############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ontoProc_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ontoProc.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '2.0.0' * 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 ... OK * checking for portable file names ... OK * checking whether package 'ontoProc' can be installed ... OK * checking installed package size ... NOTE installed size is 10.4Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb owl 3.3Mb * 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 ... OK * 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 ... OK * 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 ... NOTE Note: found 162 marked UTF-8 strings * 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 48.67 1.84 51.89 CLfeats 32.68 2.30 35.95 siblings_TAG 27.25 2.08 30.10 labels.owlents 26.95 0.66 30.33 owl2cache 21.66 0.39 22.94 getLeavesFromTerm 18.78 1.24 22.03 cleanCLOnames 16.77 0.68 17.81 fastGrep 16.47 0.94 18.18 nomenCheckup 16.00 0.75 16.90 ancestors 15.64 1.08 24.83 findCommonAncestors 13.38 1.14 16.44 common_classes 12.25 1.24 14.25 onto_plot2 11.56 0.66 14.00 liberalMap 11.11 1.00 13.86 getOnto 10.94 0.90 12.23 make_graphNEL_from_ontology_plot 10.80 0.79 12.00 TermSet-class 10.72 0.86 12.34 selectFromMap 10.36 1.11 11.70 secLevGen 10.12 0.73 11.24 mapOneNaive 8.92 0.57 9.63 plot.owlents 9.00 0.08 9.37 parents 6.61 0.06 6.78 subclasses 6.28 0.13 6.47 children_names 5.40 0.07 5.47 ancestors_names 5.32 0.08 5.40 search_labels 0.50 0.11 104.86 bioregistry_ols_resources 0.06 0.03 35.86 * 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-3.20-bioc/meat/ontoProc.Rcheck/00check.log' for details.