############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings ontoProc_2.3.9.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ontoProc/DESCRIPTION' ... OK * this is package 'ontoProc' version '2.3.9' * 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 'ontoProc' can be installed ... OK * checking installed package size ... INFO installed size is 11.5Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 3.8Mb * 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 dependencies in R code ... NOTE ':::' call which should be '::': 'ontologyPlot:::remove_uninformative_terms' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE CLfeat : prupdate: no visible binding for global variable 'PROSYM' CLfeat : prupdate: no visible binding for global variable 'PRID' CLfeat : prupdate: no visible binding for global variable 'SYMBOL' ctmarks : server: no visible binding for global variable 'text' ctmarks : server: no visible binding for global variable 'packDesc2022' ctmarks : server: no visible binding for global variable 'packDesc2021' ctmarks: no visible binding for global variable 'cumu' dropStop: no visible binding for global variable 'stopWords' getOnto: no visible binding for global variable 'rdatadateadded' getOnto: no visible binding for global variable 'title' getOnto: no visible binding for global variable 'description' ldfToTerm: no visible binding for global variable 'PROSYM' sym2CellOnto: no visible binding for global variable 'PROSYM' sym2CellOnto: no visible binding for global variable 'SYMBOL' Undefined global functions or variables: PRID PROSYM SYMBOL cumu description packDesc2021 packDesc2022 rdatadateadded stopWords text title Consider adding importFrom("graphics", "text", "title") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: findCommonAncestors.Rd: graph, DataFrame-class, List-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'plot.owlents.Rd': 'plot.owlents' The \usage entries for S3 methods should use the \method markup and not their full name. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... 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 sym2CellOnto 227.16 2.75 231.38 siblings_TAG 138.32 2.15 141.21 cleanCLOnames 123.31 1.17 131.90 nomenCheckup 96.44 0.77 97.39 CLfeats 75.81 2.68 79.91 getLeavesFromTerm 66.03 0.85 67.28 fastGrep 64.42 1.39 70.91 common_classes 59.53 1.22 65.52 liberalMap 57.32 0.90 59.23 findCommonAncestors 50.17 1.04 51.62 onto_plot2 50.38 0.70 51.17 make_graphNEL_from_ontology_plot 49.99 0.99 51.39 selectFromMap 49.00 0.74 49.88 mapOneNaive 48.11 0.86 49.25 secLevGen 47.83 0.83 48.95 TermSet-class 47.52 0.60 48.65 getOnto 47.05 0.96 48.24 labels.owlents 25.73 0.47 27.55 owl2cache 16.56 0.41 17.64 ancestors 15.01 0.75 19.03 ontoDiff 13.42 1.22 15.32 graph2paths 10.61 0.31 10.89 plot.owlents 7.07 0.16 7.22 ancestors_names 5.81 0.04 5.85 subclasses 5.28 0.08 5.36 setup_entities 5.30 0.03 5.32 children_names 5.06 0.10 5.19 search_labels 0.53 0.04 21.02 bioregistry_ols_resources 0.08 0.03 25.62 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test.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 'F:/biocbuild/bbs-3.22-bioc/meat/ontoProc.Rcheck/00check.log' for details.