printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild cran-gmp-r31 2>&1 The package 'cran-gmp-r31' will be built without being installed. Reading build dependency for cran-gmp-r31-0.5-11-1... Reading dependency for cran-gmp-r31-0.5-11-1... Reading build conflict for cran-gmp-r31-0.5-11-1... 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 'gmp5' will be installed. Reading dependency for gmp5-6.0.0a-1... Reading runtime dependency for gmp5-6.0.0a-1... 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 'gmp5-shlibs' will be installed. Reading dependency for gmp5-shlibs-6.0.0a-1... Reading runtime dependency for gmp5-shlibs-6.0.0a-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 'libgmpxx5-shlibs' will be installed. Reading dependency for libgmpxx5-shlibs-6.0.0a-1... Reading runtime dependency for libgmpxx5-shlibs-6.0.0a-1... The following package will be rebuilt: cran-gmp-r31 The following 6 additional packages will be installed: gmp5 gmp5-shlibs libgmpxx5-shlibs r-base31 r-base31-dev r-base31-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/gmp5_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb Selecting previously deselected package gmp5. (Reading database ... 7384 files and directories currently installed.) Unpacking gmp5 (from .../gmp5_6.0.0a-1_darwin-x86_64.deb) ... Selecting previously deselected package gmp5-shlibs. Unpacking gmp5-shlibs (from .../gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Selecting previously deselected package libgmpxx5-shlibs. Unpacking libgmpxx5-shlibs (from .../libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Setting up gmp5-shlibs (6.0.0a-1) ... Setting up libgmpxx5-shlibs (6.0.0a-1) ... Setting up gmp5 (6.0.0a-1) ... Clearing dependency_libs of .la files being installed * gmp: (gmp). GNU Multiple Precision Arithmetic Library. install-info(/sw/share/info/gmp.info): creating new section `GNU libraries' 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 ... 7434 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-base30-dev in favour of r-base31-dev ... dpkg: yes, will remove r-base30-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-gmp-r31-0.5-11-1 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-gmp-r31-0.5-11-1' in `/sw/build.build/fink-buildlock-cran-gmp-r31-0.5-11-1_2014.07.29-06.07.19_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-gmp-r31-0.5-11-1_2014.07.29-06.07.19_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-gmp-r31-0.5-11-1. (Reading database ... 9352 files and directories currently installed.) Unpacking fink-buildlock-cran-gmp-r31-0.5-11-1 (from .../fink-buildlock-cran-gmp-r31-0.5-11-1_2014.07.29-06.07.19_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-gmp-r31-0.5-11-1 (2014.07.29-06.07.19) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.BacKS env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/gmp_0.5-11.tar.gz gmp/ gmp/TODO gmp/inst/ gmp/inst/doc/ gmp/inst/doc/index.html gmp/inst/doc/bigintegerR_8cc.html gmp/inst/doc/classbigmod.html gmp/inst/doc/files.html gmp/inst/doc/functions.html gmp/inst/doc/annotated.html gmp/inst/doc/classbiginteger-members.html gmp/inst/doc/doxygen.css gmp/inst/doc/doxygen.png gmp/inst/doc/classbigmod-members.html gmp/inst/doc/biginteger_8h-source.html gmp/inst/doc/classbiginteger.html gmp/inst/doc/biginteger_8cc.html gmp/inst/doc/biginteger__operator_8cc.html gmp/inst/doc/globals.html gmp/configure.in gmp/tests/ gmp/tests/gmp-test.Rout.save gmp/tests/arith-ex.R gmp/tests/basic-ex.R gmp/tests/gmp-test.R gmp/src/ gmp/src/matrix.cc gmp/src/primes.h gmp/src/init.cc gmp/src/bigintegerR.h gmp/src/bigrationalR.cc gmp/src/biginteger.h gmp/src/factorize.h gmp/src/bigrational.cc gmp/src/bigvec_q.cc gmp/src/extract_matrix.h gmp/src/factor.cc gmp/src/biginteger.cc gmp/src/matrixq.cc gmp/src/Rgmp.h gmp/src/apply.h gmp/src/bigrationalR.h gmp/src/solve.h gmp/src/Makevars.in gmp/src/bigvec.cc gmp/src/factor.h gmp/src/bigintegerR.cc gmp/src/apply.cc gmp/src/bigmod.h gmp/src/bigvec_q.h gmp/src/Makevars.win gmp/src/extract_matrix.cc gmp/src/factorize.cc gmp/src/matrixq.h gmp/src/bigmod.cc gmp/src/solve.cc gmp/src/bigrational.h gmp/src/bigvec.h gmp/src/matrix.h gmp/NAMESPACE gmp/Done gmp/data/ gmp/data/Oakley2.R gmp/data/Oakley1.R gmp/R/ gmp/R/matrixz.R gmp/R/matrix-prods.R gmp/R/AllClasses-etc.R gmp/R/biginteger.R gmp/R/Stirling-n-etc.R gmp/R/zzz.R gmp/R/matrixq.R gmp/R/bigq.R gmp/MD5 gmp/DESCRIPTION gmp/Changes gmp/configure gmp/ChangeLog gmp/man/ gmp/man/frexpZ.Rd gmp/man/operators_bigq.Rd gmp/man/extreme.Rd gmp/man/bigrational.Rd gmp/man/comp.bigq.Rd gmp/man/solve.Rd gmp/man/matrix.Rd gmp/man/factorialZ.Rd gmp/man/is.whole.Rd gmp/man/Oakley.Rd gmp/man/utils.Rd gmp/man/gcdex.Rd gmp/man/biginteger.rand.Rd gmp/man/modulus.Rd gmp/man/cumsum.Rd gmp/man/add.biginteger.Rd gmp/man/asNumeric.Rd gmp/man/comp.biginteger.Rd gmp/man/nextprime.Rd gmp/man/fibonacci.Rd gmp/man/biginteger.Rd gmp/man/factor.Rd gmp/man/apply.Rd gmp/man/Stirling.Rd gmp/man/formatN.Rd gmp/man/gcd.Rd gmp/man/extract.Rd gmp/man/sizeinbase.Rd gmp/man/isprime.Rd gmp/man/powm.Rd gmp/cleanup sudo -u fink-bld [ENV] sh -c /tmp/fink._hymI /tmp/fink.yDYmv #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-gmp-r31-0.5-11-1/gmp/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R perl -pi -e 's|-I/usr/local/include/||g' configure perl -pi -e 's|-L/usr/local/lib/||g' configure pushd .. /sw/build.build/cran-gmp-r31-0.5-11-1 /sw/build.build/cran-gmp-r31-0.5-11-1/gmp if [[ 3.1 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes gmp else $BIN_R --verbose CMD build --no-vignettes gmp fi * checking for file 'gmp/DESCRIPTION' ... OK * preparing 'gmp': * checking DESCRIPTION meta-information ... OK * cleaning src * running 'cleanup' * 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 'gmp_0.5-11.tar.gz' /bin/rm -rf /sw/build.build/root-cran-gmp-r31-0.5-11-1 /bin/mkdir -p /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw /bin/mkdir -p /sw/build.build/root-cran-gmp-r31-0.5-11-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-gmp-r31-0.5-11-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.VXi6n /tmp/fink.wU4Nb #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R mkdir -p /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/lib/R/3.1/site-library pushd /sw/build.build/cran-gmp-r31-0.5-11-1/gmp/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/lib/R/3.1/site-library gmp /sw/build.build/cran-gmp-r31-0.5-11-1 /sw/build.build/cran-gmp-r31-0.5-11-1/gmp * installing *source* package 'gmp' ... file 'configure' has the wrong MD5 checksum creating cache ./config.cache checking for __gmpz_ui_sub in -lgmp... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c apply.cc -o apply.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c biginteger.cc -o biginteger.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c bigintegerR.cc -o bigintegerR.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c bigmod.cc -o bigmod.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c bigrational.cc -o bigrational.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c bigrationalR.cc -o bigrationalR.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c bigvec.cc -o bigvec.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c bigvec_q.cc -o bigvec_q.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c extract_matrix.cc -o extract_matrix.o In file included from extract_matrix.cc:1: ./extract_matrix.h:336:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else { // matrix case: ^ 1 warning generated. flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c factor.cc -o factor.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c factorize.cc -o factorize.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c init.cc -o init.o In file included from init.cc:11: ./extract_matrix.h:336:9: warning: add explicit braces to avoid dangling else [-Wdangling-else] } else { // matrix case: ^ 1 warning generated. flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c matrix.cc -o matrix.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c matrixq.cc -o matrixq.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c solve.cc -o solve.o flag-sort -r g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o gmp.dylib apply.o biginteger.o bigintegerR.o bigmod.o bigrational.o bigrationalR.o bigvec.o bigvec_q.o extract_matrix.o factor.o factorize.o init.o matrix.o matrixq.o solve.o -lgmp -L/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation installing to /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/lib/R/3.1/site-library/gmp/libs ** R ** data ** inst ** preparing package for lazy loading Creating a generic function for 'which.max' from package 'base' in package 'gmp' Creating a generic function for 'which.min' from package 'base' in package 'gmp' ** help *** installing help indices ** building package indices Attaching package: 'gmp' The following objects are masked from 'package:base': %*%, apply, crossprod, matrix, tcrossprod ** testing if installed package can be loaded * DONE (gmp) install_name_tool -id /sw/lib/R/3.1/site-library/gmp/libs/gmp.dylib /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/lib/R/3.1/site-library/gmp/libs/gmp.dylib sudo -u fink-bld [ENV] sh -c /tmp/fink.nihv0 /bin/rm -f /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/info/dir /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/info/dir.old /sw/build.build/root-cran-gmp-r31-0.5-11-1/sw/share/info/dir /sw/build.build/root-cran-gmp-r31-0.5-11-1/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-gmp-r31-0.5-11-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `cran-gmp-r31' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/cran-gmp-r31_0.5-11-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-gmp-r31-0.5-11-1 (Reading database ... 9353 files and directories currently installed.) Removing fink-buildlock-cran-gmp-r31-0.5-11-1 ...