MAJIQ INSTALLATION ERROR IN MAC OS.

Ankush Bansal

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May 15, 2019, 12:54:41 PM5/15/19

to majiq_voila

Hi,

I was trying to install MAJIQ from last 3-4 weeks, but I am not able to install it on my MAC OS. I was able to install it on other Centos system perfectly.

Could you please tell me where I am making error in installing. I have attached file for reference.

1 warning generated.

g++ -bundle -undefined dynamic_lookup -arch x86_64 -g build/temp.macosx-10.9-x86_64-3.7/majiq/src/polyfitnb.o -o build/lib/majiq/src/polyfitnb.cpython-37m-darwin.so

building 'majiq.src.build' extension

creating build/temp.macosx-10.9-x86_64-3.7/majiq/src/internals

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch x86_64 -g -I./majiq/src/internals -I./voila/c -Imajiq/src/internals -Ivoila/c -I/usr/local/include/env/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include/env/include -I/Library/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c majiq/src/build.cpp -o build/temp.macosx-10.9-x86_64-3.7/majiq/src/build.o -fopenmp -DSCYTHE_COMPILE_DIRECT -DSCYTHE_PTHREAD

clang: error: unsupported option '-fopenmp'

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Command "/usr/local/include/env/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/private/tmp/pip-install-9_slyp38/majiq/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/tmp/pip-record-jcsz4i9c/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/include/env/include/site/python3.7/majiq" failed with error code 1 in /private/tmp/pip-install-9_slyp38/majiq/

Please help me to resolve this problem as I am not able to figure it out.

Thank you very much.

Thanks and Regards,

Ankush Bansal

Error_log.rtf

Ankush Bansal

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May 15, 2019, 1:51:32 PM5/15/19

to majiq_voila

Hi Botao Liu,

Thank you for your swift response.

I tried to install clang compiler in following way as per given link.

brew install llvm

LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib"

echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> ~/.bash_profile

export LDFLAGS="-L/usr/local/opt/llvm/lib"

export CPPFLAGS="-I/usr/local/opt/llvm/include"

But, still getting same error. I have attached file for reference.

Should I use any other way of installing Clang Compiler ?

Thanks and Regards,

Ankush bansal

Error_Log_2.rtf

Jordi Vaquero

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May 17, 2019, 1:54:38 PM5/17/19

to Ankush Bansal, majiq_voila

Hello,

The problem is installing openmp compatibilities for clang. But the best approach is installing GNU C++. That is an easy process using homebrew, for example

Jordi

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Allison Cote

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Jun 27, 2019, 2:14:28 PM6/27/19

to majiq_voila

I am having the same issue trying to install MAJIQ2 on my mac desktop. I've tried to install gcc using homebrew, but it doesn't seem to help (brew install gcc). I think missing openmp support is definitely the issue, but how do I force OSX to point to the appropriate compiler? I tried creating a new virtual environment with gcc=4.8.5 and got a different error (below, but I'm not sure it's relevant).

creating build/temp.macosx-10.9-x86_64-3.7/majiq/src

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda2/envs/forlongread/include -arch x86_64 -I/anaconda2/envs/forlongread/include -arch x86_64 -I/usr/local/opt/llvm/include -I/Users/allisoncote/code/K562_seq/env/lib/python3.7/site-packages/numpy/core/include -I/Users/allisoncote/code/K562_seq/env/include -I/anaconda2/envs/forlongread/include/python3.7m -c majiq/src/polyfitnb.cpp -o build/temp.macosx-10.9-x86_64-3.7/majiq/src/polyfitnb.o

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]

In file included from /anaconda2/envs/formajiq/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0,

from /anaconda2/envs/formajiq/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34,

from /anaconda2/envs/forlongread/include/python3.7m/Python.h:11,

from majiq/src/polyfitnb.cpp:24:

/anaconda2/envs/formajiq/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

#include_next <limits.h> /* recurse down to the real one */

^

compilation terminated.

error: command 'gcc' failed with exit status 1

----------------------------------------

ERROR: Command "/Users/allisoncote/code/K562_seq/env/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/private/var/folders/5m/5q4sfxwd4l32t87jlyl94bwc0000gn/T/pip-install-ptt80jzw/majiq/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/5m/5q4sfxwd4l32t87jlyl94bwc0000gn/T/pip-record-24omc5pp/install-record.txt --single-version-externally-managed --compile --install-headers /Users/allisoncote/code/K562_seq/env/include/site/python3.7/majiq" failed with error code 1 in /private/var/folders/5m/5q4sfxwd4l32t87jlyl94bwc0000gn/T/pip-install-ptt80jzw/majiq/

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Jordi Vaquero

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Jun 27, 2019, 2:41:30 PM6/27/19

to Allison Cote, majiq_voila

If you installed the gcc with homebrew you can try something like

CC=/usr/local/bin/gcc-8 CXX=/usr/local/bin/g++-8 pip install ……

jordi

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Allison Cote

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Jun 27, 2019, 2:49:43 PM6/27/19

to majiq_voila

That worked, thanks!!

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Taylor Floyd

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Jul 30, 2019, 3:38:36 PM7/30/19

to majiq_voila

Hello Jordi,

I followed all the aforementioned installation instructions, as well as making sure my compilers are up to date. I'm still unable to install majiq2.1 and get the attached error messages. Any help would be great! Thank you for your time.

To view this discussion on the web visit https://groups.google.com/d/msgid/majiq_voila/263c468b-76ee-414f-9519-e146b626534a%40googlegroups.com.

MAJIQ.Error.1.png

Paul Jewell

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Jul 30, 2019, 4:16:27 PM7/30/19

to majiq_voila

Hi Taylor,

I can see the error mention at the time, but I am not able to see a standard error message / reason that I would usually expect following the commandline call. Would you be able to scroll down to the bottom to show the full output, or just copy+paste the text of the full run?

Thanks,

-Paul

Taylor Floyd

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Jul 30, 2019, 4:40:55 PM7/30/19

to majiq_voila

Hi Paul,

Here's the full run:

(env) MAC202754:~ tlf2002$ pip install git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

Collecting majiq from git+https://bitbucket.org/biociphers/majiq_stable.git#egg=majiq

Cloning https://bitbucket.org/biociphers/majiq_stable.git to /private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq

Running command git clone -q https://bitbucket.org/biociphers/majiq_stable.git /private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq

Building wheels for collected packages: majiq

Building wheel for majiq (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /Users/tlf2002/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq/setup.py'"'"'; __file__='"'"'/private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq/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 /private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-wheel-zvxxm7e4 --python-tag cp37

cwd: /private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq/

Complete output (324 lines):

running bdist_wheel

running build

installing to build/bdist.macosx-10.14-x86_64/wheel

running install

0

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/io.pyx because it changed.

Compiling voila/c/splice_graph_sql.pyx because it changed.

[1/6] Cythonizing majiq/src/build.pyx

[2/6] Cythonizing majiq/src/calc_psi.pyx

[3/6] Cythonizing majiq/src/deltapsi.pyx

[4/6] Cythonizing majiq/src/io.pyx

[5/6] Cythonizing majiq/src/polyfitnb.pyx

[6/6] Cythonizing voila/c/splice_graph_sql.pyx

running install_lib

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/vlsv.py -> build/lib/voila

copying voila/classifier.py -> build/lib/voila

copying voila/as_types.py -> build/lib/voila

copying voila/config.py -> build/lib/voila

copying voila/index.py -> build/lib/voila

copying voila/io_voila.py -> build/lib/voila

copying voila/constants.py -> build/lib/voila

copying voila/__init__.py -> build/lib/voila

copying voila/tsv.py -> build/lib/voila

copying voila/run_voila.py -> build/lib/voila

copying voila/exceptions.py -> build/lib/voila

copying voila/voila_log.py -> build/lib/voila

creating 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/__init__.py -> build/lib/majiq/src

copying majiq/src/logger.py -> build/lib/majiq/src

copying majiq/src/gff.py -> build/lib/majiq/src

copying majiq/src/basic_pipeline.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/tools

copying voila/tools/lsv_venns.py -> build/lib/voila/tools

copying voila/tools/binary_like_arrays.py -> build/lib/voila/tools

copying voila/tools/flattened_arrays.py -> build/lib/voila/tools

copying voila/tools/remove_dpsi_priors.py -> build/lib/voila/tools

copying voila/tools/lookup.py -> build/lib/voila/tools

copying voila/tools/__init__.py -> build/lib/voila/tools

copying voila/tools/junction_dictionary.py -> build/lib/voila/tools

copying voila/tools/putative_cryptic_junctions.py -> build/lib/voila/tools

copying voila/tools/interactive.py -> build/lib/voila/tools

copying voila/tools/example_tool.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/ctrl_psi_dictionary.py -> build/lib/voila/tools

copying voila/tools/tests.py -> build/lib/voila/tools

copying voila/tools/relatively_uniq.py -> build/lib/voila/tools

copying voila/tools/find_binary_lsvs.py -> build/lib/voila/tools

copying voila/tools/tool.py -> build/lib/voila/tools

copying voila/tools/non_redundant_sets.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/psi.py -> build/lib/voila/view

copying voila/view/splicegraph.py -> build/lib/voila/view

copying voila/view/heterogen.py -> build/lib/voila/view

copying voila/view/__init__.py -> build/lib/voila/view

copying voila/view/forms.py -> build/lib/voila/view

copying voila/view/deltapsi.py -> build/lib/voila/view

copying voila/view/datatables.py -> build/lib/voila/view

copying voila/view/views.py -> build/lib/voila/view

creating build/lib/voila/api

copying voila/api/matrix_hdf5.py -> build/lib/voila/api

copying voila/api/view_splice_graph.py -> build/lib/voila/api

copying voila/api/matrix_utils.py -> build/lib/voila/api

copying voila/api/__init__.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

creating build/lib/voila/c

copying voila/c/__init__.py -> build/lib/voila/c

creating build/lib/voila/tools/unittests

copying voila/tools/unittests/test_junction_dictionary.py -> build/lib/voila/tools/unittests

copying voila/tools/unittests/test_find_files.py -> build/lib/voila/tools/unittests

copying voila/tools/unittests/__init__.py -> build/lib/voila/tools/unittests

copying voila/tools/unittests/test_example_tool.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_find_voila_files.py -> build/lib/voila/tools/unittests

copying voila/tools/unittests/test_util_print_hello.py -> build/lib/voila/tools/unittests

copying voila/tools/unittests/test_hello_caleb.py -> build/lib/voila/tools/unittests

creating build/lib/voila/tools/utils

copying voila/tools/utils/compare_dpsis.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/__init__.py -> build/lib/voila/tools/utils

copying voila/tools/utils/calebs_xrange.py -> build/lib/voila/tools/utils

copying voila/tools/utils/string_to_bool.py -> build/lib/voila/tools/utils

copying voila/tools/utils/all_pairwise.py -> build/lib/voila/tools/utils

copying voila/tools/utils/io_caleb.py -> build/lib/voila/tools/utils

copying voila/tools/utils/percent_through_list.py -> build/lib/voila/tools/utils

copying voila/tools/utils/index_all.py -> build/lib/voila/tools/utils

copying voila/tools/utils/find_files.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

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 majiq/src/build.cpp -> build/lib/majiq/src

copying majiq/src/calc_psi.cpp -> build/lib/majiq/src

copying majiq/src/deltapsi.cpp -> build/lib/majiq/src

copying majiq/src/io.cpp -> build/lib/majiq/src

copying majiq/src/polyfitnb.cpp -> build/lib/majiq/src

copying majiq/src/internals/grimoire.cpp -> build/lib/majiq/src/internals

copying majiq/src/internals/io_bam.cpp -> build/lib/majiq/src/internals

copying majiq/src/internals/psi.cpp -> build/lib/majiq/src/internals

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

copying voila/api/model.sql -> build/lib/voila/api

copying voila/c/splice_graph_sql.cpp -> build/lib/voila/c

copying voila/c/sqlite3.c -> build/lib/voila/c

running build_ext

building 'majiq.src.polyfitnb' extension

creating build/temp.macosx-10.14-x86_64-3.7

creating build/temp.macosx-10.14-x86_64-3.7/majiq

creating build/temp.macosx-10.14-x86_64-3.7/majiq/src

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/opt/llvm/include -I/Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/Users/tlf2002/env/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c majiq/src/polyfitnb.cpp -o build/temp.macosx-10.14-x86_64-3.7/majiq/src/polyfitnb.o

In file included from majiq/src/polyfitnb.cpp:632:

In file included from /Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:

In file included from /Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:

/Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

#warning "Using deprecated NumPy API, disable it with " \

^

1 warning generated.

clang++ -bundle -undefined dynamic_lookup -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -L/usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include build/temp.macosx-10.14-x86_64-3.7/majiq/src/polyfitnb.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -o build/lib/majiq/src/polyfitnb.cpython-37m-darwin.so

building 'majiq.src.build' extension

creating build/temp.macosx-10.14-x86_64-3.7/majiq/src/internals

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/opt/llvm/include -I./majiq/src/internals -I./voila/c -Imajiq/src/internals -Ivoila/c -I/Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/Users/tlf2002/env/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c majiq/src/build.cpp -o build/temp.macosx-10.14-x86_64-3.7/majiq/src/build.o -fopenmp -DSCYTHE_COMPILE_DIRECT -DSCYTHE_PTHREAD

In file included from majiq/src/build.cpp:673:

In file included from /Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:

In file included from /Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830:

/Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

#warning "Using deprecated NumPy API, disable it with " \

^

In file included from majiq/src/build.cpp:675:

./majiq/src/internals/grimoire.hpp:232:18: warning: 'grimoire::Exon::set_simpl_fltr' hides overloaded virtual function [-Woverloaded-virtual]

void set_simpl_fltr(bool val) {};

^

./majiq/src/internals/grimoire.hpp:68:27: note: hidden overloaded virtual function 'grimoire::_Region::set_simpl_fltr' declared here: different number of parameters (2 vs 1)

virtual void set_simpl_fltr(bool val, bool in) { cerr << "NOT SHOW\n" ;}

^

./majiq/src/internals/grimoire.hpp:431:21: warning: 'grimoire::Gene::set_simpl_fltr' hides overloaded virtual function [-Woverloaded-virtual]

void set_simpl_fltr(bool val) {};

^

./majiq/src/internals/grimoire.hpp:68:27: note: hidden overloaded virtual function 'grimoire::_Region::set_simpl_fltr' declared here: different number of parameters (2 vs 1)

virtual void set_simpl_fltr(bool val, bool in) { cerr << "NOT SHOW\n" ;}

^

majiq/src/build.cpp:5452:21: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:5452:13: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

majiq/src/build.cpp:4346:21: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:4346:13: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

majiq/src/build.cpp:7767:25: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:7767:17: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

majiq/src/build.cpp:10290:25: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:10290:17: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

majiq/src/build.cpp:9420:33: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:9420:25: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

majiq/src/build.cpp:11289:21: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:11289:13: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

majiq/src/build.cpp:10907:21: warning: code will never be executed [-Wunreachable-code]

if (1 == 0) abort();

^~~~~

majiq/src/build.cpp:10907:13: note: silence by adding parentheses to mark code as explicitly dead

if (1 == 0) abort();

^

/* DISABLES CODE */ ( )

10 warnings generated.

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/opt/llvm/include -I./majiq/src/internals -I./voila/c -Imajiq/src/internals -Ivoila/c -I/Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/Users/tlf2002/env/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c majiq/src/internals/io_bam.cpp -o build/temp.macosx-10.14-x86_64-3.7/majiq/src/internals/io_bam.o -fopenmp -DSCYTHE_COMPILE_DIRECT -DSCYTHE_PTHREAD

In file included from majiq/src/internals/io_bam.cpp:11:

In file included from ./majiq/src/internals/io_bam.hpp:7:

./majiq/src/internals/grimoire.hpp:232:18: warning: 'grimoire::Exon::set_simpl_fltr' hides overloaded virtual function [-Woverloaded-virtual]

void set_simpl_fltr(bool val) {};

^

./majiq/src/internals/grimoire.hpp:68:27: note: hidden overloaded virtual function 'grimoire::_Region::set_simpl_fltr' declared here: different number of parameters (2 vs 1)

virtual void set_simpl_fltr(bool val, bool in) { cerr << "NOT SHOW\n" ;}

^

./majiq/src/internals/grimoire.hpp:431:21: warning: 'grimoire::Gene::set_simpl_fltr' hides overloaded virtual function [-Woverloaded-virtual]

void set_simpl_fltr(bool val) {};

^

./majiq/src/internals/grimoire.hpp:68:27: note: hidden overloaded virtual function 'grimoire::_Region::set_simpl_fltr' declared here: different number of parameters (2 vs 1)

virtual void set_simpl_fltr(bool val, bool in) { cerr << "NOT SHOW\n" ;}

^

2 warnings generated.

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/opt/llvm/include -I./majiq/src/internals -I./voila/c -Imajiq/src/internals -Ivoila/c -I/Users/tlf2002/env/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/Users/tlf2002/env/include -I/usr/local/Cellar/python/3.7.4/Frameworks/Python.framework/Versions/3.7/include/python3.7m -c majiq/src/internals/grimoire.cpp -o build/temp.macosx-10.14-x86_64-3.7/majiq/src/internals/grimoire.o -fopenmp -DSCYTHE_COMPILE_DIRECT -DSCYTHE_PTHREAD

In file included from majiq/src/internals/grimoire.cpp:12:

./majiq/src/internals/grimoire.hpp:232:18: warning: 'grimoire::Exon::set_simpl_fltr' hides overloaded virtual function [-Woverloaded-virtual]

void set_simpl_fltr(bool val) {};

^

./majiq/src/internals/grimoire.hpp:68:27: note: hidden overloaded virtual function 'grimoire::_Region::set_simpl_fltr' declared here: different number of parameters (2 vs 1)

virtual void set_simpl_fltr(bool val, bool in) { cerr << "NOT SHOW\n" ;}

^

./majiq/src/internals/grimoire.hpp:431:21: warning: 'grimoire::Gene::set_simpl_fltr' hides overloaded virtual function [-Woverloaded-virtual]

void set_simpl_fltr(bool val) {};

^

./majiq/src/internals/grimoire.hpp:68:27: note: hidden overloaded virtual function 'grimoire::_Region::set_simpl_fltr' declared here: different number of parameters (2 vs 1)

virtual void set_simpl_fltr(bool val, bool in) { cerr << "NOT SHOW\n" ;}

^

2 warnings generated.

clang++ -bundle -undefined dynamic_lookup -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -L/usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include build/temp.macosx-10.14-x86_64-3.7/majiq/src/build.o build/temp.macosx-10.14-x86_64-3.7/majiq/src/internals/io_bam.o build/temp.macosx-10.14-x86_64-3.7/majiq/src/internals/grimoire.o -L/usr/local/lib -Lmajiq/src/internals -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -L/usr/local/lib -Lmajiq/src/internals -lhts -lz -o build/lib/majiq/src/build.cpython-37m-darwin.so -lgomp

ld: library not found for -lgomp

clang-8: error: linker command failed with exit code 1 (use -v to see invocation)

error: command 'clang++' failed with exit status 1

----------------------------------------

ERROR: Failed building wheel for majiq

Running setup.py clean for majiq

Failed to build majiq

Installing collected packages: majiq

Running setup.py install for majiq ... error

ERROR: Command errored out with exit status 1:

command: /Users/tlf2002/env/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq/setup.py'"'"'; __file__='"'"'/private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-record-mdzbozk_/install-record.txt --single-version-externally-managed --compile --install-headers /Users/tlf2002/env/include/site/python3.7/majiq

cwd: /private/var/folders/1x/tf2vf0915dx36fbdm5kxd_c00000gp/T/pip-install-bcywb88i/majiq/

Complete output (307 lines):