############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ontoProc.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ontoProc_2.1.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ontoProc/DESCRIPTION’ ... OK * this is package ‘ontoProc’ version ‘2.1.4’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘ontoProc’ can be installed ... OK * checking installed package size ... INFO installed size is 9.7Mb sub-directories of 1Mb or more: app 1.6Mb data 1.8Mb ontoRda 2.7Mb owl 3.0Mb * 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 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 73.282 5.798 83.039 siblings_TAG 33.336 4.505 39.853 owl2cache 30.033 2.598 34.774 CLfeats 29.050 3.523 33.369 labels.owlents 27.603 2.179 35.830 nomenCheckup 23.432 2.061 26.546 getLeavesFromTerm 16.963 1.221 18.428 liberalMap 15.050 1.599 19.242 fastGrep 15.263 1.153 16.658 cleanCLOnames 14.899 0.968 16.172 ontoDiff 12.023 2.242 15.628 common_classes 12.312 1.279 13.883 make_graphNEL_from_ontology_plot 12.082 1.385 13.730 ancestors 12.299 1.072 14.787 mapOneNaive 12.188 1.039 14.739 getOnto 10.991 1.001 18.281 findCommonAncestors 8.708 0.986 9.990 secLevGen 8.291 1.190 9.984 TermSet-class 8.376 0.983 9.778 selectFromMap 8.384 0.834 9.471 plot.owlents 8.296 0.431 8.755 subclasses 8.020 0.636 8.818 onto_plot2 7.751 0.894 8.886 parents 6.652 0.354 7.035 ldfToTerms 4.816 0.076 5.480 search_labels 0.676 0.093 182.766 bioregistry_ols_resources 0.039 0.013 13.416 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/ontoProc.Rcheck/00check.log’ for details.