printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild cran-wccsom-r30 2>&1 The package 'cran-wccsom-r30' will be built without being installed. Reading build dependency for cran-wccsom-r30-1.2.8-1... Reading dependency for cran-wccsom-r30-1.2.8-1... Reading build conflict for cran-wccsom-r30-1.2.8-1... 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 'cran-class-r30' will be installed. Reading dependency for cran-class-r30-7.3-10-2... Reading runtime dependency for cran-class-r30-7.3-10-2... 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 '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 following package will be rebuilt: cran-wccsom-r30 The following 5 additional packages will be installed: cran-class-r30 cran-mass-r30 r-base30 r-base30-dev r-base30-shlibs Do you want to continue? [Y/n] (assuming default) 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 ... 7371 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. dpkg: considering removing r-base31-dev in favour of r-base30-dev ... dpkg: yes, will remove r-base31-dev in favour of 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/cran-mass-r30_7.3-32-2_darwin-x86_64.deb Selecting previously deselected package cran-mass-r30. (Reading database ... 9300 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-class-r30_7.3-10-2_darwin-x86_64.deb Selecting previously deselected package cran-class-r30. (Reading database ... 9368 files and directories currently installed.) Unpacking cran-class-r30 (from .../cran-class-r30_7.3-10-2_darwin-x86_64.deb) ... Setting up cran-class-r30 (7.3-10-2) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-wccsom-r30-1.2.8-1 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-wccsom-r30-1.2.8-1' in `/sw/build.build/fink-buildlock-cran-wccsom-r30-1.2.8-1_2014.08.01-01.37.42_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-wccsom-r30-1.2.8-1_2014.08.01-01.37.42_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-wccsom-r30-1.2.8-1. (Reading database ... 9411 files and directories currently installed.) Unpacking fink-buildlock-cran-wccsom-r30-1.2.8-1 (from .../fink-buildlock-cran-wccsom-r30-1.2.8-1_2014.08.01-01.37.42_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-wccsom-r30-1.2.8-1 (2014.08.01-01.37.42) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.oPfwQ env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/wccsom_1.2.8.tar.gz wccsom/ wccsom/MD5 wccsom/src/ wccsom/src/wccsom.c wccsom/man/ wccsom/man/wccmap.Rd wccsom/man/classvec2classmat.Rd wccsom/man/bucket.Rd wccsom/man/degelder.Rd wccsom/man/wccsom.Rd wccsom/man/predict.wccsom.Rd wccsom/man/cepha.Rd wccsom/man/plot.wccsom.Rd wccsom/man/wcc.Rd wccsom/man/wccxyf.Rd wccsom/man/wccsom-internal.Rd wccsom/man/summary.wccsom.Rd wccsom/man/expand.som.Rd wccsom/man/unit.distances.Rd wccsom/man/wccassign.Rd wccsom/NAMESPACE wccsom/data/ wccsom/data/cepha.rda wccsom/data/degelder.rda wccsom/DESCRIPTION wccsom/R/ wccsom/R/predict.wccsom.R wccsom/R/wccmap.R wccsom/R/wccxyf.R wccsom/R/wccassign.R wccsom/R/plot.R wccsom/R/expand.R wccsom/R/summary.R wccsom/R/classvec2classmat.R wccsom/R/wccsom.R sudo -u fink-bld [ENV] sh -c /tmp/fink.zg7PQ /tmp/fink.g9mwW #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-wccsom-r30-1.2.8-1/wccsom/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R pushd .. /sw/build.build/cran-wccsom-r30-1.2.8-1 /sw/build.build/cran-wccsom-r30-1.2.8-1/wccsom if [[ 3.0 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes wccsom else $BIN_R --verbose CMD build --no-vignettes wccsom fi WARNING: ignoring environment value of R_HOME * checking for file 'wccsom/DESCRIPTION' ... OK * preparing 'wccsom': * checking DESCRIPTION meta-information ... OK * cleaning src * 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 * building 'wccsom_1.2.8.tar.gz' /bin/rm -rf /sw/build.build/root-cran-wccsom-r30-1.2.8-1 /bin/mkdir -p /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw /bin/mkdir -p /sw/build.build/root-cran-wccsom-r30-1.2.8-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-wccsom-r30-1.2.8-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.dhTTU /tmp/fink.s0roi #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R mkdir -p /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/lib/R/3.0/site-library pushd /sw/build.build/cran-wccsom-r30-1.2.8-1/wccsom/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/lib/R/3.0/site-library wccsom /sw/build.build/cran-wccsom-r30-1.2.8-1 /sw/build.build/cran-wccsom-r30-1.2.8-1/wccsom WARNING: ignoring environment value of R_HOME * installing *source* package 'wccsom' ... ** package 'wccsom' successfully unpacked and MD5 sums checked ** libs flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c wccsom.c -o wccsom.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 wccsom.dylib wccsom.o -L/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation installing to /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/lib/R/3.0/site-library/wccsom/libs ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (wccsom) install_name_tool -id /sw/lib/R/3.0/site-library/wccsom/libs/wccsom.dylib /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/lib/R/3.0/site-library/wccsom/libs/wccsom.dylib sudo -u fink-bld [ENV] sh -c /tmp/fink.DEVP2 /bin/rm -f /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/info/dir /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/info/dir.old /sw/build.build/root-cran-wccsom-r30-1.2.8-1/sw/share/info/dir /sw/build.build/root-cran-wccsom-r30-1.2.8-1/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-cran-wccsom-r30-1.2.8-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `cran-wccsom-r30' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/cran-wccsom-r30_1.2.8-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-wccsom-r30-1.2.8-1 (Reading database ... 9412 files and directories currently installed.) Removing fink-buildlock-cran-wccsom-r30-1.2.8-1 ...