printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild cran-r.matlab-r31 2>&1 The package 'cran-r.matlab-r31' will be built without being installed. Reading build dependency for cran-r.matlab-r31-2.2.3-1... Reading dependency for cran-r.matlab-r31-2.2.3-1... Reading build conflict for cran-r.matlab-r31-2.2.3-1... The package 'r-base31-dev' will be installed. Reading dependency for r-base31-dev-3.1.1-2... Reading runtime dependency for r-base31-dev-3.1.1-2... The package 'r-base31' will be installed. Reading dependency for r-base31-3.1.1-2... Reading runtime dependency for r-base31-3.1.1-2... The package 'cran-r.methodss3-r31' will be installed. Reading dependency for cran-r.methodss3-r31-1.6.1-1... Reading runtime dependency for cran-r.methodss3-r31-1.6.1-1... The package 'cran-r.oo-r31' will be installed. Reading dependency for cran-r.oo-r31-1.18.0-1... Reading runtime dependency for cran-r.oo-r31-1.18.0-1... The package 'cran-r.utils-r31' will be installed. Reading dependency for cran-r.utils-r31-1.29.8-1... Reading runtime dependency for cran-r.utils-r31-1.29.8-1... The package 'r-base31-shlibs' will be installed. Reading dependency for r-base31-shlibs-3.1.1-2... Reading runtime dependency for r-base31-shlibs-3.1.1-2... 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 '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: cran-r.matlab-r31 The following 31 additional packages will be installed: cairo-shlibs cran-r.methodss3-r31 cran-r.oo-r31 cran-r.utils-r31 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-base31 r-base31-dev r-base31-shlibs readline6-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. (Reading database ... 4296 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... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/flag-sort_0.5-1_darwin-x86_64.deb Selecting previously deselected package flag-sort. (Reading database ... 4301 files and directories currently installed.) Unpacking flag-sort (from .../flag-sort_0.5-1_darwin-x86_64.deb) ... Setting up flag-sort (0.5-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/freetype219-shlibs_2.4.12-1_darwin-x86_64.deb Selecting previously deselected package freetype219-shlibs. 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All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/cran-r.oo-r31_1.18.0-1_darwin-x86_64.deb Selecting previously deselected package cran-r.oo-r31. (Reading database ... 7313 files and directories currently installed.) Unpacking cran-r.oo-r31 (from .../cran-r.oo-r31_1.18.0-1_darwin-x86_64.deb) ... Setting up cran-r.oo-r31 (1.18.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/cran-r.utils-r31_1.29.8-1_darwin-x86_64.deb Selecting previously deselected package cran-r.utils-r31. (Reading database ... 7343 files and directories currently installed.) Unpacking cran-r.utils-r31 (from .../cran-r.utils-r31_1.29.8-1_darwin-x86_64.deb) ... Setting up cran-r.utils-r31 (1.29.8-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-r.matlab-r31-2.2.3-1 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-r.matlab-r31-2.2.3-1' in `/sw/build.build/fink-buildlock-cran-r.matlab-r31-2.2.3-1_2014.08.01-08.49.42_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-r.matlab-r31-2.2.3-1_2014.08.01-08.49.42_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-r.matlab-r31-2.2.3-1. (Reading database ... 7372 files and directories currently installed.) Unpacking fink-buildlock-cran-r.matlab-r31-2.2.3-1 (from .../fink-buildlock-cran-r.matlab-r31-2.2.3-1_2014.08.01-08.49.42_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-r.matlab-r31-2.2.3-1 (2014.08.01-08.49.42) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.VXvWw env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/R.matlab_2.2.3.tar.gz R.matlab/ R.matlab/inst/ R.matlab/inst/mat-files/ R.matlab/inst/mat-files/nonsignedByte1.mat R.matlab/inst/mat-files/emptyStrings.mat R.matlab/inst/mat-files/structLooped.mat R.matlab/inst/mat-files/SparseMatrix-v5.mat R.matlab/inst/mat-files/ExampleMat4.mat R.matlab/inst/mat-files/NestedMiMATRIX,problem4,v5,compressed.mat R.matlab/inst/mat-files/Matrix-v4.mat R.matlab/inst/mat-files/SparseMatrix3-v5.mat R.matlab/inst/mat-files/SparseMatrix-v4.mat R.matlab/inst/mat-files/SparseLogicalDouble-v5.mat R.matlab/inst/mat-files/SparseMatrix2-v5.mat R.matlab/inst/mat-files/nonsignedByte2.mat R.matlab/inst/mat-files/NestedMiMATRIX,problem3,v5,compressed.mat R.matlab/inst/mat-files/struct-v5.mat R.matlab/inst/mat-files/ABC.mat R.matlab/inst/mat-files/TwoMATs.stream R.matlab/inst/mat-files/SparseMatrix3-v4.mat R.matlab/inst/mat-files/SparseMatrixPage20-v5.mat R.matlab/inst/mat-files/ExampleMat5.mat R.matlab/inst/mat-files/unsignedByte.mat R.matlab/inst/mat-files/Matrix-BigEndian-v4.mat R.matlab/inst/mat-files/NestedMiMATRIX,problem1,v5,compressed.mat R.matlab/inst/mat-files/Matrix-LittleEndian-v5.mat R.matlab/inst/mat-files/SparseLogicalDouble-v4.mat R.matlab/inst/mat-files/NestedMiMATRIX,problem2,v5,compressed.mat R.matlab/inst/mat-files/Matrix-v5.mat R.matlab/inst/mat-files/StructWithSparseMatrix-v4,compressed.mat R.matlab/inst/mat-files/MatlabStructure.mat R.matlab/inst/mat-files/unsignedInt.mat R.matlab/inst/externals/ R.matlab/inst/externals/MatlabServer.m R.matlab/inst/externals/InputStreamByteWrapper.java R.matlab/inst/externals/InputStreamByteWrapper.class R.matlab/tests/ R.matlab/tests/readMat.R R.matlab/tests/Matlab.R R.matlab/tests/readMat,noattach.R R.matlab/tests/writeMat.R R.matlab/NAMESPACE R.matlab/NEWS R.matlab/R/ R.matlab/R/000.R R.matlab/R/readMat.R R.matlab/R/901.MatlabServer.R R.matlab/R/Matlab.R R.matlab/R/006.fixVarArgs.R R.matlab/R/Sys.setenv.patch.R R.matlab/R/999.NonDocumentedObjects.R R.matlab/R/999.package.R R.matlab/R/zzz.R R.matlab/R/writeMat.R R.matlab/MD5 R.matlab/DESCRIPTION R.matlab/man/ R.matlab/man/startServer.Matlab.Rd R.matlab/man/Matlab.Rd R.matlab/man/Sys.setenv.Rd R.matlab/man/R.matlab-package.Rd R.matlab/man/writeMat.Rd R.matlab/man/as.character.Matlab.Rd R.matlab/man/evaluate.Matlab.Rd R.matlab/man/open.Matlab.Rd R.matlab/man/1._The_MATLAB_server_running_in_MATLAB.Rd R.matlab/man/setOption.Matlab.Rd R.matlab/man/readMat.Rd R.matlab/man/isOpen.Matlab.Rd R.matlab/man/getVariable.Matlab.Rd R.matlab/man/readResult.Matlab.Rd R.matlab/man/setFunction.Matlab.Rd R.matlab/man/setVariable.Matlab.Rd R.matlab/man/getOption.Matlab.Rd R.matlab/man/writeCommand.Matlab.Rd R.matlab/man/finalize.Matlab.Rd R.matlab/man/close.Matlab.Rd R.matlab/man/Non-documented_objects.Rd R.matlab/man/setVerbose.Matlab.Rd sudo -u fink-bld [ENV] sh -c /tmp/fink.1F_Yj /tmp/fink.afU_9 #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-r.matlab-r31-2.2.3-1/R.matlab/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R pushd .. /sw/build.build/cran-r.matlab-r31-2.2.3-1 /sw/build.build/cran-r.matlab-r31-2.2.3-1/R.matlab $BIN_R --verbose CMD build --no-build-vignettes R.matlab * checking for file 'R.matlab/DESCRIPTION' ... OK * preparing 'R.matlab': * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'R.matlab_2.2.3.tar.gz' /bin/rm -rf /sw/build.build/root-cran-r.matlab-r31-2.2.3-1 /bin/mkdir -p /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/sw /bin/mkdir -p /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-r.matlab-r31-2.2.3-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.IAa3T /tmp/fink.PGoZR #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R mkdir -p /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/sw/lib/R/3.1/site-library pushd /sw/build.build/cran-r.matlab-r31-2.2.3-1/R.matlab/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-r.matlab-r31-2.2.3-1/sw/lib/R/3.1/site-library R.matlab /sw/build.build/cran-r.matlab-r31-2.2.3-1 /sw/build.build/cran-r.matlab-r31-2.2.3-1/R.matlab * installing *source* package 'R.matlab' ... ** package 'R.matlab' successfully unpacked and MD5 sums checked ** R ** inst ** preparing package for lazy loading Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function getOption to getOption.default, which was defined in environment base. ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (R.matlab) sudo -u fink-bld [ENV] sh -c /tmp/fink.y6AlQ /bin/rm -f /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/sw/info/dir /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/sw/info/dir.old /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/sw/share/info/dir /sw/build.build/root-cran-r.matlab-r31-2.2.3-1/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-cran-r.matlab-r31-2.2.3-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `cran-r.matlab-r31' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/cran-r.matlab-r31_2.2.3-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-r.matlab-r31-2.2.3-1 (Reading database ... 7373 files and directories currently installed.) Removing fink-buildlock-cran-r.matlab-r31-2.2.3-1 ...