MISO Installation Errer on Mac OS
0
0
Entering edit mode
6.4 years ago

Please help me find out the reason of MISO installation error.

python2 -m pip install misopy
Collecting misopy
  Using cached misopy-0.5.4.tar.gz
Requirement already satisfied: matplotlib in /anaconda2/lib/python2.7/site-packages (from misopy)
Requirement already satisfied: numpy>=1.5.0 in /anaconda2/lib/python2.7/site-packages (from misopy)
Requirement already satisfied: scipy>=0.9.0 in /anaconda2/lib/python2.7/site-packages (from misopy)
Requirement already satisfied: pysam>=0.6.0 in /anaconda2/lib/python2.7/site-packages (from misopy)
Requirement already satisfied: six>=1.10 in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Requirement already satisfied: python-dateutil>=2.0 in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Requirement already satisfied: backports.functools_lru_cache in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Requirement already satisfied: subprocess32 in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Requirement already satisfied: pytz in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Requirement already satisfied: cycler>=0.10 in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /anaconda2/lib/python2.7/site-packages (from matplotlib->misopy)
Building wheels for collected packages: misopy
  Running setup.py bdist_wheel for misopy ... error
  Complete output from command /anaconda2/bin/python2 -u -c "import setuptools, tokenize;__file__='/private/var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/pip-build-iDBF1r/misopy/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 /var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/tmppYenk6pip-wheel- --python-tag cp27:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.6-x86_64-2.7
  creating build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/credible_intervals.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/miso_utils.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/samples_utils.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/pickle_utils.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/kde_subclass.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/parse_gene.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/json_utils.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/module_availability.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/read_simulator.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  copying misopy/pe_utils.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
  creating build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot
  copying misopy/sashimi_plot/plot.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot
  copying misopy/sashimi_plot/Sashimi.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot
  copying misopy/sashimi_plot/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot
  copying misopy/sashimi_plot/sashimi_plot.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot
  creating build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
  copying misopy/sashimi_plot/plot_utils/plot_settings.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
  copying misopy/sashimi_plot/plot_utils/samples_plotter.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
  copying misopy/sashimi_plot/plot_utils/plotting.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
  copying misopy/sashimi_plot/plot_utils/plot_gene.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
  copying misopy/sashimi_plot/plot_utils/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
  creating build/lib.macosx-10.6-x86_64-2.7/pysplicing
  copying pysplicing/pysplicing/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/pysplicing
  running build_ext
  building 'pysplicing.pysplicing' extension
  creating build/temp.macosx-10.6-x86_64-2.7
  creating build/temp.macosx-10.6-x86_64-2.7/pysplicing
  creating build/temp.macosx-10.6-x86_64-2.7/pysplicing/src
  creating build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/lapack
  creating build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/f2c
  gcc -fno-strict-aliasing -I/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/anaconda2/include/python2.7 -c pysplicing/src/simulator.c -o build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/simulator.o
  pysplicing/src/simulator.c: In function ‘splicing_create_gene’:
  pysplicing/src/simulator.c:16:10: warning: unused variable ‘exlen’ [-Wunused-variable]
     size_t exlen=splicing_vector_int_size(exons);
            ^
  pysplicing/src/simulator.c: In function ‘splicing_simulate_reads’:
  pysplicing/src/simulator.c:76:13: warning: unused variable ‘p’ [-Wunused-variable]
     size_t i, p, noiso, goodiso=0, nogenes;
               ^
  gcc -fno-strict-aliasing -I/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/anaconda2/include/python2.7 -c pysplicing/src/pyrandom.c -o build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/pyrandom.o
  gcc -fno-strict-aliasing -I/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/anaconda2/include/python2.7 -c pysplicing/src/memory.c -o build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/memory.o
  In file included from /usr/include/Availability.h:198:0,
                   from /usr/include/stdlib.h:61,
                   from pysplicing/include/splicing_memory.h:6,
                   from pysplicing/src/memory.c:3:
  /usr/include/AvailabilityInternal.h:27982:74: error: missing binary operator before token "("
   #if defined(__has_feature) && defined(__has_attribute) && __has_attribute(availability)
                                                                            ^
  In file included from /usr/include/stdlib.h:61:0,
                   from pysplicing/include/splicing_memory.h:6,
                   from pysplicing/src/memory.c:3:
  /usr/include/Availability.h:391:74: error: missing binary operator before token "("
   #if defined(__has_feature) && defined(__has_attribute) && __has_attribute(availability)
                                                                            ^
  error: command 'gcc' failed with exit status 1

  ----------------------------------------
  Failed building wheel for misopy
  Running setup.py clean for misopy
Failed to build misopy
Installing collected packages: misopy
  Running setup.py install for misopy ... error
    Complete output from command /anaconda2/bin/python2 -u -c "import setuptools, tokenize;__file__='/private/var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/pip-build-iDBF1r/misopy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/pip-yIA9aA-record/install-record.txt --single-version-externally-managed --compile:
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.6-x86_64-2.7
    creating build/lib.macosx-10.6-x86_64-2.7/misopy
    copying misopy/credible_intervals.py -> build/lib.macosx-10.6-x86_64-2.7/misopy
    copying misopy/sashimi_plot/sashimi_plot.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot
    creating build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
    copying misopy/sashimi_plot/plot_utils/plot_settings.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
    copying misopy/sashimi_plot/plot_utils/samples_plotter.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
    copying misopy/sashimi_plot/plot_utils/plotting.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
    copying misopy/sashimi_plot/plot_utils/plot_gene.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
    copying misopy/sashimi_plot/plot_utils/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/misopy/sashimi_plot/plot_utils
    creating build/lib.macosx-10.6-x86_64-2.7/pysplicing
    copying pysplicing/pysplicing/__init__.py -> build/lib.macosx-10.6-x86_64-2.7/pysplicing
    running build_ext
    building 'pysplicing.pysplicing' extension
    creating build/temp.macosx-10.6-x86_64-2.7
    creating build/temp.macosx-10.6-x86_64-2.7/pysplicing
    creating build/temp.macosx-10.6-x86_64-2.7/pysplicing/src
    creating build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/lapack
    creating build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/f2c
    gcc -fno-strict-aliasing -I/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/anaconda2/include/python2.7 -c pysplicing/src/simulator.c -o build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/simulator.o
    pysplicing/src/simulator.c: In function ‘splicing_create_gene’:
    pysplicing/src/simulator.c:16:10: warning: unused variable ‘exlen’ [-Wunused-variable]
       size_t exlen=splicing_vector_int_size(exons);
              ^
    pysplicing/src/simulator.c: In function ‘splicing_simulate_reads’:
    pysplicing/src/simulator.c:76:13: warning: unused variable ‘p’ [-Wunused-variable]
       size_t i, p, noiso, goodiso=0, nogenes;
                 ^
    gcc -fno-strict-aliasing -I/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/anaconda2/include/python2.7 -c pysplicing/src/pyrandom.c -o build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/pyrandom.o
    gcc -fno-strict-aliasing -I/anaconda2/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/anaconda2/include/python2.7 -c pysplicing/src/memory.c -o build/temp.macosx-10.6-x86_64-2.7/pysplicing/src/memory.o
    In file included from /usr/include/Availability.h:198:0,
                     from /usr/include/stdlib.h:61,
                     from pysplicing/include/splicing_memory.h:6,
                     from pysplicing/src/memory.c:3:
    /usr/include/AvailabilityInternal.h:27982:74: error: missing binary operator before token "("
     #if defined(__has_feature) && defined(__has_attribute) && __has_attribute(availability)
                                                                              ^
    In file included from /usr/include/stdlib.h:61:0,
                     from pysplicing/include/splicing_memory.h:6,
                     from pysplicing/src/memory.c:3:
    /usr/include/Availability.h:391:74: error: missing binary operator before token "("
     #if defined(__has_feature) && defined(__has_attribute) && __has_attribute(availability)
                                                                              ^
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/anaconda2/bin/python2 -u -c "import setuptools, tokenize;__file__='/private/var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/pip-build-iDBF1r/misopy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/pip-yIA9aA-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/tj/4x295k0j5056b1vbhyjf_1s00000gn/T/pip-build-iDBF1r/misopy/
software error • 1.9k views
ADD COMMENT •
0
Entering edit mode

What version of macOS are you installing on? Do you have all latest patches/updates applied to macOS? Do you have the latest command line tools/Xcode installed?

ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 2911 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6