printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild cran-som-r31 2>&1 The package 'cran-som-r31' will be built without being installed. Reading build dependency for cran-som-r31-0.3-5-2... Reading dependency for cran-som-r31-0.3-5-2... Reading build conflict for cran-som-r31-0.3-5-2... 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 '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 following package will be rebuilt: cran-som-r31 The following 3 additional packages will be installed: r-base31 r-base31-dev r-base31-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/som_0.3-5.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 6 243k 6 15686 0 0 46554 0 0:00:05 --:--:-- 0:00:05 46545 100 243k 100 243k 0 0 320k 0 --:--:-- --:--:-- --:--:-- 320k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/r-base31_3.1.1-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base31-shlibs_3.1.1-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base31-dev_3.1.1-2_darwin-x86_64.deb Selecting previously deselected package r-base31. (Reading database ... 7557 files and directories currently installed.) Unpacking r-base31 (from .../r-base31_3.1.1-2_darwin-x86_64.deb) ... Selecting previously deselected package r-base31-shlibs. Unpacking r-base31-shlibs (from .../r-base31-shlibs_3.1.1-2_darwin-x86_64.deb) ... Selecting previously deselected package r-base31-dev. dpkg: considering removing r-base215-dev in favour of r-base31-dev ... dpkg: yes, will remove r-base215-dev in favour of r-base31-dev. Unpacking r-base31-dev (from .../r-base31-dev_3.1.1-2_darwin-x86_64.deb) ... Setting up r-base31-shlibs (3.1.1-2) ... Setting up r-base31-dev (3.1.1-2) ... Setting up r-base31 (3.1.1-2) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-som-r31-0.3-5-2 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-som-r31-0.3-5-2' in `/sw/build.build/fink-buildlock-cran-som-r31-0.3-5-2_2014.07.29-18.53.26_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-som-r31-0.3-5-2_2014.07.29-18.53.26_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-som-r31-0.3-5-2. (Reading database ... 9474 files and directories currently installed.) Unpacking fink-buildlock-cran-som-r31-0.3-5-2 (from .../fink-buildlock-cran-som-r31-0.3-5-2_2014.07.29-18.53.26_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-som-r31-0.3-5-2 (2014.07.29-18.53.26) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.zV3_g env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/som_0.3-5.tar.gz som/ som/NAMESPACE som/DESCRIPTION som/INDEX som/man/ som/man/filtering.Rd som/man/yeast.Rd som/man/normalize.Rd som/man/som-internal.Rd som/man/summary.Rd som/man/qerror.Rd som/man/som.Rd som/man/plot.som.Rd som/src/ som/src/som.cc som/src/Makevars som/src/sub.h som/src/tntsupp.h som/src/SomParam.h som/src/tnt/ som/src/tnt/qr.h som/src/tnt/triang.h som/src/tnt/transv.h som/src/tnt/version.h som/src/tnt/index.h som/src/tnt/fortran.h som/src/tnt/tntreqs.h som/src/tnt/stopwatch.h som/src/tnt/trisolve.h som/src/tnt/fspvec.h som/src/tnt/subscript.h som/src/tnt/lapack.h som/src/tnt/region1d.h som/src/tnt/vecadaptor.h som/src/tnt/lu.h som/src/tnt/tntmath.h som/src/tnt/fmat.h som/src/tnt/tnt.h som/src/tnt/vec.h som/src/tnt/region2d.h som/src/tnt/cmat.h som/src/tnt/fcscmat.h som/src/tnt/cholesky.h som/data/ som/data/yeast.tab som/R/ som/R/som.R som/R/zzz.R som/Changes sudo -u fink-bld [ENV] sh -c /tmp/fink.m9VSK /tmp/fink.A8Scc #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-som-r31-0.3-5-2/som/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R pushd .. /sw/build.build/cran-som-r31-0.3-5-2 /sw/build.build/cran-som-r31-0.3-5-2/som if [[ 3.1 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes som else $BIN_R --verbose CMD build --no-vignettes som fi * checking for file 'som/DESCRIPTION' ... OK * preparing 'som': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... NO * use '--force' to remove the existing 'INDEX' * 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 tabular files * building 'som_0.3-5.tar.gz' /bin/rm -rf /sw/build.build/root-cran-som-r31-0.3-5-2 /bin/mkdir -p /sw/build.build/root-cran-som-r31-0.3-5-2/sw /bin/mkdir -p /sw/build.build/root-cran-som-r31-0.3-5-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-som-r31-0.3-5-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.pHc6h /tmp/fink.DHEMD #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R mkdir -p /sw/build.build/root-cran-som-r31-0.3-5-2/sw/lib/R/3.1/site-library pushd /sw/build.build/cran-som-r31-0.3-5-2/som/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-som-r31-0.3-5-2/sw/lib/R/3.1/site-library som /sw/build.build/cran-som-r31-0.3-5-2 /sw/build.build/cran-som-r31-0.3-5-2/som * installing *source* package 'som' ... ** libs flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I. -I/sw/include -fPIC -g -O3 -c som.cc -o som.o flag-sort -r g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o som.dylib som.o -L/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation installing to /sw/build.build/root-cran-som-r31-0.3-5-2/sw/lib/R/3.1/site-library/som/libs ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (som) install_name_tool -id /sw/lib/R/3.1/site-library/som/libs/som.dylib /sw/build.build/root-cran-som-r31-0.3-5-2/sw/lib/R/3.1/site-library/som/libs/som.dylib sudo -u fink-bld [ENV] sh -c /tmp/fink.bkEup /bin/rm -f /sw/build.build/root-cran-som-r31-0.3-5-2/sw/info/dir /sw/build.build/root-cran-som-r31-0.3-5-2/sw/info/dir.old /sw/build.build/root-cran-som-r31-0.3-5-2/sw/share/info/dir /sw/build.build/root-cran-som-r31-0.3-5-2/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-som-r31-0.3-5-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `cran-som-r31' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/cran-som-r31_0.3-5-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-som-r31-0.3-5-2 (Reading database ... 9475 files and directories currently installed.) Removing fink-buildlock-cran-som-r31-0.3-5-2 ...