starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/bin:/gnu/store/bkcd6iqgxhikvbl54vwiy2jih981vrz1-tar-1.34/bin:/gnu/store/4ly70ncfklcln1vvilpq5fih53227p4b-gzip-1.12/bin:/gnu/store/d66iz5kkh2kravdfa21x58bd53s7acvp-bzip2-1.0.8/bin:/gnu/store/bzj02l1bgp7ibhxvdmpga2k5af0c4npa-file-5.44/bin:/gnu/store/mydmggf3qs7ha5ajkz7x250dy7cnmi2v-diffutils-3.8/bin:/gnu/store/jzk30pqyk3z7xlizbq6013krgyyyys39-patch-2.7.6/bin:/gnu/store/5sksczis0ssy8nhln62lsjfm80np01rc-findutils-4.9.0/bin:/gnu/store/qll484d4kizx5s1lgyjgrq2nqzq177q6-gawk-5.2.1/bin:/gnu/store/bjjyfa71m9zy8iyriqc9wbpg95skad90-sed-4.8/bin:/gnu/store/j0h6z30j13wrbch7pax9l9859c0wfvsl-grep-3.8/bin:/gnu/store/drsra005pzksg8z11jp4yn96sk8gkmq9-xz-5.2.8/bin:/gnu/store/sinrqfmja2a3ys1kmlwgpb629l4sh5rr-coreutils-9.1/bin:/gnu/store/kgdnsfsw8f226s6j5vldaqvc767hn8ff-make-4.3/bin:/gnu/store/9q7cmydxbzfpc79ybn1yn257wq547kvz-bash-minimal-5.1.16/bin:/gnu/store/py7qrzdb70jzkyjhggp15w57iqldv8hc-ld-wrapper-0/bin:/gnu/store/a7v86dd2kbi1rn9rwcw5mfw85aw9m3cf-binutils-2.38/bin:/gnu/store/dcrdgy1rjkh0kibpkw6v2mia7f921b27-gcc-11.3.0/bin:/gnu/store/3imvi8mfcsib1aiiidgr2znypih8nhmv-glibc-2.35/bin:/gnu/store/3imvi8mfcsib1aiiidgr2znypih8nhmv-glibc-2.35/sbin' environment variable `R_LIBS_SITE' set to `/gnu/store/j2654ifvzb3iqn5xhnkgvcr35dyn102a-r-knitr-1.44/site-library/:/gnu/store/5rprp5nc5974dllskw0pb8spx6zs28bh-r-biobase-2.60.0/site-library/:/gnu/store/873b2fz6fj4l8p8irk2h90w6vv997i7p-r-edger-3.42.4/site-library/:/gnu/store/xmzfk1cyp8b3566lm1csdxnaldy5i3j2-r-rcpp-1.0.11/site-library/:/gnu/store/gr1300zdvbrnyka532c1m3krxbr940rg-r-yaml-2.3.7/site-library/:/gnu/store/6a6jxnr3zmv92cmyr3bgcissmvd4x4s4-r-xfun-0.40/site-library/:/gnu/store/84xfinkynhwadxbknxj6dqgwbdpb070l-r-highr-0.10/site-library/:/gnu/store/pa9k94k97p47si9kfy1llz52by6ls7sx-r-evaluate-0.21/site-library/:/gnu/store/vva2nqifmq1kc2psjw144f2n4vy7daw2-r-biocgenerics-0.46.0/site-library/:/gnu/store/wz9m2jqrvwff582dp397nbbxjc0yayzs-r-locfit-1.5-9.8/site-library/:/gnu/store/q3qbnnnnr9mj0rflyph4knw40sw5cfnw-r-limma-3.56.2/site-library/:/gnu/store/gqzlag4h2mb0662q5s3zfb7rh5in0gq7-r-lattice-0.21-8/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/d66iz5kkh2kravdfa21x58bd53s7acvp-bzip2-1.0.8/include:/gnu/store/bzj02l1bgp7ibhxvdmpga2k5af0c4npa-file-5.44/include:/gnu/store/qll484d4kizx5s1lgyjgrq2nqzq177q6-gawk-5.2.1/include:/gnu/store/drsra005pzksg8z11jp4yn96sk8gkmq9-xz-5.2.8/include:/gnu/store/kgdnsfsw8f226s6j5vldaqvc767hn8ff-make-4.3/include:/gnu/store/a7v86dd2kbi1rn9rwcw5mfw85aw9m3cf-binutils-2.38/include:/gnu/store/dcrdgy1rjkh0kibpkw6v2mia7f921b27-gcc-11.3.0/include:/gnu/store/3imvi8mfcsib1aiiidgr2znypih8nhmv-glibc-2.35/include:/gnu/store/6qj8b1i9ynscrl6a8nqgkw787nvnf8fi-linux-libre-headers-5.15.49/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/d66iz5kkh2kravdfa21x58bd53s7acvp-bzip2-1.0.8/include:/gnu/store/bzj02l1bgp7ibhxvdmpga2k5af0c4npa-file-5.44/include:/gnu/store/qll484d4kizx5s1lgyjgrq2nqzq177q6-gawk-5.2.1/include:/gnu/store/drsra005pzksg8z11jp4yn96sk8gkmq9-xz-5.2.8/include:/gnu/store/kgdnsfsw8f226s6j5vldaqvc767hn8ff-make-4.3/include:/gnu/store/a7v86dd2kbi1rn9rwcw5mfw85aw9m3cf-binutils-2.38/include:/gnu/store/dcrdgy1rjkh0kibpkw6v2mia7f921b27-gcc-11.3.0/include/c++:/gnu/store/dcrdgy1rjkh0kibpkw6v2mia7f921b27-gcc-11.3.0/include:/gnu/store/3imvi8mfcsib1aiiidgr2znypih8nhmv-glibc-2.35/include:/gnu/store/6qj8b1i9ynscrl6a8nqgkw787nvnf8fi-linux-libre-headers-5.15.49/include' environment variable `LIBRARY_PATH' set to `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib:/gnu/store/d66iz5kkh2kravdfa21x58bd53s7acvp-bzip2-1.0.8/lib:/gnu/store/bzj02l1bgp7ibhxvdmpga2k5af0c4npa-file-5.44/lib:/gnu/store/qll484d4kizx5s1lgyjgrq2nqzq177q6-gawk-5.2.1/lib:/gnu/store/drsra005pzksg8z11jp4yn96sk8gkmq9-xz-5.2.8/lib:/gnu/store/a7v86dd2kbi1rn9rwcw5mfw85aw9m3cf-binutils-2.38/lib:/gnu/store/3imvi8mfcsib1aiiidgr2znypih8nhmv-glibc-2.35/lib:/gnu/store/qqpiqxw7n69ikd28cvm78zi5z7g8y0qh-glibc-2.35-static/lib:/gnu/store/83rdr33pwjzimv4n0ch33lc6yf1acbry-glibc-utf8-locales-2.35/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/83rdr33pwjzimv4n0ch33lc6yf1acbry-glibc-utf8-locales-2.35/lib/locale' phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' BioQC/DESCRIPTION BioQC/LICENSE BioQC/NAMESPACE BioQC/NEWS BioQC/R/ BioQC/R/AllClasses.R BioQC/R/AllMethods.R BioQC/R/GmtList-funcs.R BioQC/R/appendGmtList.R BioQC/R/as.GmtList.R BioQC/R/entropy.R BioQC/R/gini.R BioQC/R/leadingEdge.R BioQC/R/matchGenes.R BioQC/R/prettySigNames.R BioQC/R/readCurrentSignatures.R BioQC/R/readGmt.R BioQC/R/readSignedGmt.R BioQC/R/uniqGenesetsByNamespace.R BioQC/R/utils.R BioQC/R/wmwTest.R BioQC/README.md BioQC/build/ BioQC/build/vignette.rds BioQC/inst/ BioQC/inst/CITATION BioQC/inst/Rscript/ BioQC/inst/Rscript/bioqc.Rscript BioQC/inst/doc/ BioQC/inst/doc/BioQC.R BioQC/inst/doc/BioQC.Rmd BioQC/inst/doc/BioQC.html BioQC/inst/doc/bioqc-efficiency.R BioQC/inst/doc/bioqc-efficiency.Rmd BioQC/inst/doc/bioqc-efficiency.html BioQC/inst/doc/bioqc-introduction.R BioQC/inst/doc/bioqc-introduction.Rmd BioQC/inst/doc/bioqc-introduction.html BioQC/inst/doc/bioqc-signedGenesets.R BioQC/inst/doc/bioqc-signedGenesets.Rmd BioQC/inst/doc/bioqc-signedGenesets.html BioQC/inst/doc/bioqc-simulation.R BioQC/inst/doc/bioqc-simulation.Rmd BioQC/inst/doc/bioqc-simulation.html BioQC/inst/doc/bioqc-wmw-test-performance.R BioQC/inst/doc/bioqc-wmw-test-performance.Rmd BioQC/inst/doc/bioqc-wmw-test-performance.html BioQC/inst/extdata/ BioQC/inst/extdata/GSE20113.rda BioQC/inst/extdata/exp.tissuemark.affy.roche.symbols.gmt BioQC/inst/extdata/exp.tissuemark.bioqc.roche.symbols.gmt BioQC/inst/extdata/kidney_example.rda BioQC/inst/extdata/test.gct BioQC/inst/extdata/test.gmt BioQC/man/ BioQC/man/BaseIndexList-class.Rd BioQC/man/GmtList-class.Rd BioQC/man/GmtList.Rd BioQC/man/IndexList-class.Rd BioQC/man/IndexList.Rd BioQC/man/SignedGenesets-class.Rd BioQC/man/SignedGenesets.Rd BioQC/man/SignedIndexList-class.Rd BioQC/man/SignedIndexList.Rd BioQC/man/absLog10p.Rd BioQC/man/appendGmtList.Rd BioQC/man/as.GmtList.Rd BioQC/man/entropy.Rd BioQC/man/entropyDiversity.Rd BioQC/man/entropySpecificity.Rd BioQC/man/figures/ BioQC/man/figures/kidney_heatmap.png BioQC/man/filterBySize.Rd BioQC/man/filterPmat.Rd BioQC/man/getLeadingEdgeIndexFromVector.Rd BioQC/man/gini.Rd BioQC/man/gmtlist2signedGenesets.Rd BioQC/man/gsDesc.Rd BioQC/man/gsGeneCount.Rd BioQC/man/gsGenes.Rd BioQC/man/gsName.Rd BioQC/man/gsNamespace.Rd BioQC/man/hasNamespace.Rd BioQC/man/isValidBaseIndexList.Rd BioQC/man/isValidGmtList.Rd BioQC/man/isValidIndexList.Rd BioQC/man/isValidSignedGenesets.Rd BioQC/man/isValidSignedIndexList.Rd BioQC/man/matchGenes.Rd BioQC/man/offset-set.Rd BioQC/man/offset.Rd BioQC/man/prettySigNames.Rd BioQC/man/readCurrentSignatures.Rd BioQC/man/readGmt.Rd BioQC/man/readSignedGmt.Rd BioQC/man/sampleSpecialization.Rd BioQC/man/setDescAsNamespace.Rd BioQC/man/setGsNamespace.Rd BioQC/man/setNamespace.Rd BioQC/man/show-GmtList-method.Rd BioQC/man/show-IndexList-method.Rd BioQC/man/show-SignedGenesets-method.Rd BioQC/man/show-SignedIndexList-method.Rd BioQC/man/simplifyMatrix.Rd BioQC/man/sub-.GmtList.Rd BioQC/man/sub-sub-.GmtList.Rd BioQC/man/uniqGenesetsByNamespace.Rd BioQC/man/valTypes.Rd BioQC/man/wmwLeadingEdge.Rd BioQC/man/wmwTest.Rd BioQC/man/wmwTestInR.Rd BioQC/src/ BioQC/src/Makevars BioQC/src/gini.c BioQC/src/init.c BioQC/src/init.h BioQC/src/read_gmt.cpp BioQC/src/read_gmt.h BioQC/src/stat_rank.c BioQC/src/stat_rank.h BioQC/src/wmw_test.c BioQC/tests/ BioQC/tests/testthat/ BioQC/tests/testthat.R BioQC/tests/testthat/test-gini.R BioQC/tests/testthat/test-indexlist.R BioQC/tests/testthat/test-matchGene.R BioQC/tests/testthat/test-normalzed.R BioQC/tests/testthat/test-out-of-range.R BioQC/tests/testthat/test-readgmt.R BioQC/tests/testthat/test-u1u2.R BioQC/tests/testthat/test-wmwTest.R BioQC/vignettes/ BioQC/vignettes/BioQC.Rmd BioQC/vignettes/bioqc-efficiency.Rmd BioQC/vignettes/bioqc-introduction.Rmd BioQC/vignettes/bioqc-signedGenesets.Rmd BioQC/vignettes/bioqc-simulation.Rmd BioQC/vignettes/bioqc-wmw-test-performance.Rmd BioQC/vignettes/simulation-benchmark.RData BioQC/vignettes/wmw-speedup.png BioQC/vignettes/wmw-speedup.svg phase `unpack' succeeded after 0.3 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' patch-shebang: ./inst/Rscript/bioqc.Rscript: warning: no binary for interpreter `tcsh' found in $PATH phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `patch-generated-file-shebangs' patch-shebang: ./inst/Rscript/bioqc.Rscript: warning: no binary for interpreter `tcsh' found in $PATH phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' * installing *source* package ‘BioQC’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 11.3.0’ using C++ compiler: ‘g++ (GCC) 11.3.0’ gcc -I"/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/include" -DNDEBUG `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/gnu/store/xmzfk1cyp8b3566lm1csdxnaldy5i3j2-r-rcpp-1.0.11/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gini.c -o gini.o gcc -I"/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/include" -DNDEBUG `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/gnu/store/xmzfk1cyp8b3566lm1csdxnaldy5i3j2-r-rcpp-1.0.11/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c init.c -o init.o g++ -std=gnu++17 -I"/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/include" -DNDEBUG `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/gnu/store/xmzfk1cyp8b3566lm1csdxnaldy5i3j2-r-rcpp-1.0.11/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c read_gmt.cpp -o read_gmt.o gcc -I"/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/include" -DNDEBUG `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/gnu/store/xmzfk1cyp8b3566lm1csdxnaldy5i3j2-r-rcpp-1.0.11/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c stat_rank.c -o stat_rank.o gcc -I"/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/include" -DNDEBUG `/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/gnu/store/xmzfk1cyp8b3566lm1csdxnaldy5i3j2-r-rcpp-1.0.11/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c wmw_test.c -o wmw_test.o g++ -std=gnu++17 -shared -L/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/lib -L/usr/local/lib -o BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -L/gnu/store/0fhaz0n6mrsba5ij2k3m36vglg3jpdns-r-minimal-4.3.1/lib/R/lib -lR installing to /gnu/store/ib6l5d0dhra7jjsaqg3a02wxa7k6a04f-r-bioqc-1.28.0/site-library/00LOCK-BioQC/00new/BioQC/libs ** R ** inst ** tests ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BioQC) phase `install' succeeded after 134.9 seconds starting phase `check' Testing examples for package ‘BioQC’ Running specific tests for package ‘BioQC’ Running ‘testthat.R’ phase `check' succeeded after 21.5 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `make-dynamic-linker-cache' phase `make-dynamic-linker-cache' succeeded after 0.0 seconds starting phase `install-license-files' installing 1 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds