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.974][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:06:32.974][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:06:32.974][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:06:32.974][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:06:32.974][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:06:32.975][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:32.976][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:32.977][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:32.978][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:32.979][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:32.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:32.982][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:32.983][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:32.984][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:32.985][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:32.986][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.987][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:32.989][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:06:32.991][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.992][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:06:32.993][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.994][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:32.996][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:32.997][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:32.998][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:32.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:33.000][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:06:33.002][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:33.003][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.004][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:06:33.005][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:33.006][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.008][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.009][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.010][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:33.011][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:33.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:33.013][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:33.014][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:33.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:33.017][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:33.018][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.019][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:33.020][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:33.021][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.022][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.024][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:06:33.026][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.027][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:06:33.028][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.029][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:33.031][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:06:33.033][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:33.035][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:06:33.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:33.040][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.041][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:06:33.042][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:33.043][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.044][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.045][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.047][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:06:33.048][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:33.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:33.050][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:33.051][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:33.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:33.054][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:33.055][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.056][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:33.057][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:33.058][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.060][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.063][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:06:33.064][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.066][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.072][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.078][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.083][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.089][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.095][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.105][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.116][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.121][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.127][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.132][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.138][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.143][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.148][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.155][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.162][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.168][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:06:33.172][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:06:33.173][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:06:33.175][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:06:33.176][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:06:33.178][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:06:33.179][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:06:33.181][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:06:33.183][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:06:33.185][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:06:33.187][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:06:33.189][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:06:33.190][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:06:33.192][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:06:33.194][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:06:33.195][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:06:33.197][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:06:33.198][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:06:33.200][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:06:33.201][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:06:33.203][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:06:33.204][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:06:33.206][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:06:33.207][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:06:33.209][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:06:33.211][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:06:33.212][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:06:33.214][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:06:33.215][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:06:33.217][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:06:33.218][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:06:33.220][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:06:33.221][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:06:33.223][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:06:33.225][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:06:33.226][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:06:33.228][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:06:33.229][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:06:33.231][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:06:33.232][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:06:33.234][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:06:33.235][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:06:33.237][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:06:33.238][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:06:33.240][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:06:33.242][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:06:33.243][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:06:33.245][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:06:33.246][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:06:33.248][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:06:33.249][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:06:33.251][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:06:33.253][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:06:33.254][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:06:33.256][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:06:33.257][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:06:33.259][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:06:33.260][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:06:33.262][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:06:33.264][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:06:33.265][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:06:33.267][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:06:33.268][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:06:33.270][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:06:33.271][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:06:33.273][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:06:33.274][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:06:33.276][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:06:33.278][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:06:33.279][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:06:33.281][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:06:33.282][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:06:33.284][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:06:33.285][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:06:33.287][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:06:33.288][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:06:33.290][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:06:33.292][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:06:33.293][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:06:33.295][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:06:33.296][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:06:33.298][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:06:33.299][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:06:33.347][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:06:33.350][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:06:33.353][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:06:33.354][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.356][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.361][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.369][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.377][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.384][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.392][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.399][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.407][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.414][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.422][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.429][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.437][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.444][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.452][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.460][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.467][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.475][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.482][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.488][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[2024-05-04 16:06:33.490][biodb$getConfig()$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:06:33.491][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:06:33.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:06:33.500][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml". biodb.DEBUG[2024-05-04 16:06:33.509][self$getDbsInfo()$define] Define connector hmdb.metabolites. biodb.DEBUG[2024-05-04 16:06:33.512][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.513][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-05-04 16:06:33.514][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.515][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:06:33.516][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.518][self$setPropertyValue] Setting property "dwnld.ext" to "zip". biodb.DEBUG[2024-05-04 16:06:33.519][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.520][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:06:33.521][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-05-04 16:06:33.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:06:33.524][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.525][self$setPropertyValue] Setting property "name" to "HMDB Metabolites". biodb.DEBUG[2024-05-04 16:06:33.526][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//inchi". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//smiles". biodb.DEBUG[2024-05-04 16:06:33.527][self$setPropertyValue] Setting property "parsing.expr" to "//super_class". biodb.DEBUG[2024-05-04 16:06:33.529][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:06:33.530][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:06:33.530][self$setPropertyValue] Setting property "searchable.fields" to "description". biodb.DEBUG[2024-05-04 16:06:33.530][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions". biodb.DEBUG[2024-05-04 16:06:33.531][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:06:33.532][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:33.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:33.534][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:06:33.536][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:06:33.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:06:33.538][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:06:33.539][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/". biodb.DEBUG[2024-05-04 16:06:33.539][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". biodb.DEBUG[2024-05-04 16:06:33.540][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:06:33.541][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:06:33.542][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:06:33.544][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:06:33.577][self$getEntryFields()$define] Define field secondary_accessions. biodb.DEBUG[2024-05-04 16:06:33.579][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:06:33.580][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:06:33.582][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:06:33.584][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:06:33.606][initialize] Initialize connector hmdb.metabolites. biodb.DEBUG[2024-05-04 16:06:33.607][initialize] Register connector hmdb.metabolites with the request scheduler biodb.DEBUG[2024-05-04 16:06:33.611][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites. biodb.DEBUG[2024-05-04 16:06:33.615][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites". biodb.DEBUG[2024-05-04 16:06:33.618][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:06:33.619][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:06:33.621][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca". biodb.DEBUG[2024-05-04 16:06:33.622][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites . biodb.INFO [2024-05-04 16:06:33.632][biodb::testThat] biodb.INFO [2024-05-04 16:06:33.633][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 16:06:33.634][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:33.635][biodb::testThat] biodb.TRACE[2024-05-04 16:06:33.641][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml". biodb.DEBUG[2024-05-04 16:06:33.643][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s). biodb.DEBUG[2024-05-04 16:06:33.646][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries. biodb.DEBUG[2024-05-04 16:06:33.653][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:06:33.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:06:33.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:06:33.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:06:33.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:06:33.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:06:33.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:06:33.685][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.687][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.688][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.689][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.706][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:33.707][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:33.708][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.710][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.732][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:33.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:33.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.737][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:33.739][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:33.740][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.741][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.743][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:33.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:33.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.748][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:33.749][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:33.750][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.751][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.753][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:33.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:33.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.758][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.759][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.760][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.761][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.768][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:33.769][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:33.770][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.771][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:33.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:33.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.788][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.789][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.790][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.792][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.793][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:33.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.798][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.800][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.801][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.802][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.803][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:33.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.808][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.810][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.811][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.812][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.814][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:33.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.819][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:33.820][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:33.821][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.822][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.824][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:33.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:33.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.829][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.830][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.831][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.832][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.834][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:33.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:33.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.841][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:33.842][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:33.843][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.844][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:33.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:33.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.851][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:33.852][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:33.853][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.854][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:33.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:33.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.861][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.862][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.863][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.864][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:33.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.871][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.872][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.873][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.875][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:33.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:33.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.881][ef$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:33.882][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:33.883][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.884][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.886][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:33.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:33.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.891][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:33.892][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:33.893][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.894][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.896][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:33.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:33.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.901][ef$get] Asked field names are: super.class. biodb.TRACE[2024-05-04 16:06:33.902][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:33.903][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.904][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.906][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class. biodb.TRACE[2024-05-04 16:06:33.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:33.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:33.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:33.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.957][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:33.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:33.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.963][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:33.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:33.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.968][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:33.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:33.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.972][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:33.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:33.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.978][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:33.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:33.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.982][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:33.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:33.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:33.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:33.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:33.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.026][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.030][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.035][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.040][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.045][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.049][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.054][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.059][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.064][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.069][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.073][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:34.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:34.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:34.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:34.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:34.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:34.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:34.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:34.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:34.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.117][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.122][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.131][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.160][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.165][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.170][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.175][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.179][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.184][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.208][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-04 16:06:34.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:34.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:34.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:34.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.227][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY. biodb.TRACE[2024-05-04 16:06:34.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:34.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.252][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.262][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.271][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.276][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.286][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:06:34.325][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001. biodb.TRACE[2024-05-04 16:06:34.328][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:34.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:34.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.333][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:06:34.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:06:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:34.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:06:34.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.342][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:34.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:06:34.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.387][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.429][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.434][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.439][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id. biodb.TRACE[2024-05-04 16:06:34.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.470][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.471][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.473][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.474][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:34.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:34.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.495][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.500][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.505][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.510][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.511][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.513][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.514][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.515][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:34.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.544][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.546][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.547][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.548][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:34.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.564][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.569][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.574][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.579][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.580][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.581][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.582][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:34.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.613][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.615][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.616][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.617][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:34.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.633][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.638][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.643][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.648][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.649][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.650][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.651][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.653][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:34.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.682][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.687][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.688][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.690][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.691][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:34.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:34.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.707][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.712][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.717][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.722][ef$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.723][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.724][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.725][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.727][self$getBiodb()$getEntryFields()$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:34.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:34.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.757][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.758][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.759][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.760][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:34.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:34.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.779][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:34.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:34.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.784][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:34.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:34.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.789][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:34.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:34.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.794][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:34.795][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:34.796][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.797][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.798][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.829][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.830][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.831][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.832][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:34.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.848][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.867][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.872][ef$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.873][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.874][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.875][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.877][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:34.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.898][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.903][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.908][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.909][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.910][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.911][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.914][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:34.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.939][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.943][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.948][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.950][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.951][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.952][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.953][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:34.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.973][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.978][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.983][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.984][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.985][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.986][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:34.987][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:34.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:34.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:34.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:35.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:35.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:35.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:35.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:35.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:35.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.017][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:35.018][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:35.019][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.020][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:35.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:35.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:35.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:35.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:35.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:35.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.051][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:35.057][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:35.059][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.060][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.076][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:35.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:35.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.081][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:35.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:35.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:35.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:35.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.093][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:35.094][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:35.096][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.097][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.099][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:35.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:35.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.114][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:06:35.116][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:06:35.117][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.118][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.124][ef$get] Asked field names are: average.mass. biodb.TRACE[2024-05-04 16:06:35.126][ef$get] Realnames of fields are: average.mass. biodb.TRACE[2024-05-04 16:06:35.127][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.128][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.135][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:06:35.136][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:06:35.137][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.138][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.145][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-05-04 16:06:35.146][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-05-04 16:06:35.147][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.148][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.155][ef$get] Asked field names are: chemspider.id. biodb.TRACE[2024-05-04 16:06:35.156][ef$get] Realnames of fields are: chemspider.id. biodb.TRACE[2024-05-04 16:06:35.157][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.158][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.165][ef$get] Asked field names are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:35.166][ef$get] Realnames of fields are: comp.iupac.name.syst. biodb.TRACE[2024-05-04 16:06:35.167][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.169][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.175][ef$get] Asked field names are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:35.176][ef$get] Realnames of fields are: comp.iupac.name.trad. biodb.TRACE[2024-05-04 16:06:35.177][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.179][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.185][ef$get] Asked field names are: comp.super.class. biodb.TRACE[2024-05-04 16:06:35.186][ef$get] Realnames of fields are: comp.super.class. biodb.TRACE[2024-05-04 16:06:35.187][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.189][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.195][ef$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:06:35.196][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:06:35.197][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.199][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.205][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:06:35.206][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:06:35.207][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.209][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.215][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:06:35.216][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:06:35.218][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.219][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.225][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:06:35.227][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:06:35.228][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.229][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.235][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:35.236][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-05-04 16:06:35.238][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.239][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.245][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:35.246][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-05-04 16:06:35.248][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.249][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.260][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:06:35.261][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:06:35.263][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.264][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.270][ef$get] Asked field names are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:35.272][ef$get] Realnames of fields are: ncbi.pubchem.comp.id. biodb.TRACE[2024-05-04 16:06:35.273][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.274][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.281][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:35.282][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:06:35.283][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.284][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:06:35.291][ef$get] Asked field names are: smiles. biodb.TRACE[2024-05-04 16:06:35.292][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-05-04 16:06:35.293][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:06:35.294][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:06:35.306][biodb::testThat] biodb.INFO [2024-05-04 16:06:35.308][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 16:06:35.309][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:06:35.310][biodb::testThat] biodb.DEBUG[2024-05-04 16:06:35.323][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2024-05-04 16:06:35.329][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.INFO [2024-05-04 16:06:35.335][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34". biodb.DEBUG[2024-05-04 16:06:35.337][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded. biodb.INFO [2024-05-04 16:06:35.338][self$download] Downloading whole database of hmdb.metabolites. biodb.INFO [2024-05-04 16:06:35.340][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ... biodb.DEBUG[2024-05-04 16:06:35.342][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip". trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' Content type 'application/zip' length 953913010 bytes (909.7 MB) ================================================== downloaded 909.7 MB biodb.TRACE[2024-05-04 16:06:52.836][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites215902eae6c0dzip". biodb.TRACE[2024-05-04 16:06:52.838][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip". biodb.DEBUG[2024-05-04 16:06:53.025][cch$addFilesToCache] Done adding files. biodb.DEBUG[2024-05-04 16:06:53.027][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip". biodb.DEBUG[2024-05-04 16:06:53.029][self$download] Downloading of hmdb.metabolites completed. biodb.TRACE[2024-05-04 16:06:53.033][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker21590450c6728marker". biodb.TRACE[2024-05-04 16:06:53.035][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker". biodb.DEBUG[2024-05-04 16:06:53.040][self$addFilesToCache] Done adding files. biodb.DEBUG[2024-05-04 16:06:53.042][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.INFO [2024-05-04 16:06:53.043][self$download] Extract whole database of hmdb.metabolites. biodb.INFO [2024-05-04 16:06:53.045][private$doExtractDownload] Extracting content of downloaded', ' HMDB metabolite database... biodb.DEBUG[2024-05-04 16:06:53.046][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip". biodb.DEBUG[2024-05-04 16:06:53.048][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp... biodb.INFO [2024-05-04 16:07:00.882][biodb::testThat] biodb.INFO [2024-05-04 16:07:00.884][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 16:07:00.885][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:00.886][biodb::testThat] biodb.TRACE[2024-05-04 16:07:00.889][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:07:00.891][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:07:00.892][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:00.893][ef$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:07:00.895][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name". biodb.DEBUG[2024-05-04 16:07:00.919][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2024-05-04 16:07:00.965][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-04 16:07:00.968][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-04 16:07:00.969][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.INFO [2024-05-04 16:07:00.971][self$download] Extract whole database of hmdb.metabolites. biodb.INFO [2024-05-04 16:07:00.982][private$doExtractDownload] Extracting content of downloaded', ' HMDB metabolite database... biodb.DEBUG[2024-05-04 16:07:00.984][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip". biodb.DEBUG[2024-05-04 16:07:00.985][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp... biodb.INFO [2024-05-04 16:07:11.208][biodb::testThat] biodb.INFO [2024-05-04 16:07:11.209][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 16:07:11.210][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:11.212][biodb::testThat] biodb.DEBUG[2024-05-04 16:07:11.222][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2024-05-04 16:07:11.223][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-04 16:07:11.225][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-04 16:07:11.228][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.INFO [2024-05-04 16:07:11.230][self$download] Extract whole database of hmdb.metabolites. biodb.INFO [2024-05-04 16:07:11.231][private$doExtractDownload] Extracting content of downloaded', ' HMDB metabolite database... biodb.DEBUG[2024-05-04 16:07:11.233][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip". biodb.DEBUG[2024-05-04 16:07:11.234][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp... biodb.INFO [2024-05-04 16:07:23.604][biodb::testThat] biodb.INFO [2024-05-04 16:07:23.605][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 16:07:23.606][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:23.607][biodb::testThat] biodb.DEBUG[2024-05-04 16:07:23.612][private$loadEntries] Creating entries from ids [1]: "HMDB0000001". biodb.DEBUG[2024-05-04 16:07:23.614][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)... biodb.DEBUG[2024-05-04 16:07:23.616][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.DEBUG[2024-05-04 16:07:23.618][self$isDownloaded] Database hmdb.metabolites has already been downloaded. biodb.INFO [2024-05-04 16:07:23.619][self$download] Extract whole database of hmdb.metabolites. biodb.INFO [2024-05-04 16:07:23.621][private$doExtractDownload] Extracting content of downloaded', ' HMDB metabolite database... biodb.DEBUG[2024-05-04 16:07:23.623][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip". biodb.DEBUG[2024-05-04 16:07:23.624][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp... biodb.INFO [2024-05-04 16:07:34.196][biodb::testThat] biodb.INFO [2024-05-04 16:07:34.197][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 16:07:34.199][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:34.200][biodb::testThat] biodb.INFO [2024-05-04 16:07:34.211][biodb::testThat] biodb.INFO [2024-05-04 16:07:34.212][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 16:07:34.213][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:34.214][biodb::testThat] biodb.INFO [2024-05-04 16:07:34.225][biodb::testThat] biodb.INFO [2024-05-04 16:07:34.227][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 16:07:34.228][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:34.229][biodb::testThat] biodb.DEBUG[2024-05-04 16:07:34.234][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001". biodb.DEBUG[2024-05-04 16:07:34.629][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001. biodb.INFO [2024-05-04 16:07:56.856][biodb::testThat] biodb.INFO [2024-05-04 16:07:56.858][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 16:07:56.860][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:07:56.861][biodb::testThat] biodb.DEBUG[2024-05-04 16:07:57.000][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png. biodb.TRACE[2024-05-04 16:07:59.759][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:07:59.761][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:07:59.762][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:59.763][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:07:59.765][ef$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:07:59.766][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:07:59.768][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:59.769][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:07:59.770][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:07:59.772][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:07:59.773][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:59.774][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:07:59.776][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:07:59.777][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:07:59.778][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:59.779][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:07:59.780][ef$get] Asked field names are: description. biodb.TRACE[2024-05-04 16:07:59.784][ef$get] Realnames of fields are: description. biodb.TRACE[2024-05-04 16:07:59.787][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:59.788][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:07:59.789][ef$get] Asked field names are: secondary.accessions. biodb.TRACE[2024-05-04 16:07:59.791][ef$get] Realnames of fields are: secondary.accessions. biodb.TRACE[2024-05-04 16:07:59.792][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:07:59.793][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:07:59.795][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:07:59.796][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler biodb.INFO [2024-05-04 16:07:59.797][self$deleteConn] Connector "hmdb.metabolites" deleted. biodb.DEBUG[2024-05-04 16:07:59.800][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:07:59.801][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:07:59.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:07:59.804][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:07:59.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:07:59.808][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:07:59.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 4 | WARN 0 | SKIP 0 | PASS 113 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ── Error in `zip::unzip(zip.path, exdir = extract.dir)`: zip error: Cannot extract entry `hmdb_metabolites.xml` from archive `C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34\download.zip` in file zip.c:220 Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`) 3. └─conn$getBiodb()$getFactory()$getEntry(...) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doExtractDownload() 8. └─zip::unzip(zip.path, exdir = extract.dir) ── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ── Error in `zip::unzip(zip.path, exdir = extract.dir)`: zip error: Cannot extract entry `hmdb_metabolites.xml` from archive `C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34\download.zip` in file zip.c:220 Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`) 3. └─conn$getEntry(id, drop = TRUE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─self$download() 8. └─private$doExtractDownload() 9. └─zip::unzip(zip.path, exdir = extract.dir) ── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ── Error in `zip::unzip(zip.path, exdir = extract.dir)`: zip error: Cannot extract entry `hmdb_metabolites.xml` from archive `C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34\download.zip` in file zip.c:220 Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`) 3. └─conn$getEntry(id, drop = TRUE) 4. └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop) 5. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 6. └─conn$getEntryContent(ids) 7. └─self$download() 8. └─private$doExtractDownload() 9. └─zip::unzip(zip.path, exdir = extract.dir) ── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ── Error in `zip::unzip(zip.path, exdir = extract.dir)`: zip error: Cannot extract entry `hmdb_metabolites.xml` from archive `C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34\download.zip` in file zip.c:220 Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`) 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doExtractDownload() 10. └─zip::unzip(zip.path, exdir = extract.dir) [ FAIL 4 | WARN 0 | SKIP 0 | PASS 113 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck' * using R version 4.4.0 beta (2024-04-15 r86425 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'biodbHmdb/DESCRIPTION' ... OK * this is package 'biodbHmdb' 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 whether package 'biodbHmdb' can be installed ... WARNING Found the following significant warnings: EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder] EntryMaker.hpp:22:14: warning: 'bool EntryMaker::closed' [-Wreorder] EntryMaker.cpp:5:1: warning: when initialized here [-Wreorder] See 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details. * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'zip' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite' All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking files in 'vignettes' ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... OK * checking tests in 'longtests' ... Running 'testthat.R' ERROR Running the tests in 'longtests/testthat.R' failed. Last 13 lines of output: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`) 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doExtractDownload() 10. └─zip::unzip(zip.path, exdir = extract.dir) [ FAIL 4 | WARN 0 | SKIP 0 | PASS 113 ] Error: Test failures Execution halted * DONE Status: 1 ERROR, 2 WARNINGs, 1 NOTE See 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log' for details.
biodbHmdb.Rcheck/00install.out
* installing *source* package 'biodbHmdb' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c EntryMaker.cpp -o EntryMaker.o In file included from EntryMaker.cpp:1: EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()': EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder] 23 | TagDetector accession_tag; | ^~~~~~~~~~~~~ EntryMaker.hpp:22:14: warning: 'bool EntryMaker::closed' [-Wreorder] 22 | bool closed; | ^~~~~~ EntryMaker.cpp:5:1: warning: when initialized here [-Wreorder] 5 | EntryMaker::EntryMaker() : | ^~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileEntryMaker.cpp -o FileEntryMaker.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TagDetector.cpp -o TagDetector.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c XmlSplitter.cpp -o XmlSplitter.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractXmlEntries.cpp -o extractXmlEntries.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-100-TagDetector.cpp -o test-100-TagDetector.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/testthat/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help No man pages found in package 'biodbHmdb' *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbHmdb)