printf ' ' | fink --no-use-binary-dist --yes rebuild cran-kernlab-r30 2>&1 The package 'cran-kernlab-r30' will be built without being installed. Reading build dependency for cran-kernlab-r30-0.9-19-1... Reading dependency for cran-kernlab-r30-0.9-19-1... Reading build conflict for cran-kernlab-r30-0.9-19-1... The following package will be rebuilt: cran-kernlab-r30 Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-kernlab-r30-0.9-19-1 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-kernlab-r30-0.9-19-1' in `/sw/build.build/fink-buildlock-cran-kernlab-r30-0.9-19-1_2014.08.01-14.31.28_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-kernlab-r30-0.9-19-1_2014.08.01-14.31.28_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-kernlab-r30-0.9-19-1. (Reading database ... 7384 files and directories currently installed.) Unpacking fink-buildlock-cran-kernlab-r30-0.9-19-1 (from .../fink-buildlock-cran-kernlab-r30-0.9-19-1_2014.08.01-14.31.28_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-kernlab-r30-0.9-19-1 (2014.08.01-14.31.28) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.FUZik env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/kernlab_0.9-19.tar.gz kernlab/ kernlab/inst/ kernlab/inst/CITATION kernlab/inst/COPYRIGHTS kernlab/inst/doc/ kernlab/inst/doc/kernlab.R kernlab/inst/doc/kernlab.pdf kernlab/inst/doc/kernlab.Rnw kernlab/src/ kernlab/src/iweightfactory.h kernlab/src/stringkernel.h kernlab/src/introsort.h kernlab/src/Makevars kernlab/src/dbreakpt.c kernlab/src/kspectrumweight.h kernlab/src/dtron.c kernlab/src/wkasailcp.cpp kernlab/src/dgpnrm.c kernlab/src/dtrpcg.c kernlab/src/inductionsort.h kernlab/src/ctable.cpp kernlab/src/misc.c kernlab/src/expdecayweight.h kernlab/src/dcauchy.c kernlab/src/wmsufsort.cpp kernlab/src/dspcg.c kernlab/src/datatype.h kernlab/src/lcp.h kernlab/src/stringk.c kernlab/src/dtrqsol.c kernlab/src/esa.cpp kernlab/src/esa.h kernlab/src/cweight.cpp kernlab/src/errorcode.h kernlab/src/dprsrch.c kernlab/src/kspectrumweight.cpp kernlab/src/svm.h kernlab/src/dprecond.c kernlab/src/msufsort.h kernlab/src/wkasailcp.h kernlab/src/stringkernel.cpp kernlab/src/ctable.h kernlab/src/brweight.h kernlab/src/isafactory.h kernlab/src/inductionsort.cpp kernlab/src/lcp.cpp kernlab/src/wmsufsort.h kernlab/src/svm.cpp kernlab/src/solvebqp.c kernlab/src/stack.h kernlab/src/Makevars.win kernlab/src/dgpstep.c kernlab/src/brweight.cpp kernlab/src/expdecayweight.cpp kernlab/src/ilcpfactory.h kernlab/src/msufsort.cpp kernlab/src/cweight.h kernlab/NAMESPACE kernlab/data/ kernlab/data/spirals.rda kernlab/data/reuters.rda kernlab/data/income.rda kernlab/data/spam.rda kernlab/data/promotergene.rda kernlab/data/musk.rda kernlab/data/ticdata.rda kernlab/R/ kernlab/R/kkmeans.R kernlab/R/gausspr.R kernlab/R/inchol.R kernlab/R/csi.R kernlab/R/lssvm.R kernlab/R/kcca.R kernlab/R/kmmd.R kernlab/R/kqr.R kernlab/R/onlearn.R kernlab/R/kha.R kernlab/R/aobjects.R kernlab/R/kpca.R kernlab/R/kernels.R kernlab/R/ranking.R kernlab/R/specc.R kernlab/R/kfa.R kernlab/R/sigest.R kernlab/R/kernelmatrix.R kernlab/R/couplers.R kernlab/R/ksvm.R kernlab/R/ipop.R kernlab/R/rvm.R kernlab/vignettes/ kernlab/vignettes/jss.bib kernlab/vignettes/A.cls kernlab/vignettes/kernlab.Rnw kernlab/MD5 kernlab/build/ kernlab/build/vignette.rds kernlab/DESCRIPTION kernlab/man/ kernlab/man/rvm-class.Rd kernlab/man/onlearn.Rd kernlab/man/kqr.Rd kernlab/man/couple.Rd kernlab/man/kpca.Rd kernlab/man/spirals.Rd kernlab/man/predict.gausspr.Rd kernlab/man/kqr-class.Rd kernlab/man/kfa-class.Rd kernlab/man/kmmd.Rd kernlab/man/as.kernelMatrix.Rd kernlab/man/musk.Rd kernlab/man/csi.Rd kernlab/man/ksvm-class.Rd kernlab/man/csi-class.Rd kernlab/man/vm-class.Rd kernlab/man/ticdata.Rd kernlab/man/inlearn.Rd kernlab/man/prc-class.Rd kernlab/man/promotergene.Rd kernlab/man/stringdot.Rd kernlab/man/ranking.Rd kernlab/man/dots.Rd kernlab/man/kmmd-class.Rd kernlab/man/kha-class.Rd kernlab/man/rvm.Rd kernlab/man/spam.Rd kernlab/man/kernelMatrix.Rd kernlab/man/gausspr-class.Rd kernlab/man/onlearn-class.Rd kernlab/man/ranking-class.Rd kernlab/man/kernel-class.Rd kernlab/man/lssvm-class.Rd kernlab/man/kfa.Rd kernlab/man/ksvm.Rd kernlab/man/inchol.Rd kernlab/man/kha.Rd kernlab/man/kkmeans.Rd kernlab/man/kpca-class.Rd kernlab/man/ipop-class.Rd kernlab/man/reuters.Rd kernlab/man/inchol-class.Rd kernlab/man/kcca.Rd kernlab/man/kcca-class.Rd kernlab/man/ipop.Rd kernlab/man/lssvm.Rd kernlab/man/sigest.Rd kernlab/man/plot.Rd kernlab/man/specc-class.Rd kernlab/man/gausspr.Rd kernlab/man/income.Rd kernlab/man/specc.Rd kernlab/man/predict.ksvm.Rd kernlab/man/predict.kqr.Rd sudo -u fink-bld [ENV] sh -c /tmp/fink.Pk6ZG /tmp/fink.pzCjl #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-kernlab-r30-0.9-19-1/kernlab/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R pushd .. /sw/build.build/cran-kernlab-r30-0.9-19-1 /sw/build.build/cran-kernlab-r30-0.9-19-1/kernlab if [[ 3.0 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes kernlab else $BIN_R --verbose CMD build --no-vignettes kernlab fi * checking for file 'kernlab/DESCRIPTION' ... OK * preparing 'kernlab': * checking DESCRIPTION meta-information ... OK * cleaning src * checking vignette meta-information ... OK * 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 'kernlab_0.9-19.tar.gz' /bin/rm -rf /sw/build.build/root-cran-kernlab-r30-0.9-19-1 /bin/mkdir -p /sw/build.build/root-cran-kernlab-r30-0.9-19-1/sw /bin/mkdir -p /sw/build.build/root-cran-kernlab-r30-0.9-19-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-kernlab-r30-0.9-19-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.IBylH /tmp/fink.8A0sS #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R mkdir -p /sw/build.build/root-cran-kernlab-r30-0.9-19-1/sw/lib/R/3.0/site-library pushd /sw/build.build/cran-kernlab-r30-0.9-19-1/kernlab/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-kernlab-r30-0.9-19-1/sw/lib/R/3.0/site-library kernlab /sw/build.build/cran-kernlab-r30-0.9-19-1 /sw/build.build/cran-kernlab-r30-0.9-19-1/kernlab * installing *source* package 'kernlab' ... ** package 'kernlab' successfully unpacked and MD5 sums checked ** libs flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c brweight.cpp -o brweight.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c ctable.cpp -o ctable.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c cweight.cpp -o cweight.o 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 dbreakpt.c -o dbreakpt.o 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 dcauchy.c -o dcauchy.o 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 dgpnrm.c -o dgpnrm.o 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 dgpstep.c -o dgpstep.o 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 dprecond.c -o dprecond.o 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 dprsrch.c -o dprsrch.o 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 dspcg.c -o dspcg.o 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 dtron.c -o dtron.o 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 dtrpcg.c -o dtrpcg.o 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 dtrqsol.c -o dtrqsol.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c esa.cpp -o esa.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c expdecayweight.cpp -o expdecayweight.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c inductionsort.cpp -o inductionsort.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c kspectrumweight.cpp -o kspectrumweight.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c lcp.cpp -o lcp.o 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 misc.c -o misc.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c msufsort.cpp -o msufsort.o 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 solvebqp.c -o solvebqp.o 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 stringk.c -o stringk.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c stringkernel.cpp -o stringkernel.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c svm.cpp -o svm.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c wkasailcp.cpp -o wkasailcp.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c wmsufsort.cpp -o wmsufsort.o flag-sort -r g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o kernlab.dylib brweight.o ctable.o cweight.o dbreakpt.o dcauchy.o dgpnrm.o dgpstep.o dprecond.o dprsrch.o dspcg.o dtron.o dtrpcg.o dtrqsol.o esa.o expdecayweight.o inductionsort.o kspectrumweight.o lcp.o misc.o msufsort.o solvebqp.o stringk.o stringkernel.o svm.o wkasailcp.o wmsufsort.o -framework Accelerate -framework Accelerate -L/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1 -L/sw/lib/gcc4.9/lib -lgfortran -lquadmath -lm -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/sw/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.3.0/4.9.1' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [kernlab.dylib] Error 1 ERROR: compilation failed for package 'kernlab' * removing '/sw/build.build/root-cran-kernlab-r30-0.9-19-1/sw/lib/R/3.0/site-library/kernlab' ### execution of /tmp/fink.8A0sS failed, exit code 1 ### execution of /tmp/fink.IBylH failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-kernlab-r30-0.9-19-1 (Reading database ... 7385 files and directories currently installed.) Removing fink-buildlock-cran-kernlab-r30-0.9-19-1 ... Failed: phase installing: cran-kernlab-r30-0.9-19-1 failed Before reporting any errors, please run "fink selfupdate" and try again. Also try using "fink configure" to set your maximum build jobs to 1 and attempt to build the package again. If you continue to have issues, please check to see if the FAQ on Fink's website solves the problem. If not, ask on one (not both, please) of these mailing lists: The Fink Users List The Fink Beginners List , with a carbon copy to the maintainer: David Fang Note that this is preferable to emailing just the maintainer directly, since most fink package maintainers do not have access to all possible hardware and software configurations. Please try to include the complete error message in your report. This generally consists of a compiler line starting with e.g. "gcc" or "g++" followed by the actual error output from the compiler. Also include the following system information: Package manager version: 0.37.0 Distribution version: selfupdate-cvs Thu Jul 24 20:26:24 2014, 10.9, x86_64 Trees: local/main stable/main Xcode.app: 5.1.1 Xcode command-line tools: 6.0.0.0.1.1405597879 Max. Fink build jobs: 8