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/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/bin:/gnu/store/ikc2qn1h260f8mdhjz2cwndv2i7n753z-tar-1.34/bin:/gnu/store/v5l2251ck0r4n3w2rjw3l5dzyqsb9zj1-gzip-1.10/bin:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/bin:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/bin:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/bin:/gnu/store/s49sxmz9g4xmzz222cay9k04ziy3qgmj-diffutils-3.8/bin:/gnu/store/m96snvbl92ivkd32giqh5f3d21bc2n5x-patch-2.7.6/bin:/gnu/store/l8l2y2dlya5rs9hfypmcb4saay7iwn0q-findutils-4.8.0/bin:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/bin:/gnu/store/7cddr79rydhc1m4hxr921mq17pz1jj3z-sed-4.8/bin:/gnu/store/ldkm5jwql0qsrfh3ax6rljjsrk0jzv7z-grep-3.6/bin:/gnu/store/25gv43v5rm05i26z39ajrd6nsxa5r461-coreutils-8.32/bin:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/bin:/gnu/store/vx6vfbmmazvfi7vp8xyjn2mcyylvw9gn-bash-minimal-5.1.8/bin:/gnu/store/k452f0r5bk6n0cbsf5ndxbp5qcf6bpfw-ld-wrapper-0/bin:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/bin:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/bin:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/bin:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/sbin' environment variable `R_LIBS_SITE' set to `/gnu/store/drxhpk02mipa2c32hsyabzjhvbg9dhsl-r-biocgenerics-0.40.0/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/include:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/include:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/include:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/include:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/include:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/include:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/include:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/include:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/include:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/include:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/include:/gnu/store/l8kxrs01lll3pzjrd590p45l8k045q6q-make-4.3/include:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/include:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include/c++:/gnu/store/vakvgvrb839igv16jkif4lmx11d25jqb-gcc-10.3.0/include:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/include:/gnu/store/99a2njzz22dkzd8pz75fsi5nbgv9ww0x-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to `/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib:/gnu/store/w6zv2mz56wyxr471q38a3cmzm4iqimy8-bzip2-1.0.8/lib:/gnu/store/72kpdqplq4nc87fm7ch47kxy3nlkzsyx-xz-5.2.5/lib:/gnu/store/jazwfsj2v41yih2yzw5nydqgdz1hgfm4-file-5.39/lib:/gnu/store/v45pjc1yqmy59j9ff913p3ywn9qk4lqx-gawk-5.1.0/lib:/gnu/store/6mqcv52gwn2dnbislgv9k99525mzmrrs-binutils-2.37/lib:/gnu/store/2fk1gz2s7ppdicynscra9b19byrrr866-glibc-2.33/lib:/gnu/store/3ywv7s8d38rgcq7ljmc1s084358a2m3h-glibc-2.33-static/lib:/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/0brdikxqk59hdr47qabcm3sya001d8vf-glibc-utf8-locales-2.33/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' Biobase/DESCRIPTION Biobase/NAMESPACE Biobase/NEWS Biobase/R/ Biobase/R/AllGenerics.R Biobase/R/DataClasses.R Biobase/R/VersionedClasses.R Biobase/R/VersionsClass.R Biobase/R/anyMissing.R Biobase/R/environment.R Biobase/R/methods-AnnotatedDataFrame.R Biobase/R/methods-AssayData.R Biobase/R/methods-ExpressionSet.R Biobase/R/methods-MIAME.R Biobase/R/methods-MIAxE.R Biobase/R/methods-MultiSet.R Biobase/R/methods-NChannelSet.R Biobase/R/methods-ScalarObject.R Biobase/R/methods-SnpSet.R Biobase/R/methods-VersionedClass.R Biobase/R/methods-VersionsNull.R Biobase/R/methods-aggregator.R Biobase/R/methods-container.R Biobase/R/methods-eSet.R Biobase/R/packages.R Biobase/R/rowOp-methods.R Biobase/R/strings.R Biobase/R/tools.R Biobase/R/updateObjectTo.R Biobase/R/vignettes.R Biobase/R/zzz.R Biobase/README.md Biobase/build/ Biobase/build/vignette.rds Biobase/data/ Biobase/data/SW.rda Biobase/data/aaMap.R Biobase/data/geneCov.R Biobase/data/geneCovariate.rda Biobase/data/geneData.R Biobase/data/reporter.rda Biobase/data/sample.ExpressionSet.rda Biobase/data/sample.MultiSet.rda Biobase/data/seD.rda Biobase/inst/ Biobase/inst/CITATION Biobase/inst/Code/ Biobase/inst/Code/DESCRIPTION Biobase/inst/Code/R/ Biobase/inst/Code/R/get@PKGNAME@.R Biobase/inst/Code/man/ Biobase/inst/Code/man/@PKGNAME@.Rd Biobase/inst/Code/man/get@PKGNAME@.Rd Biobase/inst/ExpressionSet/ Biobase/inst/ExpressionSet/DESCRIPTION Biobase/inst/ExpressionSet/man/ Biobase/inst/ExpressionSet/man/@PKGNAME@.Rd Biobase/inst/doc/ Biobase/inst/doc/BiobaseDevelopment.R Biobase/inst/doc/BiobaseDevelopment.Rnw Biobase/inst/doc/BiobaseDevelopment.pdf Biobase/inst/doc/ExpressionSetIntroduction.R Biobase/inst/doc/ExpressionSetIntroduction.Rnw Biobase/inst/doc/ExpressionSetIntroduction.pdf Biobase/inst/doc/esApply.R Biobase/inst/doc/esApply.Rnw Biobase/inst/doc/esApply.pdf Biobase/inst/extdata/ Biobase/inst/extdata/exprsData.txt Biobase/inst/extdata/pData.txt Biobase/inst/scripts/ Biobase/inst/scripts/esetTesting.R Biobase/inst/scripts/getBioC.R Biobase/inst/scripts/getBioCHelp Biobase/inst/scripts/getBioCPkgNames.R Biobase/inst/scripts/makeExpressionSetPackage.R Biobase/inst/scripts/query.packages.R Biobase/inst/testClass.R Biobase/inst/unitTests/ Biobase/inst/unitTests/VersionedClass_data/ Biobase/inst/unitTests/VersionedClass_data/1.8/ Biobase/inst/unitTests/VersionedClass_data/1.8/AnnotatedDataFrame.Rda Biobase/inst/unitTests/VersionedClass_data/1.8/ExpressionSet.Rda Biobase/inst/unitTests/VersionedClass_data/1.8/MIAME.Rda Biobase/inst/unitTests/VersionedClass_data/1.8/exprSet.Rda Biobase/inst/unitTests/VersionedClass_data/1.8/phenoData.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/ Biobase/inst/unitTests/VersionedClass_data/2.0/AnnotatedDataFrame.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/ExpressionSet.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/MIAME.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/MultiSet.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/ScalarCharacter.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/SnpSet.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/Versioned.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/VersionedBiobase.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/Versions.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/VersionsNull.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/aggregator.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/container.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/exprSet.Rda Biobase/inst/unitTests/VersionedClass_data/2.0/phenoData.Rda Biobase/inst/unitTests/VersionedClass_data/devel/ Biobase/inst/unitTests/VersionedClass_data/devel/AnnotatedDataFrame.Rda Biobase/inst/unitTests/VersionedClass_data/devel/ExpressionSet.Rda Biobase/inst/unitTests/VersionedClass_data/devel/MIAME.Rda Biobase/inst/unitTests/VersionedClass_data/devel/MultiSet.Rda Biobase/inst/unitTests/VersionedClass_data/devel/NChannelSet.Rda Biobase/inst/unitTests/VersionedClass_data/devel/SWPD.rda Biobase/inst/unitTests/VersionedClass_data/devel/ScalarCharacter.Rda Biobase/inst/unitTests/VersionedClass_data/devel/ScalarInteger.Rda Biobase/inst/unitTests/VersionedClass_data/devel/ScalarLogical.Rda Biobase/inst/unitTests/VersionedClass_data/devel/ScalarNumeric.Rda Biobase/inst/unitTests/VersionedClass_data/devel/SnpSet.Rda Biobase/inst/unitTests/VersionedClass_data/devel/Versioned.Rda Biobase/inst/unitTests/VersionedClass_data/devel/VersionedBiobase.Rda Biobase/inst/unitTests/VersionedClass_data/devel/Versions.Rda Biobase/inst/unitTests/VersionedClass_data/devel/VersionsNull.Rda Biobase/inst/unitTests/VersionedClass_data/devel/aggregator.Rda Biobase/inst/unitTests/VersionedClass_data/devel/bbsym.rda Biobase/inst/unitTests/VersionedClass_data/devel/container.Rda Biobase/inst/unitTests/VersionedClass_data/devel/eset.rda Biobase/inst/unitTests/VersionedClass_data/devel/exprSet.Rda Biobase/inst/unitTests/VersionedClass_data/devel/golubMergeSub.rda Biobase/inst/unitTests/VersionedClass_data/devel/sample.eSet.rda Biobase/inst/unitTests/VersionedClass_data/devel/sample.exprSet.1.rda Biobase/inst/unitTests/VersionedClass_data/devel/sample.exprSet.rda Biobase/inst/unitTests/VersionedClass_data/devel/swrep.rda Biobase/inst/unitTests/VersionedClass_data/raw/ Biobase/inst/unitTests/VersionedClass_data/raw/exprs.tab Biobase/inst/unitTests/VersionedClass_data/raw/pData.tab Biobase/inst/unitTests/VersionedClass_data/raw/varMetadata.tab Biobase/inst/unitTests/test_AnnotatedDataFrame.R Biobase/inst/unitTests/test_AssayData.R Biobase/inst/unitTests/test_DataClasses.R Biobase/inst/unitTests/test_EsetSubclasses.R Biobase/inst/unitTests/test_ExpressionSet.R Biobase/inst/unitTests/test_NChannelSet.R Biobase/inst/unitTests/test_SnpSet.R Biobase/inst/unitTests/test_UpdateObject.R Biobase/inst/unitTests/test_VersionedClass.R Biobase/inst/unitTests/test_cache.R Biobase/inst/unitTests/test_checkClass.R Biobase/inst/unitTests/test_combine.R Biobase/inst/unitTests/test_copyEnv.R Biobase/inst/unitTests/test_esApply.R Biobase/inst/unitTests/test_subListExtract.R Biobase/inst/unitTests/test_unsaveSetSlot.R Biobase/inst/unitTests/utilities.R Biobase/man/ Biobase/man/Aggregate.Rd Biobase/man/Biobase-package.Rd Biobase/man/ScalarObject-class.Rd Biobase/man/abstract.Rd Biobase/man/addVig2Menu.Rd Biobase/man/annotatedDataFrameFrom-methods.Rd Biobase/man/anyMissing.Rd Biobase/man/assayData.Rd Biobase/man/cache.Rd Biobase/man/channel.Rd Biobase/man/channelNames.Rd Biobase/man/class.AnnotatedDataFrame.Rd Biobase/man/class.AssayData.Rd Biobase/man/class.ExpressionSet.Rd Biobase/man/class.MIAME.Rd Biobase/man/class.MIAxE.Rd Biobase/man/class.MultiSet.Rd Biobase/man/class.NChannelSet.Rd Biobase/man/class.SnpSet.Rd Biobase/man/class.Versioned.Rd Biobase/man/class.VersionedBiobase.Rd Biobase/man/class.Versions.Rd Biobase/man/class.VersionsNull.Rd Biobase/man/class.aggregator.Rd Biobase/man/class.characterORmiame.Rd Biobase/man/class.container.Rd Biobase/man/class.eSet.Rd Biobase/man/classVersion.Rd Biobase/man/contents.Rd Biobase/man/copyEnv.Rd Biobase/man/copySubstitute.Rd Biobase/man/createPackage.Rd Biobase/man/data.aaMap.Rd Biobase/man/data.geneData.Rd Biobase/man/data.reporter.Rd Biobase/man/data.sample.ExpressionSet.Rd Biobase/man/data.sample.MultiSet.Rd Biobase/man/defunct.Rd Biobase/man/description.Rd Biobase/man/dumpPackTxt.Rd Biobase/man/esApply.Rd Biobase/man/exprs.Rd Biobase/man/featureData.Rd Biobase/man/featureNames.Rd Biobase/man/getPkgVigs.Rd Biobase/man/internals.Rd Biobase/man/isCurrent.Rd Biobase/man/isUnique.Rd Biobase/man/isVersioned.Rd Biobase/man/lcSuffix.Rd Biobase/man/listLen.Rd Biobase/man/makeDataPackage.Rd Biobase/man/matchpt.Rd Biobase/man/multiassign.Rd Biobase/man/note.Rd Biobase/man/notes.Rd Biobase/man/openPDF.Rd Biobase/man/openVignette.Rd Biobase/man/package.version.Rd Biobase/man/phenoData.Rd Biobase/man/protocolData.Rd Biobase/man/read.AnnotatedDataFrame.Rd Biobase/man/read.MIAME.Rd Biobase/man/readExpressionSet.Rd Biobase/man/reverseSplit.Rd Biobase/man/rowMedians.Rd Biobase/man/rowQ.Rd Biobase/man/selectChannels.Rd Biobase/man/selectSome.Rd Biobase/man/snpCall.Rd Biobase/man/storageMode.Rd Biobase/man/strbreak.Rd Biobase/man/subListExtract.Rd Biobase/man/testBioCConnection.Rd Biobase/man/updateObjectTo.Rd Biobase/man/updateOldESet.Rd Biobase/man/userQuery.Rd Biobase/man/validMsg.Rd Biobase/src/ Biobase/src/Rinit.c Biobase/src/anyMissing.c Biobase/src/envir.c Biobase/src/matchpt.c Biobase/src/rowMedians.c Biobase/src/rowMedians_TYPE-template.h Biobase/src/sublist_extract.c Biobase/src/templates-types.h Biobase/src/templates-types_undef.h Biobase/tests/ Biobase/tests/test-all.R Biobase/tests/test-rowMedians.R Biobase/vignettes/ Biobase/vignettes/BiobaseDevelopment.Rnw Biobase/vignettes/ExpressionSetIntroduction.Rnw Biobase/vignettes/esApply.Rnw Biobase/vignettes/legacy/ Biobase/vignettes/legacy/Biobase.Rnw Biobase/vignettes/legacy/Bioconductor.Rnw Biobase/vignettes/legacy/HowTo.Rnw Biobase/vignettes/legacy/Qviews.Rnw phase `unpack' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' * installing *source* package ‘Biobase’ ... ** using staged installation ** libs gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rinit.c -o Rinit.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c envir.c -o envir.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c matchpt.c -o matchpt.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c rowMedians.c -o rowMedians.o gcc -I"/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sublist_extract.c -o sublist_extract.o gcc -shared -L/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/gnu/store/ild13b0r1cfalbd766q1633bgjgm623i-r-minimal-4.1.2/lib/R/lib -lR installing to /gnu/store/i1g97zfp0k5sqd5c9j76iycg0a9h69hg-r-biobase-2.54.0/site-library/00LOCK-Biobase/00new/Biobase/libs ** R ** data ** inst ** tests ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (Biobase) phase `install' succeeded after 13.0 seconds starting phase `check' Testing examples for package ‘Biobase’ Running specific tests for package ‘Biobase’ Running ‘test-all.R’ phase `check' succeeded after 6.4 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 0 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