{"action":"created","issue":{"url":"https://api.github.com/repos/mit-probabilistic-computing-project/crosscat/issues/28","labels_url":"https://api.github.com/repos/mit-probabilistic-computing-project/crosscat/issues/28/labels{/name}","comments_url":"https://api.github.com/repos/mit-probabilistic-computing-project/crosscat/issues/28/comments","events_url":"https://api.github.com/repos/mit-probabilistic-computing-project/crosscat/issues/28/events","html_url":"https://github.com/mit-probabilistic-computing-project/crosscat/issues/28","id":55691158,"number":28,"title":"Unable to install CrossCat using pip","user":{"login":"yarden","id":96318,"avatar_url":"https://avatars.githubusercontent.com/u/96318?v=3","gravatar_id":"","url":"https://api.github.com/users/yarden","html_url":"https://github.com/yarden","followers_url":"https://api.github.com/users/yarden/followers","following_url":"https://api.github.com/users/yarden/following{/other_user}","gists_url":"https://api.github.com/users/yarden/gists{/gist_id}","starred_url":"https://api.github.com/users/yarden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yarden/subscriptions","organizations_url":"https://api.github.com/users/yarden/orgs","repos_url":"https://api.github.com/users/yarden/repos","events_url":"https://api.github.com/users/yarden/events{/privacy}","received_events_url":"https://api.github.com/users/yarden/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-01-27T23:28:13Z","updated_at":"2015-01-31T19:06:48Z","closed_at":null,"body":"Hi,\r\n\r\nI'm having trouble installing CrossCat using ``pip`` in my local virtual environment. I simply cloned the ``crosscat`` repository from github, and in that repository ran:\r\n\r\n``pip install .``\r\n\r\nThe results were:\r\n\r\n```\r\n$ pip install .\r\nUnpacking /ahg/regevdata/users/yarden/software/crosscat\r\n  Running setup.py egg_info for package from file:///ahg/regevdata/users/yarden/software/crosscat\r\n    which: no ccache in (/ahg/regevdata/users/yarden/myenv/bin:/home/unix/yarden/bin:/broad/lsf9/9.1/linux2.6-glibc2.3-x86_64/bin:/ahg/regevdata/users/yarden/myenv/bin:/home/unix/yarden/bin:/ahg/regevdata/users/yarden/myenv/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/emacs_24.2/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/mysql_5.6.20/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/perl_5.14.2/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bioperl_1.6.923/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/sqlite_3.6.19/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/tophat_2.0.10/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bowtie2_2.0.5:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bowtie_0.12.9:/broad/software/free/Linux/redhat_6_x86_64/pkgs/samtools/samtools_0.1.19/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/zlib_1.2.6/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bedtools_version-2.16.1/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/scipy_0.13.0-python-2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/matplotlib_1.3.1-python-2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/db_4.7.25/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/tcltk8.5.9/bin:/broad/lsf9/9.1/linux2.6-glibc2.3-x86_64/etc:/broad/software/free/Linux/redhat_6_x86_64/pkgs/lsf_drmaa-1.1.1/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.1.0-bioconductor-2.14/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/bin:/home/unix/yarden/bin:/broad/tools/NoArch/pkgs/local:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/)\r\n    \r\nRequirement already satisfied (use --upgrade to upgrade): scipy>=0.11.0 in /broad/software/free/Linux/redhat_6_x86_64/pkgs/scipy_0.13.0-python-2.7.1-sqlite3-rtrees/lib/python2.7/site-packages (from CrossCat==0.1)\r\nRequirement already satisfied (use --upgrade to upgrade): numpy>=1.7.0 in /ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages (from CrossCat==0.1)\r\nInstalling collected packages: CrossCat\r\n  Running setup.py install for CrossCat\r\n    which: no ccache in (/ahg/regevdata/users/yarden/myenv/bin:/home/unix/yarden/bin:/broad/lsf9/9.1/linux2.6-glibc2.3-x86_64/bin:/ahg/regevdata/users/yarden/myenv/bin:/home/unix/yarden/bin:/ahg/regevdata/users/yarden/myenv/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/emacs_24.2/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/mysql_5.6.20/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/perl_5.14.2/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bioperl_1.6.923/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/sqlite_3.6.19/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/tophat_2.0.10/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bowtie2_2.0.5:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bowtie_0.12.9:/broad/software/free/Linux/redhat_6_x86_64/pkgs/samtools/samtools_0.1.19/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/zlib_1.2.6/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bedtools_version-2.16.1/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/scipy_0.13.0-python-2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/matplotlib_1.3.1-python-2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/db_4.7.25/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/tcltk8.5.9/bin:/broad/lsf9/9.1/linux2.6-glibc2.3-x86_64/etc:/broad/software/free/Linux/redhat_6_x86_64/pkgs/lsf_drmaa-1.1.1/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.1.0-bioconductor-2.14/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/bin:/home/unix/yarden/bin:/broad/tools/NoArch/pkgs/local:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/)\r\n    building 'crosscat.cython_code.CyclicComponentModel' extension\r\n    gcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c crosscat/cython_code/CyclicComponentModel.c -o build/temp.linux-x86_64-2.7/crosscat/cython_code/CyclicComponentModel.o\r\n    gcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o\r\n    gcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o\r\n    gcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o\r\n    gcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o\r\n    gcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/CyclicComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/CyclicComponentModel.o\r\n    gcc: error: crosscat/cython_code/CyclicComponentModel.c: No such file or directory\r\n    gcc: fatal error: no input files\r\n    compilation terminated.\r\n    error: command 'gcc' failed with exit status 1\r\n    Complete output from command /ahg/regevdata/users/yarden/myenv/bin/python -c \"import setuptools;__file__='/tmp/pip-ZYN_sU-build/setup.py';exec(compile(open(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))\" install --record /tmp/pip-5armZF-record/install-record.txt --single-version-externally-managed --install-headers /ahg/regevdata/users/yarden/myenv/include/site/python2.7:\r\n    which: no ccache in (/ahg/regevdata/users/yarden/myenv/bin:/home/unix/yarden/bin:/broad/lsf9/9.1/linux2.6-glibc2.3-x86_64/bin:/ahg/regevdata/users/yarden/myenv/bin:/home/unix/yarden/bin:/ahg/regevdata/users/yarden/myenv/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/emacs_24.2/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/mysql_5.6.20/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/perl_5.14.2/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bioperl_1.6.923/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/sqlite_3.6.19/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/tophat_2.0.10/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bowtie2_2.0.5:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bowtie_0.12.9:/broad/software/free/Linux/redhat_6_x86_64/pkgs/samtools/samtools_0.1.19/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/zlib_1.2.6/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/bedtools_version-2.16.1/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/scipy_0.13.0-python-2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/matplotlib_1.3.1-python-2.7.1-sqlite3-rtrees/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/db_4.7.25/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/tcltk8.5.9/bin:/broad/lsf9/9.1/linux2.6-glibc2.3-x86_64/etc:/broad/software/free/Linux/redhat_6_x86_64/pkgs/lsf_drmaa-1.1.1/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/r_3.1.0-bioconductor-2.14/bin:/broad/software/free/Linux/redhat_6_x86_64/pkgs/gcc_4.9.0/bin:/home/unix/yarden/bin:/broad/tools/NoArch/pkgs/local:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/:/home/unix/yarden/regevdata/bedtools2/bin:/home/unix/yarden/regevdata/software/sratoolkit.2.4.2-ubuntu64/bin:/home/unix/yarden/regevdata/software/ncftp-3.2.5/bin:/home/unix/yarden/bin/)\r\n\r\nrunning install\r\n\r\nrunning build\r\n\r\nrunning build_py\r\n\r\ncreating build\r\n\r\ncreating build/lib.linux-x86_64-2.7\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/JSONRPCEngine.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/CrossCatClient.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/MultiprocessingEngine.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/LocalEngine.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/__init__.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/starcluster_plugin.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/EngineTemplate.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/HadoopEngine.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/IPClusterEngine.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncopying crosscat/settings.py -> build/lib.linux-x86_64-2.7/crosscat\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/convergence_test_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/api_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/diagnostic_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/inference_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/xnet_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/hadoop_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/mutual_information_test_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/enumerate_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/timing_test_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/validate_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/plot_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/geweke_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/sample_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/useCase_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/file_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/data_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncopying crosscat/utils/general_utils.py -> build/lib.linux-x86_64-2.7/crosscat/utils\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncopying crosscat/convergence_analysis/parse_convergence_results.py -> build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncopying crosscat/convergence_analysis/automated_convergence_tests.py -> build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncopying crosscat/convergence_analysis/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncopying crosscat/convergence_analysis/generate_convergence_script.py -> build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncopying crosscat/convergence_analysis/plot_convergence_results.py -> build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncopying crosscat/convergence_analysis/convergence_test.py -> build/lib.linux-x86_64-2.7/crosscat/convergence_analysis\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/jsonrpc_http\r\n\r\ncopying crosscat/jsonrpc_http/test_resume.py -> build/lib.linux-x86_64-2.7/crosscat/jsonrpc_http\r\n\r\ncopying crosscat/jsonrpc_http/stub_client_jsonrpc.py -> build/lib.linux-x86_64-2.7/crosscat/jsonrpc_http\r\n\r\ncopying crosscat/jsonrpc_http/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/jsonrpc_http\r\n\r\ncopying crosscat/jsonrpc_http/test_engine.py -> build/lib.linux-x86_64-2.7/crosscat/jsonrpc_http\r\n\r\ncopying crosscat/jsonrpc_http/server_jsonrpc.py -> build/lib.linux-x86_64-2.7/crosscat/jsonrpc_http\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/test_pred_prob_and_density.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/test_multinomial_impute.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/setup.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/test_missing_value.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/mixed_state_test.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/state_test.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/test_sample.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncopying crosscat/cython_code/continuous_component_model_test.py -> build/lib.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/test_pred_prob_and_density.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/cpp_long_tests.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/test_sampler_enumeration.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/cpp_unit_tests.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/timing_analysis.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/test_log_likelihood.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncopying crosscat/tests/geweke_on_schemas.py -> build/lib.linux-x86_64-2.7/crosscat/tests\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/synthetic_data_generator.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/test_impute_quality.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/test_mixture_inference_quality.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/test_kl_divergence_quality.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/test_component_model_quality.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/test_predictive_confidence.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncopying crosscat/tests/quality_tests/quality_test_utils.py -> build/lib.linux-x86_64-2.7/crosscat/tests/quality_tests\r\n\r\ncreating build/lib.linux-x86_64-2.7/crosscat/tests/component_model_extensions\r\n\r\ncopying crosscat/tests/component_model_extensions/MultinomialComponentModel.py -> build/lib.linux-x86_64-2.7/crosscat/tests/component_model_extensions\r\n\r\ncopying crosscat/tests/component_model_extensions/__init__.py -> build/lib.linux-x86_64-2.7/crosscat/tests/component_model_extensions\r\n\r\ncopying crosscat/tests/component_model_extensions/CyclicComponentModel.py -> build/lib.linux-x86_64-2.7/crosscat/tests/component_model_extensions\r\n\r\ncopying crosscat/tests/component_model_extensions/ContinuousComponentModel.py -> build/lib.linux-x86_64-2.7/crosscat/tests/component_model_extensions\r\n\r\nrunning build_ext\r\n\r\nbuilding 'crosscat.cython_code.CyclicComponentModel' extension\r\n\r\ncreating build/temp.linux-x86_64-2.7\r\n\r\ncreating build/temp.linux-x86_64-2.7/crosscat\r\n\r\ncreating build/temp.linux-x86_64-2.7/crosscat/cython_code\r\n\r\ncreating build/temp.linux-x86_64-2.7/cpp_code\r\n\r\ncreating build/temp.linux-x86_64-2.7/cpp_code/src\r\n\r\ngcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c crosscat/cython_code/CyclicComponentModel.c -o build/temp.linux-x86_64-2.7/crosscat/cython_code/CyclicComponentModel.o\r\n\r\ngcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/utils.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/utils.o\r\n\r\ngcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/numerics.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/numerics.o\r\n\r\ngcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/RandomNumberGenerator.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/RandomNumberGenerator.o\r\n\r\ngcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/ComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/ComponentModel.o\r\n\r\ngcc -pthread -fno-strict-aliasing -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/tcltk8.5.9/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/sqlite_3.7.5/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/db_4.7.25/include -DNDEBUG -fPIC -Icpp_code/include/CrossCat -I/ahg/regevdata/users/yarden/myenv/lib/python2.7/site-packages/numpy/core/include -I/broad/software/free/Linux/redhat_5_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/include/python2.7 -c cpp_code/src/CyclicComponentModel.cpp -o build/temp.linux-x86_64-2.7/cpp_code/src/CyclicComponentModel.o\r\n\r\ngcc: error: crosscat/cython_code/CyclicComponentModel.c: No such file or directory\r\n\r\ngcc: fatal error: no input files\r\n\r\ncompilation terminated.\r\n\r\nerror: command 'gcc' failed with exit status 1\r\n\r\n----------------------------------------\r\nCommand /ahg/regevdata/users/yarden/myenv/bin/python -c \"import setuptools;__file__='/tmp/pip-ZYN_sU-build/setup.py';exec(compile(open(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))\" install --record /tmp/pip-5armZF-record/install-record.txt --single-version-externally-managed --install-headers /ahg/regevdata/users/yarden/myenv/include/site/python2.7 failed with error code 1 in /tmp/pip-ZYN_sU-build\r\nStoring complete log in /home/unix/yarden/.pip/pip.log\r\n```\r\n\r\nAny thoughts on this?\r\n\r\nI haven't looked too closely but it looks like Cython never gets invoked so the *.c files it should produce like ``crosscat/cython_code/CyclicComponentModel.c`` are not found."},"comment":{"url":"https://api.github.com/repos/mit-probabilistic-computing-project/crosscat/issues/comments/72331149","html_url":"https://github.com/mit-probabilistic-computing-project/crosscat/issues/28#issuecomment-72331149","issue_url":"https://api.github.com/repos/mit-probabilistic-computing-project/crosscat/issues/28","id":72331149,"user":{"login":"BaxterEaves","id":1041591,"avatar_url":"https://avatars.githubusercontent.com/u/1041591?v=3","gravatar_id":"","url":"https://api.github.com/users/BaxterEaves","html_url":"https://github.com/BaxterEaves","followers_url":"https://api.github.com/users/BaxterEaves/followers","following_url":"https://api.github.com/users/BaxterEaves/following{/other_user}","gists_url":"https://api.github.com/users/BaxterEaves/gists{/gist_id}","starred_url":"https://api.github.com/users/BaxterEaves/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BaxterEaves/subscriptions","organizations_url":"https://api.github.com/users/BaxterEaves/orgs","repos_url":"https://api.github.com/users/BaxterEaves/repos","events_url":"https://api.github.com/users/BaxterEaves/events{/privacy}","received_events_url":"https://api.github.com/users/BaxterEaves/received_events","type":"User","site_admin":false},"created_at":"2015-01-31T19:06:48Z","updated_at":"2015-01-31T19:06:48Z","body":"From a virtualenv, doing `python setup.py build` and then `pip install .` worked for me without `sudo` (doing `pip install .` did not work)."}}