Error during MAJIQ/VOILA installation
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Huck Thornton
Dec 26, 2020, 12:11:06 PM12/26/20
to majiq_voila
I have been trying to install MAJIQ/VOILA but have been running into a very long error message. I have pasted the error message below.
I am very new to bioinformatics. Do you have advice about how to proceed?
Huck Thornton
[x@dev x]$ python3 -m venv env
[x@dev x]$ source env/bin/activate
(env) [x@dev x]$ pip install git+https://bitbucket.org/biociphers/majiq_academic.git#egg=majiq
Collecting majiq
Cloning https://bitbucket.org/biociphers/majiq_academic.git to /tmp/pip-install-ig7yumnw/majiq_8624b5298fcf4d5ea282b4cd555dffd8
Requirement already satisfied: Click==7.0 in ./env/lib/python3.6/site-packages (from majiq) (7.0)
Requirement already satisfied: Flask==1.0.2 in ./env/lib/python3.6/site-packages (from majiq) (1.0.2)
Requirement already satisfied: Flask-Session==0.3.1 in ./env/lib/python3.6/site-packages (from majiq) (0.3.1)
Requirement already satisfied: Flask-WTF==0.14.2 in ./env/lib/python3.6/site-packages (from majiq) (0.14.2)
Requirement already satisfied: gitdb2==2.0.6 in ./env/lib/python3.6/site-packages (from majiq) (2.0.6)
Requirement already satisfied: gunicorn==19.9.0 in ./env/lib/python3.6/site-packages (from majiq) (19.9.0)
Requirement already satisfied: h5py==2.10.0 in ./env/lib/python3.6/site-packages (from majiq) (2.10.0)
Requirement already satisfied: itsdangerous==1.1.0 in ./env/lib/python3.6/site-packages (from majiq) (1.1.0)
Requirement already satisfied: Jinja2==2.11.1 in ./env/lib/python3.6/site-packages (from majiq) (2.11.1)
Requirement already satisfied: MarkupSafe==1.1.1 in ./env/lib/python3.6/site-packages (from majiq) (1.1.1)
Requirement already satisfied: numpy==1.18.1 in ./env/lib/python3.6/site-packages (from majiq) (1.18.1)
Requirement already satisfied: scipy==1.4.1 in ./env/lib/python3.6/site-packages (from majiq) (1.4.1)
Requirement already satisfied: six==1.14.0 in ./env/lib/python3.6/site-packages (from majiq) (1.14.0)
Requirement already satisfied: smmap2==2.0.5 in ./env/lib/python3.6/site-packages (from majiq) (2.0.5)
Requirement already satisfied: waitress==1.1.0 in ./env/lib/python3.6/site-packages (from majiq) (1.1.0)
Requirement already satisfied: Werkzeug==0.16.0 in ./env/lib/python3.6/site-packages (from majiq) (0.16.0)
Requirement already satisfied: WTForms==2.2.1 in ./env/lib/python3.6/site-packages (from majiq) (2.2.1)
Collecting Cython==0.29.14
Using cached Cython-0.29.14-cp36-cp36m-manylinux1_x86_64.whl (2.1 MB)
Collecting GitPython==3.0.5
Using cached GitPython-3.0.5-py3-none-any.whl (455 kB)
Collecting psutil==5.6.7
Using cached psutil-5.6.7.tar.gz (448 kB)
Building wheels for collected packages: majiq, psutil
Building wheel for majiq (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Filers/home/psych02/x/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ig7yumnw/majiq_8624b5298fcf4d5ea282b4cd555dffd8/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ig7yumnw/majiq_8624b5298fcf4d5ea282b4cd555dffd8/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-d1pbk3qs
cwd: /tmp/pip-install-ig7yumnw/majiq_8624b5298fcf4d5ea282b4cd555dffd8/
Complete output (205 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib
creating build/lib/majiq
copying majiq/__init__.py -> build/lib/majiq
copying majiq/run_majiq.py -> build/lib/majiq
creating build/lib/voila
copying voila/__init__.py -> build/lib/voila
copying voila/as_types.py -> build/lib/voila
copying voila/classifier.py -> build/lib/voila
copying voila/config.py -> build/lib/voila
copying voila/constants.py -> build/lib/voila
copying voila/exceptions.py -> build/lib/voila
copying voila/index.py -> build/lib/voila
copying voila/io_voila.py -> build/lib/voila
copying voila/run_voila.py -> build/lib/voila
copying voila/tsv.py -> build/lib/voila
copying voila/vlsv.py -> build/lib/voila
copying voila/voila_log.py -> build/lib/voila
creating build/lib/majiq/src
copying majiq/src/__init__.py -> build/lib/majiq/src
copying majiq/src/basic_pipeline.py -> build/lib/majiq/src
copying majiq/src/config.py -> build/lib/majiq/src
copying majiq/src/constants.py -> build/lib/majiq/src
copying majiq/src/gff.py -> build/lib/majiq/src
copying majiq/src/logger.py -> build/lib/majiq/src
creating build/lib/majiq/src/internals
copying majiq/src/internals/__init__.py -> build/lib/majiq/src/internals
creating build/lib/voila/api
copying voila/api/__init__.py -> build/lib/voila/api
copying voila/api/matrix_hdf5.py -> build/lib/voila/api
copying voila/api/matrix_utils.py -> build/lib/voila/api
copying voila/api/splice_graph.py -> build/lib/voila/api
copying voila/api/view_matrix.py -> build/lib/voila/api
copying voila/api/view_splice_graph.py -> build/lib/voila/api
creating build/lib/voila/c
copying voila/c/__init__.py -> build/lib/voila/c
creating build/lib/voila/tools
copying voila/tools/__init__.py -> build/lib/voila/tools
copying voila/tools/binary_like_arrays.py -> build/lib/voila/tools
copying voila/tools/ctrl_psi_dictionary.py -> build/lib/voila/tools
copying voila/tools/example_tool.py -> build/lib/voila/tools
copying voila/tools/find_binary_lsvs.py -> build/lib/voila/tools
copying voila/tools/flattened_arrays.py -> build/lib/voila/tools
copying voila/tools/gen_voila_html_lines.py -> build/lib/voila/tools
copying voila/tools/hello_caleb.py -> build/lib/voila/tools
copying voila/tools/interactive.py -> build/lib/voila/tools
copying voila/tools/junction_dictionary.py -> build/lib/voila/tools
copying voila/tools/lookup.py -> build/lib/voila/tools
copying voila/tools/lsv_venns.py -> build/lib/voila/tools
copying voila/tools/non_redundant_sets.py -> build/lib/voila/tools
copying voila/tools/putative_cryptic_junctions.py -> build/lib/voila/tools
copying voila/tools/relatively_uniq.py -> build/lib/voila/tools
copying voila/tools/remove_dpsi_priors.py -> build/lib/voila/tools
copying voila/tools/tests.py -> build/lib/voila/tools
copying voila/tools/tool.py -> build/lib/voila/tools
creating build/lib/voila/utils
copying voila/utils/__init__.py -> build/lib/voila/utils
copying voila/utils/utils_voila.py -> build/lib/voila/utils
creating build/lib/voila/view
copying voila/view/__init__.py -> build/lib/voila/view
copying voila/view/datatables.py -> build/lib/voila/view
copying voila/view/deltapsi.py -> build/lib/voila/view
copying voila/view/forms.py -> build/lib/voila/view
copying voila/view/heterogen.py -> build/lib/voila/view
copying voila/view/psi.py -> build/lib/voila/view
copying voila/view/splicegraph.py -> build/lib/voila/view
copying voila/view/views.py -> build/lib/voila/view
creating build/lib/voila/tools/unittests
copying voila/tools/unittests/__init__.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_ctrl_psi_dictionary.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_example_tool.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_find_files.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_find_voila_files.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_hello_caleb.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_junction_dictionary.py -> build/lib/voila/tools/unittests
copying voila/tools/unittests/test_util_print_hello.py -> build/lib/voila/tools/unittests
creating build/lib/voila/tools/utils
copying voila/tools/utils/__init__.py -> build/lib/voila/tools/utils
copying voila/tools/utils/all_pairwise.py -> build/lib/voila/tools/utils
copying voila/tools/utils/calebs_xrange.py -> build/lib/voila/tools/utils
copying voila/tools/utils/compare_dpsis.py -> build/lib/voila/tools/utils
copying voila/tools/utils/find_files.py -> build/lib/voila/tools/utils
copying voila/tools/utils/index_all.py -> build/lib/voila/tools/utils
copying voila/tools/utils/io_caleb.py -> build/lib/voila/tools/utils
copying voila/tools/utils/merge_dicts.py -> build/lib/voila/tools/utils
copying voila/tools/utils/most_common_elem.py -> build/lib/voila/tools/utils
copying voila/tools/utils/percent_through_list.py -> build/lib/voila/tools/utils
copying voila/tools/utils/print_hello.py -> build/lib/voila/tools/utils
copying voila/tools/utils/random_merge_numpy.py -> build/lib/voila/tools/utils
copying voila/tools/utils/string_to_bool.py -> build/lib/voila/tools/utils
running egg_info
creating majiq.egg-info
writing majiq.egg-info/PKG-INFO
writing dependency_links to majiq.egg-info/dependency_links.txt
writing entry points to majiq.egg-info/entry_points.txt
writing requirements to majiq.egg-info/requires.txt
writing top-level names to majiq.egg-info/top_level.txt
writing manifest file 'majiq.egg-info/SOURCES.txt'
reading manifest file 'majiq.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'majiq.egg-info/SOURCES.txt'
creating build/lib/majiq/data
copying majiq/data/defaultprior.pickle -> build/lib/majiq/data
copying majiq/data/git_version -> build/lib/majiq/data
copying voila/api/model.sql -> build/lib/voila/api
creating build/lib/voila/view/static
creating build/lib/voila/view/static/css
copying voila/view/static/css/copy_lsv.css -> build/lib/voila/view/static/css
copying voila/view/static/css/custom.css -> build/lib/voila/view/static/css
copying voila/view/static/css/index.css -> build/lib/voila/view/static/css
copying voila/view/static/css/lsv.css -> build/lib/voila/view/static/css
copying voila/view/static/css/multi_input.css -> build/lib/voila/view/static/css
copying voila/view/static/css/summary.css -> build/lib/voila/view/static/css
creating build/lib/voila/view/static/css/images
copying voila/view/static/css/images/sort_asc.png -> build/lib/voila/view/static/css/images
copying voila/view/static/css/images/sort_asc_disabled.png -> build/lib/voila/view/static/css/images
copying voila/view/static/css/images/sort_both.png -> build/lib/voila/view/static/css/images
copying voila/view/static/css/images/sort_desc.png -> build/lib/voila/view/static/css/images
copying voila/view/static/css/images/sort_desc_disabled.png -> build/lib/voila/view/static/css/images
creating build/lib/voila/view/static/css/lib
copying voila/view/static/css/lib/jquery.dataTables.min.css -> build/lib/voila/view/static/css/lib
copying voila/view/static/css/lib/pure-min.css -> build/lib/voila/view/static/css/lib
copying voila/view/static/css/lib/sumoselect.min.css -> build/lib/voila/view/static/css/lib
creating build/lib/voila/view/static/img
copying voila/view/static/img/LogoOnly.svg -> build/lib/voila/view/static/img
copying voila/view/static/img/LogoOnly_white.svg -> build/lib/voila/view/static/img
copying voila/view/static/img/biociphers.png -> build/lib/voila/view/static/img
copying voila/view/static/img/biociphers_header.png -> build/lib/voila/view/static/img
copying voila/view/static/img/biociphers_wb.png -> build/lib/voila/view/static/img
copying voila/view/static/img/download.svg -> build/lib/voila/view/static/img
copying voila/view/static/img/favicon.ico -> build/lib/voila/view/static/img
copying voila/view/static/img/hide.png -> build/lib/voila/view/static/img
copying voila/view/static/img/left_arrow.svg -> build/lib/voila/view/static/img
copying voila/view/static/img/penn.jpg -> build/lib/voila/view/static/img
copying voila/view/static/img/remove.svg -> build/lib/voila/view/static/img
copying voila/view/static/img/right_arrow.svg -> build/lib/voila/view/static/img
copying voila/view/static/img/solve-icon16.png -> build/lib/voila/view/static/img
copying voila/view/static/img/ucsc.png -> build/lib/voila/view/static/img
copying voila/view/static/img/undo.png -> build/lib/voila/view/static/img
copying voila/view/static/img/zoom_in.png -> build/lib/voila/view/static/img
copying voila/view/static/img/zoom_out.png -> build/lib/voila/view/static/img
creating build/lib/voila/view/static/js
copying voila/view/static/js/ajax.js -> build/lib/voila/view/static/js
copying voila/view/static/js/colors.js -> build/lib/voila/view/static/js
copying voila/view/static/js/copy_lsv.js -> build/lib/voila/view/static/js
copying voila/view/static/js/heatmap.js -> build/lib/voila/view/static/js
copying voila/view/static/js/lsv.js -> build/lib/voila/view/static/js
copying voila/view/static/js/lsvtools.js -> build/lib/voila/view/static/js
copying voila/view/static/js/splicegraphs.js -> build/lib/voila/view/static/js
copying voila/view/static/js/splicegraphtools.js -> build/lib/voila/view/static/js
copying voila/view/static/js/table.js -> build/lib/voila/view/static/js
copying voila/view/static/js/utils.js -> build/lib/voila/view/static/js
copying voila/view/static/js/violin.js -> build/lib/voila/view/static/js
creating build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/clipboard.min.js -> build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/d3-beeswarm.js -> build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/d3.v5.min.js -> build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/jquery.ba-throttle-debounce.min.js -> build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/jquery.dataTables.min.js -> build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/jquery.min.js -> build/lib/voila/view/static/js/lib
copying voila/view/static/js/lib/jquery.sumoselect.min.js -> build/lib/voila/view/static/js/lib
creating build/lib/voila/view/templates
copying voila/view/templates/base.html -> build/lib/voila/view/templates
copying voila/view/templates/base_index.html -> build/lib/voila/view/templates
copying voila/view/templates/base_summary.html -> build/lib/voila/view/templates
copying voila/view/templates/dpsi_index.html -> build/lib/voila/view/templates
copying voila/view/templates/dpsi_summary.html -> build/lib/voila/view/templates
copying voila/view/templates/het_index.html -> build/lib/voila/view/templates
copying voila/view/templates/het_summary.html -> build/lib/voila/view/templates
copying voila/view/templates/psi_index.html -> build/lib/voila/view/templates
copying voila/view/templates/psi_summary.html -> build/lib/voila/view/templates
copying voila/view/templates/sg_summary.html -> build/lib/voila/view/templates
installing to build/bdist.linux-x86_64/wheel
running install
{'distribution': <setuptools.dist.Distribution object at 0x7fd789706898>, 'prefix': '/Filers/home/psych02/x/env', 'exec_prefix': '/Filers/home/psych02/x/env', 'home': None, 'user': 0, 'install_base': '/Filers/home/psych02/x/env', 'install_platbase': '/Filers/home/psych02/x/env', 'root': 'build/bdist.linux-x86_64/wheel', 'install_purelib': 'build/bdist.linux-x86_64/wheel/', 'install_platlib': 'build/bdist.linux-x86_64/wheel/majiq-2.2.data/platlib', 'install_headers': 'build/bdist.linux-x86_64/wheel/majiq-2.2.data/headers', 'install_lib': 'build/bdist.linux-x86_64/wheel/', 'install_scripts': 'build/bdist.linux-x86_64/wheel/majiq-2.2.data/scripts', 'install_data': 'build/bdist.linux-x86_64/wheel/majiq-2.2.data/data', 'install_userbase': '/home/psych02/x/.local', 'install_usersite': '/home/psych02/x/.local/lib/python3.6/site-packages', 'compile': False, 'optimize': None, 'extra_path': None, 'install_path_file': 1, 'force': None, 'skip_build': 0, 'warn_dir': False, 'build_base': 'build', 'build_lib': 'build/lib', 'record': None, 'old_and_unmanageable': None, 'single_version_externally_managed': True, 'voila_only': 0, 'debug_gdb': 0, 'num_threads': 0, '_dry_run': None, 'verbose': 1, 'help': 0, 'finalized': 1, 'config_vars': {'dist_name': 'majiq', 'dist_version': '2.2', 'dist_fullname': 'majiq-2.2', 'py_version': '3.6.8', 'py_version_short': '3.6', 'py_version_nodot': '36', 'sys_prefix': '/Filers/home/psych02/x/env', 'prefix': '/Filers/home/psych02/x/env', 'sys_exec_prefix': '/Filers/home/psych02/x/env', 'exec_prefix': '/Filers/home/psych02/x/env', 'abiflags': 'm', 'userbase': '/home/psych02/x/.local', 'usersite': '/home/psych02/x/.local/lib/python3.6/site-packages', 'base': '/Filers/home/psych02/x/env', 'platbase': '/Filers/home/psych02/x/env'}, 'path_file': None, 'extra_dirs': '', 'install_libbase': 'build/bdist.linux-x86_64/wheel/'}
Compiling majiq/src/polyfitnb.pyx because it changed.
Compiling majiq/src/build.pyx because it changed.
Compiling majiq/src/calc_psi.pyx because it changed.
Compiling majiq/src/deltapsi.pyx because it changed.
Compiling majiq/src/indpnt.pyx because it changed.
Compiling majiq/src/io.pyx because it changed.
Compiling voila/c/splice_graph_sql.pyx because it changed.
[1/7] Cythonizing majiq/src/build.pyx
warning: majiq/src/build.pyx:285:12: Unsigned index type not allowed before OpenMP 3.0
[2/7] Cythonizing majiq/src/calc_psi.pyx
[3/7] Cythonizing majiq/src/deltapsi.pyx
[4/7] Cythonizing majiq/src/indpnt.pyx
[5/7] Cythonizing majiq/src/io.pyx
[6/7] Cythonizing majiq/src/polyfitnb.pyx
[7/7] Cythonizing voila/c/splice_graph_sql.pyx
running install_lib
running build_ext
building 'majiq.src.polyfitnb' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/majiq
creating build/temp.linux-x86_64-3.6/majiq/src
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DNPY_NO_DEPRECATED_API=0 -I/Filers/home/psych02/x/env/lib64/python3.6/site-packages/numpy/core/include -I/Filers/home/psych02/x/env/include -I/usr/include/python3.6m -c majiq/src/polyfitnb.cpp -o build/temp.linux-x86_64-3.6/majiq/src/polyfitnb.o -fopenmp -O3 -std=c++11
majiq/src/polyfitnb.cpp:35:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for majiq
Running setup.py clean for majiq
Building wheel for psutil (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /Filers/home/psych02/x/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-gc9fi74p
cwd: /tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/
Complete output (44 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/psutil
copying psutil/__init__.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_common.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_compat.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psaix.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psosx.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psposix.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.6/psutil
creating build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/__init__.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/__main__.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/runner.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.6/psutil/tests
running build_ext
building 'psutil._psutil_linux' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/psutil
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=567 -DPSUTIL_LINUX=1 -I/Filers/home/psych02/x/env/include -I/usr/include/python3.6m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.6/psutil/_psutil_common.o
psutil/_psutil_common.c:9:20: fatal error: Python.h: No such file or directory
#include <Python.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for psutil
Running setup.py clean for psutil
Failed to build majiq psutil
Installing collected packages: psutil, GitPython, Cython, majiq
Running setup.py install for psutil ... error
ERROR: Command errored out with exit status 1:
command: /Filers/home/psych02/x/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-pse_j7yf/install-record.txt --single-version-externally-managed --compile --install-headers /Filers/home/psych02/x/env/include/site/python3.6/psutil
cwd: /tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/
Complete output (44 lines):
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/psutil
copying psutil/__init__.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_common.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_compat.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psaix.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psbsd.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_pslinux.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psosx.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_psposix.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_pssunos.py -> build/lib.linux-x86_64-3.6/psutil
copying psutil/_pswindows.py -> build/lib.linux-x86_64-3.6/psutil
creating build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/__init__.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/__main__.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/runner.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_aix.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_bsd.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_connections.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_contracts.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_linux.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_memory_leaks.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_misc.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_osx.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_posix.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_process.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_sunos.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_system.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_unicode.py -> build/lib.linux-x86_64-3.6/psutil/tests
copying psutil/tests/test_windows.py -> build/lib.linux-x86_64-3.6/psutil/tests
running build_ext
building 'psutil._psutil_linux' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/psutil
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DPSUTIL_POSIX=1 -DPSUTIL_VERSION=567 -DPSUTIL_LINUX=1 -I/Filers/home/psych02/x/env/include -I/usr/include/python3.6m -c psutil/_psutil_common.c -o build/temp.linux-x86_64-3.6/psutil/_psutil_common.o
psutil/_psutil_common.c:9:20: fatal error: Python.h: No such file or directory
#include <Python.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Filers/home/psych02/x/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ig7yumnw/psutil_6a17eb555aaa4b8ca5472052b3991d52/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-pse_j7yf/install-record.txt --single-version-externally-managed --compile --install-headers /Filers/home/psych02/x/env/include/site/python3.6/psutil Check the logs for full command output.
Paul Jewell
Jan 4, 2021, 12:52:51 PM1/4/21
to majiq_voila
Hello Huck,
Which operating system are you trying to install on?
The relevant error line in your output is:
psutil/_psutil_common.c:9:20: fatal error: Python.h: No such file or directory
This means that you will need to install python development headers to be able to compile a library (psutil in this case).
If you are using a debian-like Linux system, you would accomplish this with a command like:
$ apt install python3-dev
If you are using another operating system, you would need to look up the proper method to install the "Python.h" header file to your system properly.
Thanks,
-Paul
huck.t...@gmail.com
Jan 11, 2021, 4:10:46 AM1/11/21
to majiq_voila
As an update, the suggestion didn't work and I had the system administrator make an attempt at installation. I think it might be better if he/she does it rather than me installing it locally.
"Traceback (most recent call last):[...]
File "/package/majiq/20210108/lib/python3.8/site-packages/majiq/run_majiq.py", line 12, in <module>
from majiq.src.build import build
ModuleNotFoundError: No module named 'majiq.src.build"
Using the "majiq" command, he received the following message:
"Traceback (most recent call last):
The operating system I believe is CentOS 7 and the software is against Python 3.8.3.
I would be grateful for any help.
Huck
Paul Jewell
Jan 11, 2021, 1:57:26 PM1/11/21
to majiq_voila
Hi Huck,
It would be helpful to know how the installation was done to provide more accurate advice. For this specific error, a workaround may be using PythonPath to add the module manually. Please try these commands:
export PYTHONPATH=''
majiq --help
export PYTHONPATH='/package/majiq/20210108/lib/python3.8/site-packages/'
majiq --help
export PYTHONPATH='/package/majiq/20210108/lib/python3.8/site-packages/majiq'
majiq --help
Were you able to run the binary in any of the three cases?
Thanks,
-Paul
Huck Thornton
Jan 12, 2021, 8:29:46 AM1/12/21
to majiq_voila
Hi Paul,
My system administrator tried the suggested solutions and none of them worked.
However, he did ask the following:
"One question I have is which python module file majiq.src.build is supposed to be imported from? I've looked in /package/majiq/20210108/lib/python3.8/site-packages/majiq and it seems a lot of files are missing that appear in the online repository. I wonder if the install (which succeeded without error) has failed to add some crucial file?"
What do you think?
Huck
Huck Thornton
Jan 15, 2021, 11:17:43 AM1/15/21
to majiq_voila
Also, I should clarify that it looks like the MAJIQ installation "worked" (no error message).
However, the following error message that comes up is when I try to run the majiq command.
""Traceback (most recent call last):
[...] File "/package/majiq/20210108/lib/python3.8/site-packages/majiq/run_majiq.py", line 12, in <module> from majiq.src.build import build ModuleNotFoundError: No module named 'majiq.src.build""
[...] File "/package/majiq/20210108/lib/python3.8/site-packages/majiq/run_majiq.py", line 12, in <module> from majiq.src.build import build ModuleNotFoundError: No module named 'majiq.src.build""
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