{"action":"created","issue":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3461","repository_url":"https://api.github.com/repos/Homebrew/homebrew-science","labels_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3461/labels{/name}","comments_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3461/comments","events_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3461/events","html_url":"https://github.com/Homebrew/homebrew-science/issues/3461","id":142695720,"number":3461,"title":"Error installing metis","user":{"login":"irisvanzelst","id":7713060,"avatar_url":"https://avatars.githubusercontent.com/u/7713060?v=3","gravatar_id":"","url":"https://api.github.com/users/irisvanzelst","html_url":"https://github.com/irisvanzelst","followers_url":"https://api.github.com/users/irisvanzelst/followers","following_url":"https://api.github.com/users/irisvanzelst/following{/other_user}","gists_url":"https://api.github.com/users/irisvanzelst/gists{/gist_id}","starred_url":"https://api.github.com/users/irisvanzelst/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/irisvanzelst/subscriptions","organizations_url":"https://api.github.com/users/irisvanzelst/orgs","repos_url":"https://api.github.com/users/irisvanzelst/repos","events_url":"https://api.github.com/users/irisvanzelst/events{/privacy}","received_events_url":"https://api.github.com/users/irisvanzelst/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/Homebrew/homebrew-science/labels/build-error","name":"build-error","color":"fc2929"},{"url":"https://api.github.com/repos/Homebrew/homebrew-science/labels/Math","name":"Math","color":"eb6420"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-03-22T15:59:55Z","updated_at":"2016-03-29T02:24:56Z","closed_at":null,"body":"Hi all,\r\n\r\nI have an issue installing `metis` on OSX 10.11.2.\r\n\r\nI am using the following `clang`:\r\n\r\n```bash\r\n$ clang -v\r\nApple LLVM version 7.3.0 (clang-703.0.29)\r\nTarget: x86_64-apple-darwin15.2.0\r\nThread model: posix\r\nInstalledDir: /Library/Developer/CommandLineTools/usr/bin\r\n```\r\n\r\nSteps to reproduce:\r\n\r\n```bash\r\n$ brew tap homebrew/science\r\n$ brew install metis\r\n==> Installing metis from homebrew/science\r\n==> Downloading http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz\r\nAlready downloaded: /Library/Caches/Homebrew/metis-5.1.0.tar.gz\r\n==> make config shared=1 prefix=/usr/local/Cellar/metis/5.1.0 openmp=0\r\n==> make install\r\nLast 15 lines from /Users/irisvanzelst/Library/Logs/Homebrew/metis/02.make:\r\n[ 67%] Building C object libmetis/CMakeFiles/metis.dir/timing.c.o\r\ncd /tmp/metis20160322-8216-15gx1te/metis-5.1.0/build/Darwin-x86_64/libmetis && /usr/local/Library/ENV/4.3/clang  -Dmetis_EXPORTS -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/GKlib -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/include -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/libmetis/.  -DLINUX -D_FILE_OFFSET_BITS=64 -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -fPIC   -o CMakeFiles/metis.dir/timing.c.o   -c /tmp/metis20160322-8216-15gx1te/metis-5.1.0/libmetis/timing.c\r\n[ 68%] Building C object libmetis/CMakeFiles/metis.dir/util.c.o\r\ncd /tmp/metis20160322-8216-15gx1te/metis-5.1.0/build/Darwin-x86_64/libmetis && /usr/local/Library/ENV/4.3/clang  -Dmetis_EXPORTS -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/GKlib -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/include -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/libmetis/.  -DLINUX -D_FILE_OFFSET_BITS=64 -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -fPIC   -o CMakeFiles/metis.dir/util.c.o   -c /tmp/metis20160322-8216-15gx1te/metis-5.1.0/libmetis/util.c\r\n[ 69%] Building C object libmetis/CMakeFiles/metis.dir/wspace.c.o\r\ncd /tmp/metis20160322-8216-15gx1te/metis-5.1.0/build/Darwin-x86_64/libmetis && /usr/local/Library/ENV/4.3/clang  -Dmetis_EXPORTS -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/GKlib -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/include -I/tmp/metis20160322-8216-15gx1te/metis-5.1.0/libmetis/.  -DLINUX -D_FILE_OFFSET_BITS=64 -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -fPIC   -o CMakeFiles/metis.dir/wspace.c.o   -c /tmp/metis20160322-8216-15gx1te/metis-5.1.0/libmetis/wspace.c\r\n[ 70%] Linking C shared library libmetis.dylib\r\ncd /tmp/metis20160322-8216-15gx1te/metis-5.1.0/build/Darwin-x86_64/libmetis && /usr/local/Cellar/cmake/3.5.0/bin/cmake -E cmake_link_script CMakeFiles/metis.dir/link.txt --verbose=1\r\n/usr/local/Library/ENV/4.3/clang   -DLINUX -D_FILE_OFFSET_BITS=64 -DNDEBUG -DNDEBUG2 -DHAVE_EXECINFO_H -DHAVE_GETLINE -O3 -dynamiclib -Wl,-headerpad_max_install_names  -o libmetis.dylib -install_name /tmp/metis20160322-8216-15gx1te/metis-5.1.0/build/Darwin-x86_64/libmetis/libmetis.dylib CMakeFiles/metis.dir/__/GKlib/b64.c.o CMakeFiles/metis.dir/__/GKlib/blas.c.o CMakeFiles/metis.dir/__/GKlib/csr.c.o CMakeFiles/metis.dir/__/GKlib/error.c.o CMakeFiles/metis.dir/__/GKlib/evaluate.c.o CMakeFiles/metis.dir/__/GKlib/fkvkselect.c.o CMakeFiles/metis.dir/__/GKlib/fs.c.o CMakeFiles/metis.dir/__/GKlib/getopt.c.o CMakeFiles/metis.dir/__/GKlib/gkregex.c.o CMakeFiles/metis.dir/__/GKlib/graph.c.o CMakeFiles/metis.dir/__/GKlib/htable.c.o CMakeFiles/metis.dir/__/GKlib/io.c.o CMakeFiles/metis.dir/__/GKlib/itemsets.c.o CMakeFiles/metis.dir/__/GKlib/mcore.c.o CMakeFiles/metis.dir/__/GKlib/memory.c.o CMakeFiles/metis.dir/__/GKlib/omp.c.o CMakeFiles/metis.dir/__/GKlib/pdb.c.o CMakeFiles/metis.dir/__/GKlib/pqueue.c.o CMakeFiles/metis.dir/__/GKlib/random.c.o CMakeFiles/metis.dir/__/GKlib/rw.c.o CMakeFiles/metis.dir/__/GKlib/seq.c.o CMakeFiles/metis.dir/__/GKlib/sort.c.o CMakeFiles/metis.dir/__/GKlib/string.c.o CMakeFiles/metis.dir/__/GKlib/timers.c.o CMakeFiles/metis.dir/__/GKlib/tokenizer.c.o CMakeFiles/metis.dir/__/GKlib/util.c.o CMakeFiles/metis.dir/auxapi.c.o CMakeFiles/metis.dir/balance.c.o CMakeFiles/metis.dir/bucketsort.c.o CMakeFiles/metis.dir/checkgraph.c.o CMakeFiles/metis.dir/coarsen.c.o CMakeFiles/metis.dir/compress.c.o CMakeFiles/metis.dir/contig.c.o CMakeFiles/metis.dir/debug.c.o CMakeFiles/metis.dir/fm.c.o CMakeFiles/metis.dir/fortran.c.o CMakeFiles/metis.dir/frename.c.o CMakeFiles/metis.dir/gklib.c.o CMakeFiles/metis.dir/graph.c.o CMakeFiles/metis.dir/initpart.c.o CMakeFiles/metis.dir/kmetis.c.o CMakeFiles/metis.dir/kwayfm.c.o CMakeFiles/metis.dir/kwayrefine.c.o CMakeFiles/metis.dir/mcutil.c.o CMakeFiles/metis.dir/mesh.c.o CMakeFiles/metis.dir/meshpart.c.o CMakeFiles/metis.dir/minconn.c.o CMakeFiles/metis.dir/mincover.c.o CMakeFiles/metis.dir/mmd.c.o CMakeFiles/metis.dir/ometis.c.o CMakeFiles/metis.dir/options.c.o CMakeFiles/metis.dir/parmetis.c.o CMakeFiles/metis.dir/pmetis.c.o CMakeFiles/metis.dir/refine.c.o CMakeFiles/metis.dir/separator.c.o CMakeFiles/metis.dir/sfm.c.o CMakeFiles/metis.dir/srefine.c.o CMakeFiles/metis.dir/stat.c.o CMakeFiles/metis.dir/timing.c.o CMakeFiles/metis.dir/util.c.o CMakeFiles/metis.dir/wspace.c.o -lm \r\nld: section __DATA/__thread_bss extends beyond end of file, file 'CMakeFiles/metis.dir/__/GKlib/error.c.o' for architecture x86_64\r\nclang: error: linker command failed with exit code 1 (use -v to see invocation)\r\nmake[3]: *** [libmetis/libmetis.dylib] Error 1\r\nmake[2]: *** [libmetis/CMakeFiles/metis.dir/all] Error 2\r\nmake[1]: *** [all] Error 2\r\nmake: *** [install] Error 2\r\n```\r\n\r\n\r\nOutput of `brew doctor` (should hopefully all be unrelated):\r\n\r\n```bash\r\n brew doctor\r\nPlease note that these warnings are just used to help the Homebrew maintainers\r\nwith debugging if you file an issue. If everything you use Homebrew for is\r\nworking fine: please don't worry and just ignore them. Thanks!\r\n\r\nWarning: Some directories in /usr/local/share/man aren't writable.\r\nThis can happen if you \"sudo make install\" software that isn't managed\r\nby Homebrew. If a brew tries to add locale information to one of these\r\ndirectories, then the install will fail during the link step.\r\n\r\nYou should probably `sudo chown -R $(whoami)` them:\r\n    /usr/local/share/man/de\r\n    /usr/local/share/man/de/man1\r\n    /usr/local/share/man/mann\r\n\r\nWarning: Unbrewed dylibs were found in /usr/local/lib.\r\nIf you didn't put them there on purpose they could cause problems when\r\nbuilding Homebrew formulae, and may need to be deleted.\r\n\r\nUnexpected dylibs:\r\n    /usr/local/lib/libtcl8.6.dylib\r\n    /usr/local/lib/libtk8.6.dylib\r\n\r\nWarning: Unbrewed header files were found in /usr/local/include.\r\nIf you didn't put them there on purpose they could cause problems when\r\nbuilding Homebrew formulae, and may need to be deleted.\r\n\r\nUnexpected header files:\r\n    /usr/local/include/fakemysql.h\r\n    /usr/local/include/fakepq.h\r\n    /usr/local/include/fakesql.h\r\n    /usr/local/include/itcl.h\r\n    /usr/local/include/itcl2TclOO.h\r\n    /usr/local/include/itclDecls.h\r\n    /usr/local/include/itclInt.h\r\n    /usr/local/include/itclIntDecls.h\r\n    /usr/local/include/itclMigrate2TclCore.h\r\n    /usr/local/include/itclTclIntStubsFcn.h\r\n    /usr/local/include/mysqlStubs.h\r\n    /usr/local/include/odbcStubs.h\r\n    /usr/local/include/pqStubs.h\r\n    /usr/local/include/tcl.h\r\n    /usr/local/include/tclDecls.h\r\n    /usr/local/include/tclOO.h\r\n    /usr/local/include/tclOODecls.h\r\n    /usr/local/include/tclPlatDecls.h\r\n    /usr/local/include/tclThread.h\r\n    /usr/local/include/tclTomMath.h\r\n    /usr/local/include/tclTomMathDecls.h\r\n    /usr/local/include/tdbc.h\r\n    /usr/local/include/tdbcDecls.h\r\n    /usr/local/include/tdbcInt.h\r\n    /usr/local/include/tk.h\r\n    /usr/local/include/tkDecls.h\r\n    /usr/local/include/tkPlatDecls.h\r\n\r\nWarning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.\r\nIf you didn't put them there on purpose they could cause problems when\r\nbuilding Homebrew formulae, and may need to be deleted.\r\n\r\nUnexpected .pc files:\r\n    /usr/local/lib/pkgconfig/tcl.pc\r\n    /usr/local/lib/pkgconfig/tk.pc\r\n\r\nWarning: Unbrewed static libraries were found in /usr/local/lib.\r\nIf you didn't put them there on purpose they could cause problems when\r\nbuilding Homebrew formulae, and may need to be deleted.\r\n\r\nUnexpected static libraries:\r\n    /usr/local/lib/libtclstub8.6.a\r\n    /usr/local/lib/libtkstub8.6.a\r\n\r\nWarning: Broken symlinks were found. Remove them with `brew prune`:\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuPro-W3\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuPro-W6\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuProN-W3\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuProN-W6\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuStd-W8\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraKakuStdN-W8\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMaruPro-W4\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMaruProN-W4\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinPro-W3\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinPro-W6\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinProN-W3\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraMinProN-W6\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraginoSansGB-W3\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/HiraginoSansGB-W6\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/YuMin-Demibold\r\n    /usr/local/share/ghostscript/9.16/Resource/CIDFont/YuMin-Medium\r\n```\r\n\r\nAny ideas what the issue here is? Thanks for your help!"},"comment":{"url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/comments/202671183","html_url":"https://github.com/Homebrew/homebrew-science/issues/3461#issuecomment-202671183","issue_url":"https://api.github.com/repos/Homebrew/homebrew-science/issues/3461","id":202671183,"user":{"login":"pavelkang","id":3678342,"avatar_url":"https://avatars.githubusercontent.com/u/3678342?v=3","gravatar_id":"","url":"https://api.github.com/users/pavelkang","html_url":"https://github.com/pavelkang","followers_url":"https://api.github.com/users/pavelkang/followers","following_url":"https://api.github.com/users/pavelkang/following{/other_user}","gists_url":"https://api.github.com/users/pavelkang/gists{/gist_id}","starred_url":"https://api.github.com/users/pavelkang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pavelkang/subscriptions","organizations_url":"https://api.github.com/users/pavelkang/orgs","repos_url":"https://api.github.com/users/pavelkang/repos","events_url":"https://api.github.com/users/pavelkang/events{/privacy}","received_events_url":"https://api.github.com/users/pavelkang/received_events","type":"User","site_admin":false},"created_at":"2016-03-29T02:24:56Z","updated_at":"2016-03-29T02:24:56Z","body":"Same here. When I tried to install from source I got the same error."}}