printf ' ' | fink --no-use-binary-dist --yes rebuild cran-bayestree-r215 2>&1 The package 'cran-bayestree-r215' will be built without being installed. Reading build dependency for cran-bayestree-r215-0.3-1.1-1... Reading dependency for cran-bayestree-r215-0.3-1.1-1... Reading build conflict for cran-bayestree-r215-0.3-1.1-1... The following package will be rebuilt: cran-bayestree-r215 Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-bayestree-r215-0.3-1.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-bayestree-r215-0.3-1.1-1' in `/sw/build.build/fink-buildlock-cran-bayestree-r215-0.3-1.1-1_2014.07.31-12.43.24_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-bayestree-r215-0.3-1.1-1_2014.07.31-12.43.24_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-bayestree-r215-0.3-1.1-1. (Reading database ... 7603 files and directories currently installed.) Unpacking fink-buildlock-cran-bayestree-r215-0.3-1.1-1 (from .../fink-buildlock-cran-bayestree-r215-0.3-1.1-1_2014.07.31-12.43.24_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-bayestree-r215-0.3-1.1-1 (2014.07.31-12.43.24) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.T7REv env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/BayesTree_0.3-1.1.tar.gz BayesTree/ BayesTree/DESCRIPTION BayesTree/man/ BayesTree/man/bart.Rd BayesTree/man/makeind.Rd BayesTree/man/pdbart.Rd BayesTree/NAMESPACE BayesTree/R/ BayesTree/R/bart.R BayesTree/R/makeind.R BayesTree/R/pd2bart.R BayesTree/R/pdbart.R BayesTree/R/plot.bart.R BayesTree/R/plot.pd2bart.R BayesTree/R/plot.pdbart.R BayesTree/src/ BayesTree/src/BirthDeath.cpp BayesTree/src/BirthDeath.h BayesTree/src/ChangeRule.cpp BayesTree/src/ChangeRule.h BayesTree/src/CPriParams.h BayesTree/src/EndNodeModel.h BayesTree/src/Funs.cpp BayesTree/src/Funs.h BayesTree/src/global.h BayesTree/src/Lib.cpp BayesTree/src/Lib.h BayesTree/src/Likelihood.cpp BayesTree/src/Likelihood.h BayesTree/src/List.cpp BayesTree/src/List.h BayesTree/src/Makevars.win BayesTree/src/mbart.cpp BayesTree/src/MuS.cpp BayesTree/src/MuS.h BayesTree/src/Node.cpp BayesTree/src/Node.h BayesTree/src/Prior.cpp BayesTree/src/Prior.h BayesTree/src/Rlob.cpp BayesTree/src/Rlob.h BayesTree/src/Sdev.h BayesTree/src/Swap.cpp BayesTree/src/Swap.h sudo -u fink-bld [ENV] sh -c /tmp/fink.gJ59m /tmp/fink.M_FiL #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-bayestree-r215-0.3-1.1-1/BayesTree/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R pushd .. /sw/build.build/cran-bayestree-r215-0.3-1.1-1 /sw/build.build/cran-bayestree-r215-0.3-1.1-1/BayesTree if [[ 2.15 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes BayesTree else $BIN_R --verbose CMD build --no-vignettes BayesTree fi * checking for file 'BayesTree/DESCRIPTION' ... OK * preparing 'BayesTree': * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building 'BayesTree_0.3-1.1.tar.gz' /bin/rm -rf /sw/build.build/root-cran-bayestree-r215-0.3-1.1-1 /bin/mkdir -p /sw/build.build/root-cran-bayestree-r215-0.3-1.1-1/sw /bin/mkdir -p /sw/build.build/root-cran-bayestree-r215-0.3-1.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-bayestree-r215-0.3-1.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.vv8wI /tmp/fink.BCW_o #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R mkdir -p /sw/build.build/root-cran-bayestree-r215-0.3-1.1-1/sw/lib/R/2.15/site-library pushd /sw/build.build/cran-bayestree-r215-0.3-1.1-1/BayesTree/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-bayestree-r215-0.3-1.1-1/sw/lib/R/2.15/site-library BayesTree /sw/build.build/cran-bayestree-r215-0.3-1.1-1 /sw/build.build/cran-bayestree-r215-0.3-1.1-1/BayesTree * installing *source* package 'BayesTree' ... ** libs flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c BirthDeath.cpp -o BirthDeath.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c ChangeRule.cpp -o ChangeRule.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Funs.cpp -o Funs.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Lib.cpp -o Lib.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Likelihood.cpp -o Likelihood.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c List.cpp -o List.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c MuS.cpp -o MuS.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Node.cpp -o Node.o Node.cpp:83:15: warning: equality comparison with extraneous parentheses [-Wparentheses-equality] if((x[Var] == RuleMat[Var][i])) { ~~~~~~~^~~~~~~~~~~~~~~~~~ Node.cpp:83:15: note: remove extraneous parentheses around the comparison to silence this warning if((x[Var] == RuleMat[Var][i])) { ~ ^ ~ Node.cpp:83:15: note: use '=' to turn this equality comparison into an assignment if((x[Var] == RuleMat[Var][i])) { ^~ = 1 warning generated. flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Prior.cpp -o Prior.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Rlob.cpp -o Rlob.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c Swap.cpp -o Swap.o flag-sort -r g++ -I/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c mbart.cpp -o mbart.o flag-sort -r g++ -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/sw/lib -o BayesTree.dylib BirthDeath.o ChangeRule.o Funs.o Lib.o Likelihood.o List.o MuS.o Node.o Prior.o Rlob.o Swap.o mbart.o -L/sw/Library/Frameworks/R.framework/Versions/2.15/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation Undefined symbols for architecture x86_64: "_daxpy_", referenced from: _mbart in mbart.o "_dcopy_", referenced from: _mbart in mbart.o "_ddot_", referenced from: _mbart in mbart.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [BayesTree.dylib] Error 1 ERROR: compilation failed for package 'BayesTree' * removing '/sw/build.build/root-cran-bayestree-r215-0.3-1.1-1/sw/lib/R/2.15/site-library/BayesTree' ### execution of /tmp/fink.BCW_o failed, exit code 1 ### execution of /tmp/fink.vv8wI failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-bayestree-r215-0.3-1.1-1 (Reading database ... 7604 files and directories currently installed.) Removing fink-buildlock-cran-bayestree-r215-0.3-1.1-1 ... Failed: phase installing: cran-bayestree-r215-0.3-1.1-1 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: Jack Howarth 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