{"action":"created","issue":{"url":"https://api.github.com/repos/nubakery/bagel/issues/124","repository_url":"https://api.github.com/repos/nubakery/bagel","labels_url":"https://api.github.com/repos/nubakery/bagel/issues/124/labels{/name}","comments_url":"https://api.github.com/repos/nubakery/bagel/issues/124/comments","events_url":"https://api.github.com/repos/nubakery/bagel/issues/124/events","html_url":"https://github.com/nubakery/bagel/issues/124","id":346435860,"node_id":"MDU6SXNzdWUzNDY0MzU4NjA=","number":124,"title":"configure bagel.1.1.1 error: C compiler cannot create executables","user":{"login":"aerask","id":23361379,"node_id":"MDQ6VXNlcjIzMzYxMzc5","avatar_url":"https://avatars1.githubusercontent.com/u/23361379?v=4","gravatar_id":"","url":"https://api.github.com/users/aerask","html_url":"https://github.com/aerask","followers_url":"https://api.github.com/users/aerask/followers","following_url":"https://api.github.com/users/aerask/following{/other_user}","gists_url":"https://api.github.com/users/aerask/gists{/gist_id}","starred_url":"https://api.github.com/users/aerask/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aerask/subscriptions","organizations_url":"https://api.github.com/users/aerask/orgs","repos_url":"https://api.github.com/users/aerask/repos","events_url":"https://api.github.com/users/aerask/events{/privacy}","received_events_url":"https://api.github.com/users/aerask/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-08-01T03:36:01Z","updated_at":"2018-08-02T20:32:47Z","closed_at":"2018-08-01T20:59:32Z","author_association":"NONE","body":"Dear developers,\r\n\r\nI’m trying to install bagel.1.1.1 with boost.1.64, autotools.2.69, and gcc.4.9.4 but I’m hitting an error I believe is due to autoconf trying to compile boost’s include directory rather than boost itself (bolded) resulting in the C compiler being unable to create executables (also bolded). This was tried with both the tar.gz and github clone routes for the newest version of BAGEL and both produced the same error. Given this, could the problem be due to a missing library and/or perhaps a different version of autotools?\r\n\r\n**Configure process:**\r\n$ export BOOST_ROOT=/export/apps/Boost/1.64.0/\r\n$ export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH\r\n$ ../configure --enable-mkl --with-boost=$BOOST_ROOT --with-mpi=intel\r\n\r\n**Printout after configuring:**\r\nconfigure: WARNING: unrecognized options: --with-boost\r\nchecking for a BSD-compatible install... /usr/bin/install -c\r\nchecking whether build environment is sane... yes\r\nchecking for a thread-safe mkdir -p... /bin/mkdir -p\r\nchecking for gawk... gawk\r\nchecking whether make sets $(MAKE)... yes\r\nchecking for python... /usr/bin/python\r\nchecking for python version... 2.6\r\nchecking for python platform... linux2\r\nchecking for python script directory... ${prefix}/lib/python2.6/site-packages\r\nchecking for python extension module directory... ${exec_prefix}/lib64/python2.6/site-packages\r\nchecking for gcc... gcc\r\nchecking whether the C compiler works... no\r\nconfigure: error: in `/export/zimmerman/aerask/bagel/obj':\r\nconfigure: error: **C compiler cannot create executables**\r\nSee `config.log' for more details\r\n\r\n**Following configure.log core tests readout:**\r\nconfigure:2440: checking for a BSD-compatible install\r\nconfigure:2508: result: /usr/bin/install -c\r\nconfigure:2519: checking whether build environment is sane\r\nconfigure:2569: result: yes\r\nconfigure:2710: checking for a thread-safe mkdir -p\r\nconfigure:2749: result: /bin/mkdir -p\r\nconfigure:2762: checking for gawk\r\nconfigure:2778: found /bin/gawk\r\nconfigure:2789: result: gawk\r\nconfigure:2800: checking whether make sets $(MAKE)\r\nconfigure:2822: result: yes\r\nconfigure:2912: checking for python\r\nconfigure:2930: found /usr/bin/python\r\nconfigure:2942: result: /usr/bin/python\r\nconfigure:2963: checking for python version\r\nconfigure:2970: result: 2.6\r\nconfigure:2982: checking for python platform\r\nconfigure:2989: result: linux2\r\nconfigure:2996: checking for python script directory\r\nconfigure:3025: result: ${prefix}/lib/python2.6/site-packages\r\nconfigure:3034: checking for python extension module directory\r\nconfigure:3063: result: ${exec_prefix}/lib64/python2.6/site-packages\r\nconfigure:3147: checking for gcc\r\nconfigure:3163: found /export/apps/GCC/4.9.4/bin//gcc\r\nconfigure:3174: result: gcc\r\nconfigure:3205: checking for C compiler version\r\nconfigure:3214: gcc --version >&5\r\ngcc (GCC) 4.9.4\r\nCopyright (C) 2015 Free Software Foundation, Inc.\r\nThis is free software; see the source for copying conditions.  There is NO\r\nwarranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\r\n\r\nconfigure:3225: $? = 0\r\nconfigure:3214: gcc -v >&5\r\nUsing built-in specs.\r\nCOLLECT_GCC=gcc\r\nCOLLECT_LTO_WRAPPER=/export/apps/GCC/4.9.4/libexec/gcc/x86_64-unknown-linux-gnu/4.9.4/lto-wrapper\r\nTarget: x86_64-unknown-linux-gnu\r\nConfigured with: ./configure --prefix=/export/apps/GCC/4.9.4 --disable-multilib --enable-languages=c,c++,fortran\r\nThread model: posix\r\ngcc version 4.9.4 (GCC) \r\nconfigure:3225: $? = 0\r\nconfigure:3214: gcc -V >&5\r\ngcc: error: unrecognized command line option '-V'\r\ngcc: fatal error: no input files\r\ncompilation terminated.\r\nconfigure:3225: $? = 1\r\nconfigure:3214: gcc -qversion >&5\r\ngcc: error: unrecognized command line option '-qversion'\r\ngcc: fatal error: no input files\r\ncompilation terminated.\r\nconfigure:3225: $? = 1\r\nconfigure:3245: checking whether the C compiler works\r\n**configure:3267: gcc  /export/apps/Boost/1.64.0/include  conftest.c  >&5**\r\n**/export/apps/Boost/1.64.0/include: file not recognized: Is a directory**\r\ncollect2: error: ld returned 1 exit status\r\nconfigure:3271: $? = 1\r\nconfigure:3309: result: no\r\nconfigure: failed program was:\r\n| /* confdefs.h */\r\n| #define PACKAGE_NAME \"BAGEL\"\r\n| #define PACKAGE_TARNAME \"bagel\"\r\n| #define PACKAGE_VERSION \"1.1.1\"\r\n| #define PACKAGE_STRING \"BAGEL 1.1.1\"\r\n| #define PACKAGE_BUGREPORT \"shiozaki@northwestern.edu\"\r\n| #define PACKAGE_URL \"http://www.nubakery.org\"\r\n| #define PACKAGE \"bagel\"\r\n| #define VERSION \"1.1.1\"\r\n| /* end confdefs.h.  */\r\n| \r\n| int\r\n| main ()\r\n| {\r\n| \r\n|   ;\r\n|   return 0;\r\n| }\r\nconfigure:3314: error: in `/export/zimmerman/aerask/bagel/obj':\r\nconfigure:3316: error: **C compiler cannot create executables**\r\nSee `config.log' for more details\r\n"},"comment":{"url":"https://api.github.com/repos/nubakery/bagel/issues/comments/410058884","html_url":"https://github.com/nubakery/bagel/issues/124#issuecomment-410058884","issue_url":"https://api.github.com/repos/nubakery/bagel/issues/124","id":410058884,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMDA1ODg4NA==","user":{"login":"shiozaki","id":1324578,"node_id":"MDQ6VXNlcjEzMjQ1Nzg=","avatar_url":"https://avatars2.githubusercontent.com/u/1324578?v=4","gravatar_id":"","url":"https://api.github.com/users/shiozaki","html_url":"https://github.com/shiozaki","followers_url":"https://api.github.com/users/shiozaki/followers","following_url":"https://api.github.com/users/shiozaki/following{/other_user}","gists_url":"https://api.github.com/users/shiozaki/gists{/gist_id}","starred_url":"https://api.github.com/users/shiozaki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shiozaki/subscriptions","organizations_url":"https://api.github.com/users/shiozaki/orgs","repos_url":"https://api.github.com/users/shiozaki/repos","events_url":"https://api.github.com/users/shiozaki/events{/privacy}","received_events_url":"https://api.github.com/users/shiozaki/received_events","type":"User","site_admin":false},"created_at":"2018-08-02T20:32:47Z","updated_at":"2018-08-02T20:32:47Z","author_association":"MEMBER","body":"Just for your information, this works on our cluster with CentOS6, so it's irrelevant.\n\nOn Aug 2, 2018, at 12:01 PM, Alan Rask <notifications@github.com<mailto:notifications@github.com>> wrote:\n\n\nAlso, just to mention, we're trying to compile this on CentOS s6, not mac, in case that helps.\n\n-\nYou are receiving this because you modified the open/close state.\nReply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nubakery_bagel_issues_124-23issuecomment-2D410033747&d=DwMCaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=_sW4wj1rqBwgPzD131gHF3HraLMy78EGvg1AOgMhrkA&m=vVG64Ko2fXyJmsmx8JsrWvb1ifnF32ev33q4vn9FP9w&s=yToLxyQg-ZEkEW21U6Er8Rgf9cmoa6Gx_W-CgwzvzdY&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ABQ2Ik7wolAMxt5K-5FiluKsPhVMrsWs9Mks5uM0ylgaJpZM4Vpylq&d=DwMCaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=_sW4wj1rqBwgPzD131gHF3HraLMy78EGvg1AOgMhrkA&m=vVG64Ko2fXyJmsmx8JsrWvb1ifnF32ev33q4vn9FP9w&s=dNdEuh46q614JXnyElDagM6DXtVPEgNASpQPvr3Vrho&e=>.\n"}}
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