############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:pathview.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings pathview_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pathview.Rcheck’ * using R Under development (unstable) (2024-11-14 r87333) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘pathview/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pathview’ version ‘1.47.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘pathview’ can be installed ... OK * checking installed package size ... OK * 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 code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘BiocManager’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘pathview/R/zzz.R’: .onLoad calls: installed.packages() packageStartupMessage(wordwrap(disclaimer, 80)) Package startup functions should not call ‘installed.packages’. See section ‘Good practice’ in '?.onAttach'. Warning in formals(fun) : argument is not a function Warning in body(fun) : argument is not a function col.key: no visible binding for global variable ‘node.sizes’ cpd2kegg: no visible binding for global variable ‘rn.list’ cpdidmap: no visible binding for global variable ‘cpd.accs’ cpdkegg2name: no visible binding for global variable ‘kegg.met’ cpdname2kegg: no visible binding for global variable ‘cpd.names’ download.kegg: no visible global function definition for ‘download.file’ eg2id: no visible binding for global variable ‘gene.idtype.list’ geneannot.map: no visible binding for global variable ‘bods’ id2eg: no visible binding for global variable ‘gene.idtype.list’ kegg.species.code: no visible binding for global variable ‘korg.1’ pathview: no visible binding for global variable ‘bods’ pathview: no visible binding for global variable ‘gene.idtype.bods’ pathview: no visible binding for global variable ‘rn.list’ sim.mol.data: no visible binding for global variable ‘bods’ sim.mol.data: no visible binding for global variable ‘gene.idtype.bods’ sim.mol.data: no visible binding for global variable ‘cpd.accs’ sim.mol.data: no visible binding for global variable ‘cpd.simtypes’ sim.mol.data: no visible binding for global variable ‘rn.list’ sim.mol.data: no visible binding for global variable ‘ko.ids’ Undefined global functions or variables: bods cpd.accs cpd.names cpd.simtypes download.file gene.idtype.bods gene.idtype.list kegg.met ko.ids korg.1 node.sizes rn.list Consider adding importFrom("utils", "download.file") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) node.color.Rd:71: Escaped LaTeX specials: \# checkRd: (-1) pathview.Rd:204: Escaped LaTeX specials: \# checkRd: (-1) pathview.Rd:396: Lost braces 396 | code{keggview.graph} are both a list of graph plotting | ^ * 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 ... NOTE Auto-generated content requiring editing in Rd file 'pathview-package.Rd': \details: ‘...the package, including the most important ~~ ~~ functions ~~’ * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed pathview 8.215 0.277 10.210 sim.mol.data 0.334 0.016 7.375 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/pathview.Rcheck/00check.log’ for details.