printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioconductor-xcms-r30 2>&1 The package 'bioconductor-xcms-r30' will be built without being installed. Reading build dependency for bioconductor-xcms-r30-1.30.3-100... Reading dependency for bioconductor-xcms-r30-1.30.3-100... Reading build conflict for bioconductor-xcms-r30-1.30.3-100... The package 'r-base30-dev' will be installed. Reading dependency for r-base30-dev-3.0.3-8... Reading runtime dependency for r-base30-dev-3.0.3-8... The package 'libgettext8-dev' will be installed. Reading dependency for libgettext8-dev-0.18.3.1-2... Reading runtime dependency for libgettext8-dev-0.18.3.1-2... The package 'netcdf-c7' will be installed. Reading dependency for netcdf-c7-4.3.2-2... Reading runtime dependency for netcdf-c7-4.3.2-2... The package 'r-base30' will be installed. Reading dependency for r-base30-3.0.3-8... Reading runtime dependency for r-base30-3.0.3-8... The package 'netcdf-c7-shlibs' will be installed. Reading dependency for netcdf-c7-shlibs-4.3.2-2... Reading runtime dependency for netcdf-c7-shlibs-4.3.2-2... The package 'r-base30-shlibs' will be installed. Reading dependency for r-base30-shlibs-3.0.3-8... Reading runtime dependency for r-base30-shlibs-3.0.3-8... The package 'gettext-bin' will be installed. Reading dependency for gettext-bin-0.18.3.1-2... Reading runtime dependency for gettext-bin-0.18.3.1-2... The package 'netcdf-bin' will be installed. Reading dependency for netcdf-bin-4.3.2-2... Reading runtime dependency for netcdf-bin-4.3.2-2... The package 'flag-sort' will be installed. Reading dependency for flag-sort-0.5-1... Reading runtime dependency for flag-sort-0.5-1... The package 'hdf5.8-shlibs' will be installed. Reading dependency for hdf5.8-shlibs-1.8.13-1... Reading runtime dependency for hdf5.8-shlibs-1.8.13-1... The package 'libcurl4-shlibs' will be installed. Reading dependency for libcurl4-shlibs-7.37.1-1+10.8... Reading runtime dependency for libcurl4-shlibs-7.37.1-1+10.8... The package 'cairo-shlibs' will be installed. Reading dependency for cairo-shlibs-1.12.14-1... Reading runtime dependency for cairo-shlibs-1.12.14-1... The package 'gcc49-shlibs' will be installed. Reading dependency for gcc49-shlibs-4.9.1-1000... Reading runtime dependency for gcc49-shlibs-4.9.1-1000... The package 'glib2-shlibs' will be installed. Reading dependency for glib2-shlibs-2.22.4-8... Reading runtime dependency for glib2-shlibs-2.22.4-8... The package 'libicu48-shlibs' will be installed. Reading dependency for libicu48-shlibs-4.8.1.1-2... Reading runtime dependency for libicu48-shlibs-4.8.1.1-2... The package 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... The package 'liblzma5-shlibs' will be installed. Reading dependency for liblzma5-shlibs-5.0.5-2... Reading runtime dependency for liblzma5-shlibs-5.0.5-2... The package 'libpng16-shlibs' will be installed. Reading dependency for libpng16-shlibs-1.6.12-1... Reading runtime dependency for libpng16-shlibs-1.6.12-1... The package 'libtiff5-shlibs' will be installed. Reading dependency for libtiff5-shlibs-4.0.3-5... Reading runtime dependency for libtiff5-shlibs-4.0.3-5... The package 'pango1-xft2-ft219-shlibs' will be installed. Reading dependency for pango1-xft2-ft219-shlibs-1.24.5-9... Reading runtime dependency for pango1-xft2-ft219-shlibs-1.24.5-9... The package 'libpcre1-shlibs' will be installed. Reading dependency for libpcre1-shlibs-8.35-1... Reading runtime dependency for libpcre1-shlibs-8.35-1... The package 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... The package 'tcltk' will be installed. Reading dependency for tcltk-8.6.1-104... Reading runtime dependency for tcltk-8.6.1-104... The package 'szip-shlibs' will be installed. Reading dependency for szip-shlibs-2.1-3... Reading runtime dependency for szip-shlibs-2.1-3... The package 'librtmp-shlibs' will be installed. Reading dependency for librtmp-shlibs-2.3-4... Reading runtime dependency for librtmp-shlibs-2.3-4... The package 'libssh2.1-shlibs' will be installed. Reading dependency for libssh2.1-shlibs-1.4.3-1... Reading runtime dependency for libssh2.1-shlibs-1.4.3-1... The package 'fontconfig2-shlibs' will be installed. Reading dependency for fontconfig2-shlibs-2.10.2-1... Reading runtime dependency for fontconfig2-shlibs-2.10.2-1... The package 'freetype219-shlibs' will be installed. Reading dependency for freetype219-shlibs-2.4.12-1... Reading runtime dependency for freetype219-shlibs-2.4.12-1... The package 'pixman-shlibs' will be installed. Reading dependency for pixman-shlibs-0.32.4-1... Reading runtime dependency for pixman-shlibs-0.32.4-1... The package 'xdg-base' will be installed. Reading dependency for xdg-base-0.8-2... Reading runtime dependency for xdg-base-0.8-2... The package 'libjbig-shlibs' will be installed. Reading dependency for libjbig-shlibs-2.0-1... Reading runtime dependency for libjbig-shlibs-2.0-1... The package 'libthai-shlibs' will be installed. Reading dependency for libthai-shlibs-0.1.20-1... Reading runtime dependency for libthai-shlibs-0.1.20-1... The package 'xft2-shlibs' will be installed. Reading dependency for xft2-shlibs-2.2.0-3... Reading runtime dependency for xft2-shlibs-2.2.0-3... The package 'tcltk-shlibs' will be installed. Reading dependency for tcltk-shlibs-8.6.1-104... Reading runtime dependency for tcltk-shlibs-8.6.1-104... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The package 'fontconfig-config' will be installed. Reading dependency for fontconfig-config-2.10.2-1... Reading runtime dependency for fontconfig-config-2.10.2-1... The package 'expat1-shlibs' will be installed. Reading dependency for expat1-shlibs-2.1.0-1... Reading runtime dependency for expat1-shlibs-2.1.0-1... The package 'libdatrie1-shlibs' will be installed. Reading dependency for libdatrie1-shlibs-0.2.8-2... Reading runtime dependency for libdatrie1-shlibs-0.2.8-2... The package 'libthai' will be installed. Reading dependency for libthai-0.1.20-1... Reading runtime dependency for libthai-0.1.20-1... The following package will be rebuilt: bioconductor-xcms-r30 The following 39 additional packages will be installed: cairo-shlibs expat1-shlibs flag-sort fontconfig-config fontconfig2-shlibs freetype219-shlibs gcc49-shlibs gettext-bin glib2-shlibs hdf5.8-shlibs libcurl4-shlibs libdatrie1-shlibs libgettext8-dev libicu48-shlibs libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libpcre1-shlibs libpng16-shlibs librtmp-shlibs libssh2.1-shlibs libthai libthai-shlibs libtiff5-shlibs netcdf-bin netcdf-c7 netcdf-c7-shlibs openssl100-shlibs pango1-xft2-ft219-shlibs pixman-shlibs r-base30 r-base30-dev r-base30-shlibs readline6-shlibs szip-shlibs tcltk tcltk-shlibs xdg-base xft2-shlibs Do you want to continue? [Y/n] (assuming default) Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/expat1-shlibs_2.1.0-1_darwin-x86_64.deb Selecting previously deselected package expat1-shlibs. 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Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb Selecting previously deselected package gcc49-shlibs. (Reading database ... 4757 files and directories currently installed.) Unpacking gcc49-shlibs (from .../gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb) ... Setting up gcc49-shlibs (4.9.1-1000) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libdatrie1-shlibs_0.2.8-2_darwin-x86_64.deb Selecting previously deselected package libdatrie1-shlibs. (Reading database ... 4802 files and directories currently installed.) Unpacking libdatrie1-shlibs (from .../libdatrie1-shlibs_0.2.8-2_darwin-x86_64.deb) ... Setting up libdatrie1-shlibs (0.2.8-2) ... Reading buildlock packages... 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All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/gnome/pango1-xft2-ft219-shlibs_1.24.5-9_darwin-x86_64.deb Selecting previously deselected package pango1-xft2-ft219-shlibs. (Reading database ... 5441 files and directories currently installed.) Unpacking pango1-xft2-ft219-shlibs (from .../pango1-xft2-ft219-shlibs_1.24.5-9_darwin-x86_64.deb) ... Setting up pango1-xft2-ft219-shlibs (1.24.5-9) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/tcltk_8.6.1-104_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/tcltk-shlibs_8.6.1-104_darwin-x86_64.deb Selecting previously deselected package tcltk. (Reading database ... 5485 files and directories currently installed.) Unpacking tcltk (from .../tcltk_8.6.1-104_darwin-x86_64.deb) ... Selecting previously deselected package tcltk-shlibs. Unpacking tcltk-shlibs (from .../tcltk-shlibs_8.6.1-104_darwin-x86_64.deb) ... Setting up tcltk-shlibs (8.6.1-104) ... Setting up tcltk (8.6.1-104) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/r-base30_3.0.3-8_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base30-shlibs_3.0.3-8_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base30-dev_3.0.3-8_darwin-x86_64.deb Selecting previously deselected package r-base30. (Reading database ... 5960 files and directories currently installed.) Unpacking r-base30 (from .../r-base30_3.0.3-8_darwin-x86_64.deb) ... Selecting previously deselected package r-base30-shlibs. Unpacking r-base30-shlibs (from .../r-base30-shlibs_3.0.3-8_darwin-x86_64.deb) ... Selecting previously deselected package r-base30-dev. Unpacking r-base30-dev (from .../r-base30-dev_3.0.3-8_darwin-x86_64.deb) ... Setting up r-base30-shlibs (3.0.3-8) ... Setting up r-base30-dev (3.0.3-8) ... Setting up r-base30 (3.0.3-8) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioconductor-xcms-r30-1.30.3-100 /sw/build.build dpkg-deb: building package `fink-buildlock-bioconductor-xcms-r30-1.30.3-100' in `/sw/build.build/fink-buildlock-bioconductor-xcms-r30-1.30.3-100_2014.08.07-01.33.13_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioconductor-xcms-r30-1.30.3-100_2014.08.07-01.33.13_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioconductor-xcms-r30-1.30.3-100. (Reading database ... 7940 files and directories currently installed.) Unpacking fink-buildlock-bioconductor-xcms-r30-1.30.3-100 (from .../fink-buildlock-bioconductor-xcms-r30-1.30.3-100_2014.08.07-01.33.13_darwin-x86_64.deb) ... Setting up fink-buildlock-bioconductor-xcms-r30-1.30.3-100 (2014.08.07-01.33.13) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.kutZ6 env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/xcms_1.30.3.tar.gz xcms/ xcms/src/ xcms/src/fastMatch.c xcms/src/mzROI.c xcms/src/obiwarp/ xcms/src/obiwarp/xcms_obiwarp.cpp xcms/src/obiwarp/mat.cpp xcms/src/obiwarp/vec.h xcms/src/obiwarp/xcms_lmat.cpp xcms/src/obiwarp/mat.h xcms/src/obiwarp/xcms_dynprog.cpp xcms/src/obiwarp/lmat.h xcms/src/obiwarp/xcms_dynprog.h xcms/src/obiwarp/vec.cpp xcms/src/netCDF.h xcms/src/netCDF.c xcms/src/ramp_base64.cpp xcms/src/binarySearch.h xcms/src/mzClust_hclust.c xcms/src/ramp.cpp xcms/src/Makevars xcms/src/rampR.cpp xcms/src/xcms.c xcms/src/ramp.h xcms/src/ramp_base64.h xcms/src/Makevars.win xcms/src/win/ xcms/src/win/x64/ xcms/src/win/x64/zlib.h xcms/src/win/x64/netcdf.h xcms/src/win/x64/libz.a xcms/src/win/x64/libnetcdf.a xcms/src/win/x64/zconf.h xcms/src/win/i386/ xcms/src/win/i386/zlib.h xcms/src/win/i386/netcdf.h xcms/src/win/i386/libz.a xcms/src/win/i386/libnetcdf.a xcms/src/win/i386/zconf.h xcms/src/xcms.h xcms/src/util.h xcms/src/massifquant/ xcms/src/massifquant/Tracker.h xcms/src/massifquant/OpOverload.h xcms/src/massifquant/dpq.h xcms/src/massifquant/SegProc.cpp xcms/src/massifquant/DataKeeper.h xcms/src/massifquant/OpOverload.cpp xcms/src/massifquant/TrMgr.cpp xcms/src/massifquant/Tracker.cpp xcms/src/massifquant/SegProc.h xcms/src/massifquant/xcms_massifquant.cpp xcms/src/massifquant/DataKeeper.cpp xcms/src/massifquant/TrMgr.h xcms/src/massifquant/nmath.h xcms/src/util.c xcms/DESCRIPTION xcms/.gitignore xcms/LICENSE xcms/NAMESPACE xcms/man/ xcms/man/xcmsPeaks-class.Rd xcms/man/specDist.cosine-methods.Rd xcms/man/findPeaks.centWave-methods.Rd xcms/man/specNoise.Rd xcms/man/split.xcmsSet.Rd xcms/man/split.xcmsRaw.Rd xcms/man/xcmsRaw.Rd xcms/man/sampnames-methods.Rd xcms/man/plotEIC-methods.Rd xcms/man/profStep-methods.Rd xcms/man/retcor.obiwarp-methods.Rd xcms/man/absent-methods.Rd xcms/man/getEIC-methods.Rd xcms/man/profMethod-methods.Rd xcms/man/plotChrom-methods.Rd xcms/man/SSgauss.Rd xcms/man/getScan-methods.Rd xcms/man/profMedFilt-methods.Rd xcms/man/profRange-methods.Rd xcms/man/doubleMatrix.Rd xcms/man/getPeaks-methods.Rd xcms/man/fillPeaks.chrom-methods.Rd xcms/man/xcmsSet-class.Rd xcms/man/findEqualGreater.Rd xcms/man/na.flatfill.Rd xcms/man/specPeaks.Rd xcms/man/retexp.Rd xcms/man/plotSpec-methods.Rd xcms/man/group-methods.Rd xcms/man/group.nearest.Rd xcms/man/AutoLockMass-methods.Rd xcms/man/collect-methods.Rd xcms/man/retcor.peakgroups-methods.Rd xcms/man/findPeaks.massifquant-methods.Rd xcms/man/stitch-methods.Rd xcms/man/specDist.peakCount-methods.Rd xcms/man/findPeaks.matchedFilter-methods.Rd xcms/man/plotSurf-methods.Rd xcms/man/profGenerate.Rd xcms/man/getSpec-methods.Rd xcms/man/xcmsFragments.Rd xcms/man/peakTable-methods.Rd xcms/man/rawEIC-methods.Rd xcms/man/fillPeaks.MSW-methods.Rd xcms/man/specDist-methods.Rd xcms/man/xcmsFragments-class.Rd xcms/man/findPeaks.MS1-methods.Rd xcms/man/write.mzdata-methods.Rd xcms/man/write.cdf-methods.Rd xcms/man/specDist.meanMZmatch-methods.Rd xcms/man/netCDF.Rd xcms/man/medianFilter.Rd xcms/man/group.mzClust.Rd xcms/man/plotPeaks-methods.Rd xcms/man/retcor-methods.Rd xcms/man/colMax.Rd xcms/man/plotScan-methods.Rd xcms/man/panel.cor.Rd xcms/man/findPeaks.MSW-methods.Rd xcms/man/findPeaks-methods.Rd xcms/man/groupval-methods.Rd xcms/man/c.xcmsSet.Rd xcms/man/plot.xcmsEIC.Rd xcms/man/xcmsSet.Rd xcms/man/xcmsEIC-class.Rd xcms/man/etg.Rd xcms/man/plotTIC-methods.Rd xcms/man/xcmsPapply.Rd xcms/man/fillPeaks-methods.Rd xcms/man/pval.Rd xcms/man/descendZero.Rd xcms/man/rawMat-methods.Rd xcms/man/filtfft.Rd xcms/man/findneutral.Rd xcms/man/ramp.Rd xcms/man/rectUnique.Rd xcms/man/plotrt-methods.Rd xcms/man/groupnames-methods.Rd xcms/man/xcmsRaw-class.Rd xcms/man/image.xcmsRaw.Rd xcms/man/peakPlots-methods.Rd xcms/man/findMZ.Rd xcms/man/group.density.Rd xcms/man/calibrate.Rd xcms/man/plotRaw-methods.Rd xcms/man/diffreport-methods.Rd xcms/inst/ xcms/inst/NEWS xcms/inst/unitTests/ xcms/inst/unitTests/runit.splitCombine.R xcms/inst/unitTests/runit.findPeaksCentWave.fitGauss.plot.R xcms/inst/unitTests/runit.specDist.R xcms/inst/unitTests/runit.snames.R xcms/inst/unitTests/runit.rawMat.R xcms/inst/unitTests/runit.fillPeaks.R xcms/inst/unitTests/runit.writemzdata.R xcms/inst/unitTests/runit.absentPresent.R xcms/inst/unitTests/runit.getEIC.R xcms/inst/unitTests/runit.xcmsRawCopy.R xcms/inst/unitTests/runit.msms.R xcms/inst/unitTests/runit.ramp.R xcms/inst/unitTests/runit.phenoData.R xcms/inst/unitTests/runit.splitRaw.R xcms/inst/unitTests/runit.obiwarp.R xcms/inst/unitTests/runit.diffreport.R xcms/inst/unitTests/runit.unusedGroups.R xcms/inst/doc/ xcms/inst/doc/xcmsMSn.pdf xcms/inst/doc/xcmsDirect.pdf xcms/inst/doc/FlowChart.pdf xcms/inst/doc/xcms.bib xcms/inst/doc/xcmsMSn.Rnw xcms/inst/doc/FlowChart.graffle xcms/inst/doc/xcmsInstall.Rnw xcms/inst/doc/xcmsPreprocess.Rnw xcms/inst/doc/xcmsDirect.Rnw xcms/inst/doc/xcmsInstall.pdf xcms/inst/doc/xcmsPreprocess.pdf xcms/inst/CITATION xcms/checkoutpwiz.sh xcms/R/ xcms/R/00xcmsFragments-class.R xcms/R/models.R xcms/R/cwTools.R xcms/R/matchpeaks.R xcms/R/ramp.R xcms/R/00xcmsRaw-class.R xcms/R/init.R xcms/R/xcmsEIC.R xcms/R/unix/ xcms/R/unix/zzz.R xcms/R/00xcmsEIC-class.R xcms/R/present.R xcms/R/specDist.R xcms/R/databases.R xcms/R/xcmsFragments.R xcms/R/c.R xcms/R/mzClust.R xcms/R/MPI.R xcms/R/netCDF.R xcms/R/00xcmsSet-class.R xcms/R/fastMatch.R xcms/R/CleanData.R xcms/R/xcmsSet.R xcms/R/windows/ xcms/R/windows/zzz.R xcms/R/xcmsRaw.R xcms/R/writemzdata.R xcms/CHANGELOG xcms/tests/ xcms/tests/doRUnit.R sudo -u fink-bld [ENV] sh -c /tmp/fink.8uzLW /tmp/fink.Kcx4f #!/bin/bash -ev export TMPDIR=/sw/build.build/bioconductor-xcms-r30-1.30.3-100/xcms/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R pushd .. /sw/build.build/bioconductor-xcms-r30-1.30.3-100 /sw/build.build/bioconductor-xcms-r30-1.30.3-100/xcms $BIN_R --verbose CMD build --no-build-vignettes xcms * checking for file 'xcms/DESCRIPTION' ... OK * preparing 'xcms': * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'xcms_1.30.3.tar.gz' /bin/rm -rf /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100 /bin/mkdir -p /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw /bin/mkdir -p /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100 sudo -u fink-bld [ENV] sh -c /tmp/fink.fpA19 /tmp/fink.Ayfjn #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R mkdir -p /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/lib/R/3.0/site-library pushd /sw/build.build/bioconductor-xcms-r30-1.30.3-100/xcms/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/lib/R/3.0/site-library xcms /sw/build.build/bioconductor-xcms-r30-1.30.3-100 /sw/build.build/bioconductor-xcms-r30-1.30.3-100/xcms * installing *source* package 'xcms' ... ** libs rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c massifquant/Tracker.cpp -o massifquant/Tracker.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c massifquant/SegProc.cpp -o massifquant/SegProc.o massifquant/SegProc.cpp:358:19: warning: conversion from string literal to 'char *' is deprecated [-Wdeprecated-writable-strings] if (n <= 0.0) ML_ERR_return_NAN; ^ massifquant/nmath.h:117:29: note: expanded from macro 'ML_ERR_return_NAN' #define ML_ERR_return_NAN { ML_ERROR(ME_DOMAIN, ""); return ML_NAN; } ^ massifquant/nmath.h:125:21: note: expanded from macro 'ML_ERROR' char *msg = ""; \ ^ 1 warning generated. flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c obiwarp/mat.cpp -o obiwarp/mat.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c obiwarp/vec.cpp -o obiwarp/vec.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c obiwarp/xcms_obiwarp.cpp -o obiwarp/xcms_obiwarp.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c fastMatch.c -o fastMatch.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c mzClust_hclust.c -o mzClust_hclust.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c mzROI.c -o mzROI.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c netCDF.c -o netCDF.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c ramp_base64.cpp -o ramp_base64.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c ramp.cpp -o ramp.o ramp.cpp:1816:36: warning: expression which evaluates to zero treated as a null pointer constant of type 'const char *' [-Wnon-literal-null-conversion] pEndAttrValue = '\0'; ^~~~ ramp.cpp:1835:35: warning: expression which evaluates to zero treated as a null pointer constant of type 'const char *' [-Wnon-literal-null-conversion] pEndAttrValue = '\0'; ^~~~ 2 warnings generated. flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c rampR.cpp -o rampR.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c util.c -o util.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/usr/local/include -I/sw/include -D_LARGEFILE_SOURCE -I/sw/include -fPIC -g -O3 -c xcms.c -o xcms.o flag-sort -r g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o xcms.dylib massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o obiwarp/xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o netCDF.o ramp_base64.o ramp.o rampR.o util.o xcms.o -L/usr/local/lib -L/sw/lib -L/sw/lib -lnetcdf -lz -L/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/lib' installing to /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/lib/R/3.0/site-library/xcms/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes 'xcmsDirect.Rnw' 'xcmsInstall.Rnw' 'xcmsMSn.Rnw' 'xcmsPreprocess.Rnw' ** testing if installed package can be loaded * DONE (xcms) install_name_tool -id /sw/lib/R/3.0/site-library/xcms/libs/xcms.dylib /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/lib/R/3.0/site-library/xcms/libs/xcms.dylib sudo -u fink-bld [ENV] sh -c /tmp/fink.XO_pJ /bin/rm -f /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/info/dir /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/info/dir.old /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/sw/share/info/dir /sw/build.build/root-bioconductor-xcms-r30-1.30.3-100/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-xcms-r30-1.30.3-100 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `bioconductor-xcms-r30' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/bioconductor-xcms-r30_1.30.3-100_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioconductor-xcms-r30-1.30.3-100 (Reading database ... 7941 files and directories currently installed.) Removing fink-buildlock-bioconductor-xcms-r30-1.30.3-100 ...