############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings fgsea_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/fgsea.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 ‘fgsea/DESCRIPTION’ ... OK * this is package ‘fgsea’ version ‘1.33.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘fgsea’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... INFO installed size is 9.4Mb sub-directories of 1Mb or more: data 1.1Mb extdata 3.9Mb libs 4.1Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE setUpBPPARAM: warning in MulticoreParam(workers = nproc, progress = TRUE): partial argument match of 'progress' to 'progressbar' addGesecaScores: no visible global function definition for ‘DefaultAssay’ addGesecaScores: no visible global function definition for ‘GetAssay’ collapsePathways: no visible binding for global variable ‘pathway’ collapsePathways: no visible binding for global variable ‘ES’ collapsePathwaysGeseca: no visible binding for global variable ‘pvalCond’ collapsePathwaysGeseca: no visible binding for global variable ‘pathway’ collapsePathwaysGeseca: no visible binding for global variable ‘reciprocalPvalCond’ collapsePathwaysGeseca: no visible binding for global variable ‘pScore’ collapsePathwaysGeseca: no visible binding for global variable ‘pval’ fgseaMultilevel: no visible binding for global variable ‘modeFraction’ fgseaMultilevel: no visible binding for global variable ‘denomProb’ fora: no visible binding for global variable ‘es’ fora: no visible binding for global variable ‘k’ fora: no visible binding for global variable ‘m’ fora: no visible binding for global variable ‘pval’ geseca: no visible binding for global variable ‘gsScore’ geseca: no visible binding for global variable ‘log2err’ geseca: no visible binding for global variable ‘nGeScore’ geseca: no visible binding for global variable ‘pctVar’ geseca: no visible binding for global variable ‘size’ geseca: no visible binding for global variable ‘pathway’ geseca: no visible global function definition for ‘.’ geseca: no visible binding for global variable ‘pval’ geseca: no visible binding for global variable ‘padj’ gesecaSimple: no visible binding for global variable ‘pctVar’ gesecaSimple: no visible binding for global variable ‘size’ gesecaSimple: no visible binding for global variable ‘pval’ gesecaSimpleImpl: no visible binding for global variable ‘pval’ gesecaSimpleImpl: no visible binding for global variable ‘nGeScore’ gesecaSimpleImpl: no visible binding for global variable ‘padj’ gesecaSimpleImpl: no visible binding for global variable ‘size’ plotCoregulationProfile: no visible binding for global variable ‘id’ plotCoregulationProfile: no visible binding for global variable ‘gene’ plotCoregulationProfile: no visible binding for global variable ‘expressionValue’ plotCoregulationProfile: no visible binding for global variable ‘x’ plotCoregulationProfile: no visible binding for global variable ‘y’ plotCoregulationProfile: no visible binding for global variable ‘condition’ plotCoregulationProfileReduction: no visible global function definition for ‘DefaultAssay’ plotCoregulationProfileSpatial: no visible global function definition for ‘DefaultAssay’ plotGesecaTable: no visible global function definition for ‘modifyList’ plotGesecaTable: no visible binding for global variable ‘pathway’ plotGesecaTable: no visible binding for global variable ‘value’ plotGesecaTable : : no visible binding for global variable ‘pathway’ plotGesecaTable : : no visible binding for global variable ‘value’ plotGseaTable: no visible global function definition for ‘modifyList’ Undefined global functions or variables: . DefaultAssay ES GetAssay condition denomProb es expressionValue gene gsScore id k log2err m modeFraction modifyList nGeScore pScore padj pathway pctVar pval pvalCond reciprocalPvalCond size value x y Consider adding importFrom("utils", "modifyList") 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotGseaTable 10.691 0.631 8.979 collapsePathways 7.566 0.426 5.306 fgseaSimple 6.511 1.236 2.081 mapIdsList 6.071 0.549 5.034 fgsea 4.679 0.395 2.614 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/fgsea.Rcheck/00check.log’ for details.