Question: MISO Installation Errer on Mac OS
0
gravatar for doublefish7
15 months ago by
doublefish70 wrote:

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 • 773 views
ADD COMMENTlink modified 15 months ago by genomax62k • written 15 months ago by doublefish70

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 REPLYlink modified 15 months ago • written 15 months ago by genomax62k
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