printf '

' | fink --no-use-binary-dist --yes  --build-as-nobody rebuild bioconductor-biobase-r31 2>&1
WARNING: your info file index has not been updated for 22 days. You should
run 'fink selfupdate' to get the latest package descriptions.
The package 'bioconductor-biobase-r31' will be built without being installed.
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The following package will be rebuilt:
 bioconductor-biobase-r31
The following 30 additional packages will be installed:
 bioconductor-biocgenerics-r31 cairo-shlibs expat1-shlibs flag-sort
 fontconfig-config fontconfig2-shlibs freetype219-shlibs gettext-bin
 glib2-shlibs libdatrie1-shlibs libgettext8-dev libicu48-shlibs
 libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libpcre1-shlibs
 libpng16-shlibs libthai libthai-shlibs libtiff5-shlibs
 pango1-xft2-ft219-shlibs pixman-shlibs r-base31 r-base31-dev r-base31-shlibs
 readline6-shlibs tcltk tcltk-shlibs xdg-base xft2-shlibs
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env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner --no-same-permissions -xvf /sw/src/Biobase_2.24.0.tar.gz
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/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/sample.eSet.R
Biobase/data/sample.exprSet.1.R
Biobase/data/sample.exprSet.R
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/Bioconductor.R
Biobase/inst/doc/Bioconductor.Rnw
Biobase/inst/doc/Bioconductor.pdf
Biobase/inst/doc/ExpressionSetIntroduction.R
Biobase/inst/doc/ExpressionSetIntroduction.Rnw
Biobase/inst/doc/ExpressionSetIntroduction.pdf
Biobase/inst/doc/HowTo.R
Biobase/inst/doc/HowTo.Rnw
Biobase/inst/doc/HowTo.pdf
Biobase/inst/doc/Qviews.R
Biobase/inst/doc/Qviews.Rnw
Biobase/inst/doc/Qviews.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/dims.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/Bioconductor.Rnw
Biobase/vignettes/ExpressionSetIntroduction.Rnw
Biobase/vignettes/HowTo.Rnw
Biobase/vignettes/Qviews.Rnw
Biobase/vignettes/esApply.Rnw
Biobase/vignettes/legacy/
Biobase/vignettes/legacy/Biobase.Rnw
sudo -u fink-bld [ENV] sh -c /tmp/fink.Chijy
/tmp/fink.a7yct
#!/bin/bash -ev
  export TMPDIR=/sw/build.build/bioconductor-biobase-r31-2.24.0-1/Biobase/tmp
  BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
  
  pushd ..
/sw/build.build/bioconductor-biobase-r31-2.24.0-1 /sw/build.build/bioconductor-biobase-r31-2.24.0-1/Biobase
  $BIN_R --verbose CMD build --no-build-vignettes Biobase
* checking for file 'Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking vignette meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* re-saving .R files as .rda
  NB: *.R converted to .rda: other files may need to be removed
* building 'Biobase_2.24.0.tar.gz'

/bin/rm -rf /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1
/bin/mkdir -p /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw
/bin/mkdir -p /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1
sudo -u fink-bld [ENV] sh -c /tmp/fink.T0O8a
/tmp/fink.XeXZJ
#!/bin/sh -ev
  BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R
  
  mkdir -p /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/lib/R/3.1/site-library
  pushd /sw/build.build/bioconductor-biobase-r31-2.24.0-1/Biobase/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/lib/R/3.1/site-library Biobase
/sw/build.build/bioconductor-biobase-r31-2.24.0-1 /sw/build.build/bioconductor-biobase-r31-2.24.0-1/Biobase
* installing *source* package 'Biobase' ...
** libs
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c Rinit.c -o Rinit.o
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c anyMissing.c -o anyMissing.o
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c envir.c -o envir.o
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c matchpt.c -o matchpt.o
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c rowMedians.c -o rowMedians.o
flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG  -I/sw/include    -fPIC  -g -O3  -c sublist_extract.c -o sublist_extract.o
flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o Biobase.dylib Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation
installing to /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/lib/R/3.1/site-library/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biobase)
  install_name_tool -id /sw/lib/R/3.1/site-library/Biobase/libs/Biobase.dylib /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/lib/R/3.1/site-library/Biobase/libs/Biobase.dylib
sudo -u fink-bld [ENV] sh -c /tmp/fink.X1pUE
/bin/rm -f /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/info/dir /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/info/dir.old /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/share/info/dir /sw/build.build/root-bioconductor-biobase-r31-2.24.0-1/sw/share/info/dir.old
Reverting ownership of install dir to root
Writing control file...
Creating shlibs files...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-bioconductor-biobase-r31-2.24.0-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods
dpkg-deb: building package `bioconductor-biobase-r31' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/bioconductor-biobase-r31_2.24.0-1_darwin-x86_64.deb'.
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-bioconductor-biobase-r31-2.24.0-1
(Reading database ... 60965 files and directories currently installed.)
Removing fink-buildlock-bioconductor-biobase-r31-2.24.0-1 ...