############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/paxtoolsr.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘paxtoolsr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘paxtoolsr’ version ‘1.28.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘paxtoolsr’ can be installed ... OK * checking installed package size ... NOTE installed size is 32.2Mb sub-directories of 1Mb or more: extdata 7.3Mb java 24.5Mb * checking package directory ... OK * checking ‘build’ 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE splitSifnxByPathway: no visible global function definition for ‘%dopar%’ Undefined global functions or variables: %dopar% * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘paxtoolsr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: toSBGN > ### Title: Convert a BioPAX OWL file to SBGNML > ### Aliases: toSBGN > > ### ** Examples > > outFile <- tempfile() > results <- toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", + package="paxtoolsr"), + outFile) No Java runtime present, requesting install. 2022-04-12 16:37:41.627 R[58514:599937551] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("paxtoolsr") URL: http://www.pathwaycommons.org/pc2/get?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ06609&uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ96EB6&format=BIOPAX 2022-04-12 16:37:56,135 890 [main] INFO org.biopax.paxtools.PaxtoolsMain - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc. 2022-04-12 16:37:56,155 910 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50 2022-04-12 16:37:56,161 916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - fetched PRs: 2 2022-04-12 16:37:56,161 916 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - grouping the PRs by organism... 2022-04-12 16:37:56,173 928 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - creating GSEA/GMT entries... 2022-04-12 16:37:56,175 930 [pool-2-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - adding uniprot IDs of proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway... 2022-04-12 16:37:56,177 932 [pool-1-thread-1] INFO org.biopax.paxtools.io.gsea.GSEAConverter - - collected 1entries. 2022-04-12 16:37:56,177 932 [main] INFO org.biopax.paxtools.io.gsea.GSEAConverter - Creating entries for the rest fo (unused) PRs... 2022-04-12 16:37:59,843 4598 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html 2022-04-12 16:38:03,327 8082 [main] INFO org.biopax.paxtools.client.BiopaxValidatorClient - BioPAX Validator location: http://biopax.baderlab.org/check.html 2022-04-12 16:38:07,928 12683 [main] INFO org.biopax.paxtools.PaxtoolsMain - Elements in the result model: 240 No Java runtime present, requesting install. 2022-04-12 16:38:08.154 R[61544:599942737] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.14-bioc/meat/paxtoolsr.Rcheck/00check.log’ for details.