############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings fgsea_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/fgsea.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * 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 ‘1.28.0’ * 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 10.3Mb 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 ... 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 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 17.986 2.774 17.876 collapsePathways 12.052 0.667 9.185 mapIdsList 9.331 0.685 7.837 fgseaSimple 6.644 1.051 3.264 fgsea 7.077 0.367 3.970 fgseaMultilevel 6.764 0.415 3.615 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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 ‘/home/biocbuild/bbs-3.18-bioc/meat/fgsea.Rcheck/00check.log’ for details.