############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings rWikiPathways_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/rWikiPathways.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rWikiPathways/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rWikiPathways’ version ‘1.25.0’ * 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: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... NOTE Found the following non-portable file path: rWikiPathways/docs/articles/rWikiPathways-and-BridgeDbR_files/accessible-code-block-0.0.1/empty-anchor.js Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘rWikiPathways’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE findPathwaysByLiterature: no visible binding for global variable ‘refs’ findPathwaysByLiterature: no visible binding for global variable ‘citations’ findPathwaysByOrcid: no visible binding for global variable ‘orcids’ findPathwaysByText: no visible binding for global variable ‘citedIn’ getOntologyTerms: no visible binding for global variable ‘terms’ getPathwaysByCommunity: no visible binding for global variable ‘pathways’ getPathwaysByCommunity: no visible binding for global variable ‘community-tag’ getPathwaysByOntologyTerm: no visible binding for global variable ‘pathways’ getPathwaysByParentOntologyTerm: no visible binding for global variable ‘terms’ getPathwaysByParentOntologyTerm: no visible binding for global variable ‘terms_parent’ getRecentChanges: no visible binding for global variable ‘revision’ getRecentChanges: no visible binding for global variable ‘revision_ymd’ getRecentChanges: no visible binding for global variable ‘authors’ getRecentChanges: no visible binding for global variable ‘description’ getRecentChanges: no visible binding for global variable ‘citedIn’ listCommunities: no visible binding for global variable ‘pathways’ listPathways: no visible binding for global variable ‘species’ readPathwayGMT: no visible binding for global variable ‘pathway’ Undefined global functions or variables: authors citations citedIn community-tag description orcids pathway pathways refs revision revision_ymd species terms terms_parent Consider adding importFrom("stats", "terms") to your NAMESPACE file. * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findPathwaysByLiterature 18.053 0.204 20.682 findPathwayIdsByLiterature 13.663 0.169 15.744 findPathwayNamesByLiterature 13.397 0.168 15.068 findPathwayUrlsByLiterature 13.178 0.153 14.957 findPathwaysByText 5.609 0.059 6.675 findPathwayUrlsByText 4.985 0.043 5.705 findPathwayIdsByText 4.959 0.041 5.674 findPathwayNamesByText 4.779 0.040 5.311 findPathwayIDsByOrcid 0.773 0.037 7.157 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/rWikiPathways.Rcheck/00check.log’ for details.