############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ontoProc.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings ontoProc_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/ontoProc.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * 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 '1.24.0' * 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 7.0Mb sub-directories of 1Mb or more: app 1.9Mb data 1.8Mb ontoRda 2.8Mb * 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 R 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 Namespace in Imports field not imported from: 'BiocFileCache' All declared Imports should be used. * 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 ... OK * 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 57.59 2.03 63.94 siblings_TAG 31.20 2.03 38.16 CLfeats 30.51 1.87 33.81 common_classes 18.91 2.93 23.50 getLeavesFromTerm 15.64 0.38 16.23 fastGrep 14.53 0.61 15.69 nomenCheckup 13.40 0.75 14.23 cleanCLOnames 13.37 0.63 14.23 TermSet-class 10.19 0.74 11.27 secLevGen 8.33 0.49 8.89 selectFromMap 7.80 0.76 8.66 make_graphNEL_from_ontology_plot 8.06 0.47 8.57 mapOneNaive 7.82 0.70 8.58 getOnto 7.95 0.56 8.63 onto_plot2 7.74 0.53 8.34 findCommonAncestors 7.58 0.65 8.31 liberalMap 7.32 0.56 8.08 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.18-bioc/meat/ontoProc.Rcheck/00check.log' for details.