printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild bioconductor-siggenes-r30 2>&1 The package 'bioconductor-siggenes-r30' will be built without being installed. Reading build dependency for bioconductor-siggenes-r30-1.38.0-1... Reading dependency for bioconductor-siggenes-r30-1.38.0-1... Reading build conflict for bioconductor-siggenes-r30-1.38.0-1... 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 '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 'bioconductor-biobase-r30' will be installed. Reading dependency for bioconductor-biobase-r30-2.22.0-1... Reading runtime dependency for bioconductor-biobase-r30-2.22.0-1... The package 'bioconductor-multtest-r30' will be installed. Reading dependency for bioconductor-multtest-r30-2.20.0-1... Reading runtime dependency for bioconductor-multtest-r30-2.20.0-1... 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 'flag-sort' will be installed. Reading dependency for flag-sort-0.5-1... Reading runtime dependency for flag-sort-0.5-1... The package 'bioconductor-biocgenerics-r30' will be installed. Reading dependency for bioconductor-biocgenerics-r30-0.10.0-1... Reading runtime dependency for bioconductor-biocgenerics-r30-0.10.0-1... The package 'cran-mass-r30' will be installed. Reading dependency for cran-mass-r30-7.3-32-2... Reading runtime dependency for cran-mass-r30-7.3-32-2... The package 'cran-survival-r30' will be installed. Reading dependency for cran-survival-r30-2.37-7-2... Reading runtime dependency for cran-survival-r30-2.37-7-2... 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 '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 '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-siggenes-r30 The following 33 additional packages will be installed: bioconductor-biobase-r30 bioconductor-biocgenerics-r30 bioconductor-multtest-r30 cairo-shlibs cran-mass-r30 cran-survival-r30 expat1-shlibs flag-sort fontconfig-config fontconfig2-shlibs freetype219-shlibs gcc49-shlibs glib2-shlibs libdatrie1-shlibs libicu48-shlibs libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libpcre1-shlibs libpng16-shlibs libthai libthai-shlibs libtiff5-shlibs pango1-xft2-ft219-shlibs pixman-shlibs r-base30 r-base30-dev r-base30-shlibs readline6-shlibs tcltk tcltk-shlibs xdg-base xft2-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/siggenes_1.38.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 7 589k 7 43197 0 0 97618 0 0:00:06 --:--:-- 0:00:06 97510 100 589k 100 589k 0 0 553k 0 0:00:01 0:00:01 --:--:-- 553k 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. (Reading database ... 4740 files and directories currently installed.) Unpacking expat1-shlibs (from .../expat1-shlibs_2.1.0-1_darwin-x86_64.deb) ... Setting up expat1-shlibs (2.1.0-1) ... Reading buildlock packages... 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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 ... 5286 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 ... 5762 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) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bioconductor-biocgenerics-r30_0.10.0-1_darwin-x86_64.deb Selecting previously deselected package bioconductor-biocgenerics-r30. (Reading database ... 7742 files and directories currently installed.) Unpacking bioconductor-biocgenerics-r30 (from .../bioconductor-biocgenerics-r30_0.10.0-1_darwin-x86_64.deb) ... Setting up bioconductor-biocgenerics-r30 (0.10.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/cran-mass-r30_7.3-32-2_darwin-x86_64.deb Selecting previously deselected package cran-mass-r30. (Reading database ... 7771 files and directories currently installed.) Unpacking cran-mass-r30 (from .../cran-mass-r30_7.3-32-2_darwin-x86_64.deb) ... Setting up cran-mass-r30 (7.3-32-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/cran-survival-r30_2.37-7-2_darwin-x86_64.deb Selecting previously deselected package cran-survival-r30. (Reading database ... 7836 files and directories currently installed.) Unpacking cran-survival-r30 (from .../cran-survival-r30_2.37-7-2_darwin-x86_64.deb) ... Setting up cran-survival-r30 (2.37-7-2) ... Reading buildlock packages... 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Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-bioconductor-siggenes-r30-1.38.0-1 /sw/build.build dpkg-deb: building package `fink-buildlock-bioconductor-siggenes-r30-1.38.0-1' in `/sw/build.build/fink-buildlock-bioconductor-siggenes-r30-1.38.0-1_2014.08.05-01.36.04_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-bioconductor-siggenes-r30-1.38.0-1_2014.08.05-01.36.04_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-bioconductor-siggenes-r30-1.38.0-1. (Reading database ... 8073 files and directories currently installed.) Unpacking fink-buildlock-bioconductor-siggenes-r30-1.38.0-1 (from .../fink-buildlock-bioconductor-siggenes-r30-1.38.0-1_2014.08.05-01.36.04_darwin-x86_64.deb) ... Setting up fink-buildlock-bioconductor-siggenes-r30-1.38.0-1 (2014.08.05-01.36.04) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.WX1ST env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/siggenes_1.38.0.tar.gz siggenes/DESCRIPTION siggenes/NAMESPACE siggenes/R/ siggenes/R/EBAM-class.R siggenes/R/FindA0-class.R siggenes/R/Rfold.cal.R siggenes/R/SAM-class.R siggenes/R/add.target2href.R siggenes/R/adjust.for.mt.R siggenes/R/args.ebam.R siggenes/R/args.finda0.R siggenes/R/args.sam.R siggenes/R/build.dperm.R siggenes/R/cat.ebam.R siggenes/R/cat.null.R siggenes/R/cat.null.approx.R siggenes/R/cat.null.approx2.R siggenes/R/cat.stat.R siggenes/R/check.chipname.R siggenes/R/checkA0.R siggenes/R/checkDBs.R siggenes/R/checkFUNout.R siggenes/R/checkInitialDelta.R siggenes/R/checkQuantiles.R siggenes/R/chisq.ebam.R siggenes/R/chisq.stat.R siggenes/R/chisqClass.R siggenes/R/chisqClassSplitted.R siggenes/R/col2hex.R siggenes/R/compFailure.R siggenes/R/compFailureMat2.R siggenes/R/compFailureSubset.R siggenes/R/compFalse.R siggenes/R/compNumber.R siggenes/R/compPermStat.R siggenes/R/compRatio.R siggenes/R/computeContCols.R siggenes/R/computeRS.R siggenes/R/d.null.R siggenes/R/d.stat.R siggenes/R/delta.plot.R siggenes/R/denspr.R siggenes/R/ebam.R siggenes/R/ebam2excel.R siggenes/R/ebam2html.R siggenes/R/ebamA0.R siggenes/R/find.a0.R siggenes/R/findDelta.R siggenes/R/findFDR.R siggenes/R/findNumber.R siggenes/R/finda02html.R siggenes/R/formatSAM.R siggenes/R/fudge2.R siggenes/R/fuzzy.ebam.R siggenes/R/fuzzy.stat.R siggenes/R/getFailure.R siggenes/R/getQuantiles.R siggenes/R/getSuccesses.R siggenes/R/getTD4Affy.R siggenes/R/getTD4rs.R siggenes/R/help.ebam.R siggenes/R/help.finda0.R siggenes/R/help.sam.R siggenes/R/limma2sam.R siggenes/R/link.genes.R siggenes/R/link.siggenes.R siggenes/R/list.siggenes.R siggenes/R/make.tablecode.R siggenes/R/makeA0mat.R siggenes/R/md.plot.R siggenes/R/na.handling.R siggenes/R/na.replace.cont.R siggenes/R/nclass.wand.R siggenes/R/pairt.cl.transform.R siggenes/R/pairt.samp.R siggenes/R/pairt.samp.transform.R siggenes/R/pi0.est.R siggenes/R/pi0.est2.R siggenes/R/pi0.est3.R siggenes/R/plotArguments.R siggenes/R/plotFindArguments.R siggenes/R/quantiles.R siggenes/R/qvalue.cal.R siggenes/R/recodeVal.R siggenes/R/rowRanksWilc.R siggenes/R/rowWilcoxon.R siggenes/R/sam.R siggenes/R/sam.plot2.R siggenes/R/sam2excel.R siggenes/R/sam2html.R siggenes/R/samControl.R siggenes/R/setup.mat.samp.R siggenes/R/siggenes2excel.R siggenes/R/siggenes2html.R siggenes/R/stats.cal.R siggenes/R/sumEBAM-class.R siggenes/R/sumSAM-class.R siggenes/R/trend.ebam.R siggenes/R/trend.stat.R siggenes/R/truncZ.R siggenes/R/wilc.ebam.R siggenes/R/wilc.stat.R siggenes/R/z.ebam.R siggenes/R/z.find.R siggenes/R/zzz.R siggenes/build/ siggenes/build/vignette.rds siggenes/inst/ siggenes/inst/doc/ siggenes/inst/doc/siggenes.R siggenes/inst/doc/siggenes.Rnw siggenes/inst/doc/siggenes.pdf siggenes/man/ siggenes/man/EBAM-class.Rd siggenes/man/FindA0-class.Rd siggenes/man/SAM-class.Rd siggenes/man/chisq.ebam.Rd siggenes/man/chisq.stat.Rd siggenes/man/d.stat.Rd siggenes/man/delta.plot.Rd siggenes/man/denspr.Rd siggenes/man/ebam.Rd siggenes/man/ebamControl.Rd siggenes/man/find.a0.Rd siggenes/man/findDelta.Rd siggenes/man/fudge2.Rd siggenes/man/fuzzy.ebam.Rd siggenes/man/help.ebam.Rd siggenes/man/help.finda0.Rd siggenes/man/help.sam.Rd siggenes/man/limma2sam.Rd siggenes/man/link.genes.Rd siggenes/man/link.siggenes.Rd siggenes/man/list.siggenes.Rd siggenes/man/md.plot.Rd siggenes/man/nclass.wand.Rd siggenes/man/pi0.est.Rd siggenes/man/plotArguments.Rd siggenes/man/plotFindArguments.Rd siggenes/man/qvalue.cal.Rd siggenes/man/rowWilcoxon.Rd siggenes/man/sam.Rd siggenes/man/sam.plot2.Rd siggenes/man/samControl.Rd siggenes/man/siggenes-internal.Rd siggenes/man/siggenes2excel.Rd siggenes/man/siggenes2html.Rd siggenes/man/sumSAM-class.Rd siggenes/man/trend.ebam.Rd siggenes/man/trend.stat.Rd siggenes/man/wilc.ebam.Rd siggenes/man/wilc.stat.Rd siggenes/man/z.ebam.Rd siggenes/vignettes/ siggenes/vignettes/ebamplot.eps siggenes/vignettes/ebamplot.png siggenes/vignettes/finda0.eps siggenes/vignettes/finda0.png siggenes/vignettes/identify.sam.html siggenes/vignettes/plot.ebam.html siggenes/vignettes/plot.finda0.html siggenes/vignettes/plot.sam.html siggenes/vignettes/print.ebam.html siggenes/vignettes/print.finda0.html siggenes/vignettes/print.sam.html siggenes/vignettes/samplot.png siggenes/vignettes/samplot.ps siggenes/vignettes/siggenes.Rnw siggenes/vignettes/siggenesRnews.pdf siggenes/vignettes/summary.ebam.html siggenes/vignettes/summary.sam.html sudo -u fink-bld [ENV] sh -c /tmp/fink.EHCA3 /tmp/fink.EGknN #!/bin/bash -ev export TMPDIR=/sw/build.build/bioconductor-siggenes-r30-1.38.0-1/siggenes/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R pushd .. /sw/build.build/bioconductor-siggenes-r30-1.38.0-1 /sw/build.build/bioconductor-siggenes-r30-1.38.0-1/siggenes $BIN_R --verbose CMD build --no-build-vignettes siggenes * checking for file 'siggenes/DESCRIPTION' ... OK * preparing 'siggenes': * checking DESCRIPTION meta-information ... OK * checking vignette meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'siggenes_1.38.0.tar.gz' /bin/rm -rf /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1 /bin/mkdir -p /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw /bin/mkdir -p /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.BTfBD /tmp/fink.DGMBy #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R mkdir -p /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw/lib/R/3.0/site-library pushd /sw/build.build/bioconductor-siggenes-r30-1.38.0-1/siggenes/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw/lib/R/3.0/site-library siggenes /sw/build.build/bioconductor-siggenes-r30-1.38.0-1 /sw/build.build/bioconductor-siggenes-r30-1.38.0-1/siggenes * installing *source* package 'siggenes' ... ** R ** inst ** preparing package for lazy loading Creating a generic function for 'print' from package 'base' in package 'siggenes' Creating a generic function for 'identify' from package 'graphics' in package 'siggenes' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (siggenes) sudo -u fink-bld [ENV] sh -c /tmp/fink.TovdV /bin/rm -f /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw/info/dir /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw/info/dir.old /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw/share/info/dir /sw/build.build/root-bioconductor-siggenes-r30-1.38.0-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-bioconductor-siggenes-r30-1.38.0-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `bioconductor-siggenes-r30' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/bioconductor-siggenes-r30_1.38.0-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-bioconductor-siggenes-r30-1.38.0-1 (Reading database ... 8074 files and directories currently installed.) Removing fink-buildlock-bioconductor-siggenes-r30-1.38.0-1 ...