{"action":"created","issue":{"url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/4","labels_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/4/comments","events_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/4/events","html_url":"https://github.com/GreenleafLab/NucleoATAC/issues/4","id":76492461,"number":4,"title":"Problem building pyatac.fragments","user":{"login":"cdeboever3","id":755960,"avatar_url":"https://avatars.githubusercontent.com/u/755960?v=3","gravatar_id":"","url":"https://api.github.com/users/cdeboever3","html_url":"https://github.com/cdeboever3","followers_url":"https://api.github.com/users/cdeboever3/followers","following_url":"https://api.github.com/users/cdeboever3/following{/other_user}","gists_url":"https://api.github.com/users/cdeboever3/gists{/gist_id}","starred_url":"https://api.github.com/users/cdeboever3/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cdeboever3/subscriptions","organizations_url":"https://api.github.com/users/cdeboever3/orgs","repos_url":"https://api.github.com/users/cdeboever3/repos","events_url":"https://api.github.com/users/cdeboever3/events{/privacy}","received_events_url":"https://api.github.com/users/cdeboever3/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"AliciaSchep","id":6809790,"avatar_url":"https://avatars.githubusercontent.com/u/6809790?v=3","gravatar_id":"","url":"https://api.github.com/users/AliciaSchep","html_url":"https://github.com/AliciaSchep","followers_url":"https://api.github.com/users/AliciaSchep/followers","following_url":"https://api.github.com/users/AliciaSchep/following{/other_user}","gists_url":"https://api.github.com/users/AliciaSchep/gists{/gist_id}","starred_url":"https://api.github.com/users/AliciaSchep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AliciaSchep/subscriptions","organizations_url":"https://api.github.com/users/AliciaSchep/orgs","repos_url":"https://api.github.com/users/AliciaSchep/repos","events_url":"https://api.github.com/users/AliciaSchep/events{/privacy}","received_events_url":"https://api.github.com/users/AliciaSchep/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-05-14T21:15:53Z","updated_at":"2015-05-14T21:51:55Z","closed_at":null,"body":"Hi @AliciaSchep ,\r\n\r\nI'm trying to run `nucleoatac run` and having an issue:\r\n\r\n```\r\nnucleoatac run --bed test_sorted.bed --bam ctc1_d15_combined.bam --out test_sorted --fasta ../../external_data/hg19/hg19.fa\r\nCommand run:  /raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/bin/nucleoatac run --bed test_sorted.bed --bam ctc1_d15_combined.bam --out test_sorted --fasta ../../external_data/hg19/hg19.fa\r\nnucleoatac version 0.1.4\r\nstart run at: 2015-05-14 14:03\r\n/home/cdeboever/.pyxbld/temp.linux-x86_64-2.7/pyrex/pyatac/fragments.c:250:31: fatal error: numpy/arrayobject.h: No such file or directory\r\n #include \"numpy/arrayobject.h\"                               ^\r\ncompilation terminated.\r\nTraceback (most recent call last):\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/bin/nucleoatac\", line 217, in <module>\r\n    main()  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/bin/nucleoatac\", line 54, in main\r\n    from nucleoatac.run_occ import run_occ\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/nucleoatac/run_occ.py\", line 19, in <module>\r\n    from nucleoatac.Occupancy import FragmentMixDistribution, OccupancyParameters, OccChunk\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/nucleoatac/Occupancy.py\", line 12, in <module>\r\n    from pyatac.fragmentsizes import FragmentSizes\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/pyatac/fragmentsizes.py\", line 10, in <module>\r\n    from pyatac.fragments import getAllFragmentSizes, getFragmentSizesFromChunkList  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/pyximport/pyximport.py\", line 431, in load_module    language_level=self.language_level)\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/pyximport/pyximport.py\", line 209, in load_module\r\n    inplace=build_inplace, language_level=language_level)\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/pyximport/pyximport.py\", line 186, in build_module\r\n    reload_support=pyxargs.reload_support)\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/pyximport/pyxbuild.py\", line 100, in pyx_to_dll\r\n    dist.run_commands()\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/distutils/dist.py\", line 953, in run_commands\r\n    self.run_command(cmd)\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/distutils/dist.py\", line 972, in run_command    cmd_obj.run()\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/Cython/Distutils/build_ext.py\", line 163, in run    _build_ext.build_ext.run(self)\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/distutils/command/build_ext.py\", line 337, in run\r\n    self.build_extensions()  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/site-packages/Cython/Distutils/build_ext.py\", line 171, in build_extensions\r\n    self.build_extension(ext)  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/distutils/command/build_ext.py\", line 496, in build_extension\r\n    depends=ext.depends)  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/distutils/ccompiler.py\", line 574, in compile\r\n    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)\r\n  File \"/raid/development/cdeboever/software/anaconda1.9.1/envs/cardips-tc/lib/python2.7/distutils/unixccompiler.py\", line 122, in _compile    raise CompileError, msg\r\nImportError: Building module pyatac.fragments failed: [\"CompileError: command 'gcc' failed with exit status 1\\n\"]\r\n```\r\n\r\nI have cython 0.22 and numpy 1.9.1 installed with python 2.7.9. I'm also running on openSUSE 13.2. I'm trying to debug it a bit but I haven't used cython much so I haven't had too much luck."},"comment":{"url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/comments/102180115","html_url":"https://github.com/GreenleafLab/NucleoATAC/issues/4#issuecomment-102180115","issue_url":"https://api.github.com/repos/GreenleafLab/NucleoATAC/issues/4","id":102180115,"user":{"login":"AliciaSchep","id":6809790,"avatar_url":"https://avatars.githubusercontent.com/u/6809790?v=3","gravatar_id":"","url":"https://api.github.com/users/AliciaSchep","html_url":"https://github.com/AliciaSchep","followers_url":"https://api.github.com/users/AliciaSchep/followers","following_url":"https://api.github.com/users/AliciaSchep/following{/other_user}","gists_url":"https://api.github.com/users/AliciaSchep/gists{/gist_id}","starred_url":"https://api.github.com/users/AliciaSchep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AliciaSchep/subscriptions","organizations_url":"https://api.github.com/users/AliciaSchep/orgs","repos_url":"https://api.github.com/users/AliciaSchep/repos","events_url":"https://api.github.com/users/AliciaSchep/events{/privacy}","received_events_url":"https://api.github.com/users/AliciaSchep/received_events","type":"User","site_admin":false},"created_at":"2015-05-14T21:51:55Z","updated_at":"2015-05-14T21:51:55Z","body":"I have made a change* that I think may fix this issue in a branch called \"issue4\".  @cdeboever3, would you be able to try checking that branch out to see if the change fixes the problem on your system? \r\n\r\n*changing `pyximport.install()` to `pyximport.install(setup_args={\"include_dirs\": np.get_include()})` within all applicable scripts"}}