{"action":"created","issue":{"url":"https://api.github.com/repos/CollasLab/edd/issues/2","labels_url":"https://api.github.com/repos/CollasLab/edd/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/CollasLab/edd/issues/2/comments","events_url":"https://api.github.com/repos/CollasLab/edd/issues/2/events","html_url":"https://github.com/CollasLab/edd/issues/2","id":88676154,"number":2,"title":"Unable to install EDD","user":{"login":"dsoronellas","id":5804463,"avatar_url":"https://avatars.githubusercontent.com/u/5804463?v=3","gravatar_id":"","url":"https://api.github.com/users/dsoronellas","html_url":"https://github.com/dsoronellas","followers_url":"https://api.github.com/users/dsoronellas/followers","following_url":"https://api.github.com/users/dsoronellas/following{/other_user}","gists_url":"https://api.github.com/users/dsoronellas/gists{/gist_id}","starred_url":"https://api.github.com/users/dsoronellas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dsoronellas/subscriptions","organizations_url":"https://api.github.com/users/dsoronellas/orgs","repos_url":"https://api.github.com/users/dsoronellas/repos","events_url":"https://api.github.com/users/dsoronellas/events{/privacy}","received_events_url":"https://api.github.com/users/dsoronellas/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-06-16T09:41:56Z","updated_at":"2015-06-22T20:59:50Z","closed_at":null,"body":"Dear Developers,\r\nI'm having an error when trying to install EDD through pip, could you please help me to solve it?\r\nSeems that is trying to look for pysam (0.8.0) and finds version 0.7.5, but when I do ```$ pip freeze```\r\n```\r\n[...]\r\npysam==0.8.3\r\n[...]\r\n```\r\nBelow I paste the install log. Also I noticed some issues with **eddlib/read_bam.c**\r\n\r\n```bash\r\n$ pip install edd\r\n```\r\n```\r\nDownloading/unpacking edd\r\n  Downloading edd-1.1.13.tar.gz\r\n  Running setup.py egg_info for package edd\r\n\r\n###########\r\nWARNING\r\n###########\r\nEDD requires pysam version 0.8.0 or greater, but the detected version was 0.7.5.The installation might not work.\r\n    \r\n    \r\nRequirement already satisfied (use --upgrade to upgrade): Logbook in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): pybedtools in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): statsmodels in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): patsy in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): pandas in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): python-dateutil in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): scipy in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): numpy in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from edd)\r\nRequirement already satisfied (use --upgrade to upgrade): pytz>=2011k in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from pandas->edd)\r\nRequirement already satisfied (use --upgrade to upgrade): six>=1.5 in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages (from python-dateutil->edd)\r\n\r\nInstalling collected packages: edd\r\nRunning setup.py install for edd\r\n\r\n###########\r\nWARNING\r\n###########\r\nEDD requires pysam version 0.8.0 or greater, but the detected version was 0.7.5.The installation might not work.\r\n    \r\ncythoning eddlib/read_bam.pyx to eddlib/read_bam.c\r\nbuilding 'eddlib.read_bam' extension\r\ngcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-linux-x86_64.egg/pysam -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-linux-x86_64.egg/pysam/include/samtools -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-linux-x86_64.egg/pysam/include/tabix -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include -I/software/mb/el6.3/python/pythons/CPython-2.7.9/include/python2.7 -c eddlib/read_bam.c -o build/temp.linux-x86_64-2.7/eddlib/read_bam.o\r\nEn el fichero incluído de /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804,\r\nde /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,\r\nde /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,\r\nde eddlib/read_bam.c:250:\r\n/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: aviso: #warning \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\"\r\n\r\n\r\neddlib/read_bam.c:256:25: error: htslib_util.h: File or dir not exist\r\neddlib/read_bam.c:261:26: error: pysam_stream.h: File or dir not exist\r\neddlib/read_bam.c:265:26: error: samfile_util.h: File or dir not exist\r\neddlib/read_bam.c:855: error: expected specifier-qualifier-list before ‘kseq_t’\r\neddlib/read_bam.c:871: error: expected specifier-qualifier-list before ‘kseq_t’\r\neddlib/read_bam.c:1209: error: expected specifier-qualifier-list before ‘kseq_t’\r\nerror: command 'gcc' failed with exit status 1\r\n\r\n\r\nComplete output from command /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/bin/python -c \"import setuptools;__file__='/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/build/edd/setup.py';exec(compile(open(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))\" install --record /tmp/pip-9R4UxR-record/install-record.txt --single-version-externally-managed --install-headers /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/include/site/python2.7:\r\n\r\n###########\r\nWARNING\r\n###########\r\nEDD requires pysam version 0.8.0 or greater, but the detected version was 0.7.5.The installation might not work.\r\nrunning install\r\n\r\nrunning build\r\nrunning build_py\r\ncreating build\r\ncreating build/lib.linux-x86_64-2.7\r\ncreating build/lib.linux-x86_64-2.7/eddlib\r\ncopying eddlib/estimate.py -> build/lib.linux-x86_64-2.7/eddlib\r\ncopying eddlib/logit.py -> build/lib.linux-x86_64-2.7/eddlib\r\ncopying eddlib/load_params.py -> build/lib.linux-x86_64-2.7/eddlib\r\ncopying eddlib/experiment.py -> build/lib.linux-x86_64-2.7/eddlib\r\ncopying eddlib/__init__.py -> build/lib.linux-x86_64-2.7/eddlib\r\ncopying eddlib/util.py -> build/lib.linux-x86_64-2.7/eddlib\r\ncreating build/lib.linux-x86_64-2.7/eddlib/algorithm\r\ncopying eddlib/algorithm/unalignable_regions.py -> build/lib.linux-x86_64-2.7/eddlib/algorithm\r\ncopying eddlib/algorithm/monte_carlo.py -> build/lib.linux-x86_64-2.7/eddlib/algorithm\r\ncopying eddlib/algorithm/max_segments.py -> build/lib.linux-x86_64-2.7/eddlib/algorithm\r\ncopying eddlib/algorithm/__init__.py -> build/lib.linux-x86_64-2.7/eddlib/algorithm\r\ncopying eddlib/default_parameters.conf -> build/lib.linux-x86_64-2.7/eddlib\r\nrunning build_ext\r\ncythoning eddlib/read_bam.pyx to eddlib/read_bam.c\r\nbuilding 'eddlib.read_bam' extension\r\ncreating build/temp.linux-x86_64-2.7\r\ncreating build/temp.linux-x86_64-2.7/eddlib\r\n\r\ngcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-linux-x86_64.egg/pysam -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-linux-x86_64.egg/pysam/include/samtools -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-linux-x86_64.egg/pysam/include/tabix -I/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include -I/software/mb/el6.3/python/pythons/CPython-2.7.9/include/python2.7 -c eddlib/read_bam.c -o build/temp.linux-x86_64-2.7/eddlib/read_bam.o\r\n\r\nIn the included file of /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804,\r\nde /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,\r\nde /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,\r\nde eddlib/read_bam.c:250:\r\n\r\n/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: aviso: #warning \"Using deprecated NumPy API, disable it by \" \"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION\"\r\n\r\n\r\neddlib/read_bam.c:256:25: error: htslib_util.h: File or dir not exist\r\neddlib/read_bam.c:261:26: error: pysam_stream.h: File or dir not exist\r\neddlib/read_bam.c:265:26: error: samfile_util.h: File or dir not exist\r\neddlib/read_bam.c:855: error: expected specifier-qualifier-list before ‘kseq_t’\r\neddlib/read_bam.c:871: error: expected specifier-qualifier-list before ‘kseq_t’\r\neddlib/read_bam.c:1209: error: expected specifier-qualifier-list before ‘kseq_t’\r\nerror: command 'gcc' failed with exit status 1\r\n\r\n\r\nCleaning up...\r\nCommand /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/bin/python -c \"import setuptools;__file__='/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/build/edd/setup.py';exec(compile(open(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))\" install --record /tmp/pip-9R4UxR-record/install-record.txt --single-version-externally-managed --install-headers /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/include/site/python2.7 failed with error code 1 in /nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/build/edd\r\n\r\nTraceback (most recent call last):\r\n  File \"/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/bin/pip\", line 9, in <module>\r\n    load_entry_point('pip==1.4.1', 'console_scripts', 'pip')()\r\n  File \"/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/pip/__init__.py\", line 148, in main\r\n    return command.main(args[1:], options)\r\n  File \"/nfs/software/mb/el6.3/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/pip/basecommand.py\", line 169, in main\r\n    text = '\\n'.join(complete_log)\r\nUnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 23: ordinal not in range(128)\r\n```\r\nI'm trying to install it in a server with SL6.5:\r\n```\r\nLSB Version:\t:base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch\r\nDistributor ID:\tScientific\r\nDescription:\tScientific Linux release 6.5 (Carbon)\r\nRelease:\t6.5\r\nCodename:\tCarbon\r\n```\r\nThanks for your help,"},"comment":{"url":"https://api.github.com/repos/CollasLab/edd/issues/comments/114260738","html_url":"https://github.com/CollasLab/edd/issues/2#issuecomment-114260738","issue_url":"https://api.github.com/repos/CollasLab/edd/issues/2","id":114260738,"user":{"login":"eivindgl","id":129231,"avatar_url":"https://avatars.githubusercontent.com/u/129231?v=3","gravatar_id":"","url":"https://api.github.com/users/eivindgl","html_url":"https://github.com/eivindgl","followers_url":"https://api.github.com/users/eivindgl/followers","following_url":"https://api.github.com/users/eivindgl/following{/other_user}","gists_url":"https://api.github.com/users/eivindgl/gists{/gist_id}","starred_url":"https://api.github.com/users/eivindgl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eivindgl/subscriptions","organizations_url":"https://api.github.com/users/eivindgl/orgs","repos_url":"https://api.github.com/users/eivindgl/repos","events_url":"https://api.github.com/users/eivindgl/events{/privacy}","received_events_url":"https://api.github.com/users/eivindgl/received_events","type":"User","site_admin":false},"created_at":"2015-06-22T20:59:49Z","updated_at":"2015-06-22T20:59:49Z","body":"Hi,\r\n\r\nThe detected version of pysam when you tried to install EDD was 0.7.5. Could it be that you have multiple versions of pysam installed? Could you try to upgrade the pysam version in your virtual environment? I see that you have multiple outdated packages there, it might be better to upgrade all of them (see http://stackoverflow.com/questions/2720014/upgrading-all-packages-with-pip)."}}