############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:rWikiPathways.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rWikiPathways_1.29.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rWikiPathways/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rWikiPathways’ version ‘1.29.2’ * 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 ... 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 loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... 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 10.925 0.211 24.904 findPathwayIdsByLiterature 8.635 0.169 19.387 findPathwayUrlsByLiterature 8.192 0.192 15.880 findPathwayNamesByLiterature 8.259 0.097 15.996 findPathwaysByText 3.344 0.016 7.746 findPathwayUrlsByText 3.021 0.058 5.089 findPathwayIdsByXref 1.330 0.090 9.643 findPathwaysByXref 1.298 0.093 13.517 findPathwayNamesByXref 1.296 0.080 9.301 findPathwayUrlsByXref 1.180 0.081 15.084 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/rWikiPathways.Rcheck/00check.log’ for details.