############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GSVA_1.52.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GSVA/DESCRIPTION’ ... OK * this is package ‘GSVA’ version ‘1.52.3’ * 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 ‘GSVA’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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 ... OK * 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 line endings in shell scripts ... 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ Running ‘test_gsva_newapi.R’ Comparing ‘test_gsva_newapi.Rout’ to ‘test_gsva_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname 161c161 < KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879766 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736 --- > KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879477 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736 163c163 < KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55050994 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745 --- > KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55049088 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745 166c166 < KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35347309 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262 --- > KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35356594 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262 173c173 < KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257010 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129 --- > KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257184 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129 Running ‘test_plage_newapi.R’ Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname Running ‘test_ssgsea_newapi.R’ Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname Running ‘test_zscore_newapi.R’ Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ...16,21c16,21 < Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, < as.data.frame, basename, cbind, colnames, dirname, do.call, < duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, < lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, < pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, < union, unique, unsplit, which.max, which.min --- > anyDuplicated, aperm, append, as.data.frame, basename, cbind, > colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, > get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, > match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, > Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, > table, tapply, union, unique, unsplit, which.max, which.min 38c38 < I, expand.grid, unname --- > expand.grid, I, unname 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: 1 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck/00check.log’ for details.