############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings fgsea_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/fgsea.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fgsea/DESCRIPTION’ ... OK * this is package ‘fgsea’ version ‘1.30.0’ * 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++ (GCC) 10.3.1’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 10.2Mb sub-directories of 1Mb or more: data 1.1Mb extdata 3.9Mb libs 5.0Mb * 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 ‘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 expressionValue gene gsScore id log2err 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 19.687 0.848 17.470 collapsePathways 12.136 0.673 9.264 mapIdsList 9.274 0.625 7.682 fgseaSimple 7.459 1.129 3.227 fgsea 7.149 0.343 4.002 fgseaMultilevel 6.855 0.373 3.715 geseca 5.413 0.664 3.484 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/fgsea.Rcheck/00check.log’ for details.