Clipper installation error

Clipper installation error

(ecwheele)[ecwheele@tscc-login1 clipper]$ python setup.py install

Installed /home/ecwheele/software/clipper/.eggs/setuptools_git-1.1-py3.5.egg
running install
running bdist_egg
running egg_info
writing top-level names to clipper.egg-info/top_level.txt
writing entry points to clipper.egg-info/entry_points.txt
writing clipper.egg-info/PKG-INFO
writing requirements to clipper.egg-info/requires.txt
writing dependency_links to clipper.egg-info/dependency_links.txt
writing manifest file 'clipper.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/clipper
copying clipper/__init__.py -> build/lib.linux-x86_64-3.5/clipper
creating build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_classic.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_CLIP_analysis.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_call_peak.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_kmerdiff.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_CLIP_Analysis_Display.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_spline.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_peaks.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/test_peakfinder.py -> build/lib.linux-x86_64-3.5/clipper/test
copying clipper/test/__init__.py -> build/lib.linux-x86_64-3.5/clipper/test
creating build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/get_ce10_genomic_regions.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/count_features.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/bam_helpers.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/AS_Structure_tools.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/peakfinder.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/kmerdiff.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/call_peak.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/CLIP_analysis.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/CLIP_analysis_runner.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/__init__.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/CLIP_analysis_display.py -> build/lib.linux-x86_64-3.5/clipper/src
copying clipper/src/get_genomic_regions.py -> build/lib.linux-x86_64-3.5/clipper/src
creating build/lib.linux-x86_64-3.5/clipper/data
copying clipper/data/__init__.py -> build/lib.linux-x86_64-3.5/clipper/data
creating build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/__init__.py -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/dm3.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.5/clipper/data
copying clipper/data/ce10.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.5/clipper/data
copying clipper/data/mm10.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.5/clipper/data
copying clipper/data/hg19.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.5/clipper/data
copying clipper/data/mm9.AS.STRUCTURE.COMPILED.gff -> build/lib.linux-x86_64-3.5/clipper/data
copying clipper/data/regions/mm9_proxintron500.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_transcription_start_sites.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_five_prime_utrs.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_transcription_start_sites.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_exons.mrg.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_genes.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_genes.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_proxintron500.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_three_prime_utrs.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_cds.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_three_prime_ends.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/mm9_cds.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/mm9_genes.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_proxintron500.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_cds.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/mm9_five_prime_utrs.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_five_prime_ends.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_three_prime_utrs.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_five_prime_utrs.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/mm9_exons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_start_codons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_distintron500.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_start_codons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_stop_codons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/mm9_three_prime_utrs.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_poly_a_sites.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_introns.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_poly_a_sites.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/mm9_distintron500.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_introns.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_exons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_stop_codons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/hg19_distintron500.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_exons.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_three_prime_ends.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
copying clipper/data/regions/ce10_five_prime_ends.bed -> build/lib.linux-x86_64-3.5/clipper/data/regions
running build_ext
skipping 'clipper/src/readsToWiggle.c' Cython extension (up-to-date)
building 'clipper.src.readsToWiggle' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/clipper
creating build/temp.linux-x86_64-3.5/clipper/src
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ecwheele/anaconda3/envs/ecwheele/include/python3.5m -c clipper/src/readsToWiggle.c -o build/temp.linux-x86_64-3.5/clipper/src/readsToWiggle.o
clipper/src/readsToWiggle.c: In function ‘__Pyx_PyInt_As_int’:
clipper/src/readsToWiggle.c:2691: warning: will never be executed
clipper/src/readsToWiggle.c:2688: warning: will never be executed
clipper/src/readsToWiggle.c:2687: warning: will never be executed
clipper/src/readsToWiggle.c:2686: warning: will never be executed
clipper/src/readsToWiggle.c:2681: warning: will never be executed
clipper/src/readsToWiggle.c:2672: warning: will never be executed
clipper/src/readsToWiggle.c:2663: warning: will never be executed
clipper/src/readsToWiggle.c:2663: warning: will never be executed
clipper/src/readsToWiggle.c:2663: warning: will never be executed
clipper/src/readsToWiggle.c:2663: warning: will never be executed
clipper/src/readsToWiggle.c:2646: warning: will never be executed
clipper/src/readsToWiggle.c:2646: warning: will never be executed
clipper/src/readsToWiggle.c:2646: warning: will never be executed
clipper/src/readsToWiggle.c:2646: warning: will never be executed
clipper/src/readsToWiggle.c:2644: warning: will never be executed
clipper/src/readsToWiggle.c:2644: warning: will never be executed
clipper/src/readsToWiggle.c:2644: warning: will never be executed
clipper/src/readsToWiggle.c:2644: warning: will never be executed
clipper/src/readsToWiggle.c:2639: warning: will never be executed
clipper/src/readsToWiggle.c:2638: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__pyx_pf_7clipper_3src_13readsToWiggle_readsToWiggle_pysam’:
clipper/src/readsToWiggle.c:1505: warning: will never be executed
clipper/src/readsToWiggle.c:1498: warning: will never be executed
clipper/src/readsToWiggle.c:1112: warning: will never be executed
clipper/src/readsToWiggle.c:1105: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_IternextUnpackEndCheck’:
clipper/src/readsToWiggle.c:2584: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_PyInt_From_int’:
clipper/src/readsToWiggle.c:2748: warning: will never be executed
clipper/src/readsToWiggle.c:2744: warning: will never be executed
clipper/src/readsToWiggle.c:2738: warning: will never be executed
clipper/src/readsToWiggle.c:2736: warning: will never be executed
clipper/src/readsToWiggle.c:2734: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__pyx_bisect_code_objects’:
clipper/src/readsToWiggle.c:2882: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_ParseOptionalKeywords’:
clipper/src/readsToWiggle.c:2068: warning: will never be executed
clipper/src/readsToWiggle.c:2115: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_RaiseArgtupleInvalid’:
clipper/src/readsToWiggle.c:2027: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_PyObject_GetSlice’:
clipper/src/readsToWiggle.c:2473: warning: will never be executed
clipper/src/readsToWiggle.c:2485: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘PyInit_readsToWiggle’:
clipper/src/readsToWiggle.c:1968: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__pyx_pf_7clipper_3src_13readsToWiggle_readsToWiggle_pysam’:
clipper/src/readsToWiggle.c:2481: warning: will never be executed
clipper/src/readsToWiggle.c:2481: warning: will never be executed
clipper/src/readsToWiggle.c:2489: warning: will never be executed
clipper/src/readsToWiggle.c:2481: warning: will never be executed
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clipper/src/readsToWiggle.c:2489: warning: will never be executed
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clipper/src/readsToWiggle.c:1394: warning: will never be executed
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clipper/src/readsToWiggle.c:1549: warning: will never be executed
clipper/src/readsToWiggle.c:1562: warning: will never be executed
clipper/src/readsToWiggle.c:1649: warning: will never be executed
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clipper/src/readsToWiggle.c:1176: warning: will never be executed
clipper/src/readsToWiggle.c:1234: warning: will never be executed
clipper/src/readsToWiggle.c:1453: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__pyx_pw_7clipper_3src_13readsToWiggle_1readsToWiggle_pysam’:
clipper/src/readsToWiggle.c:2030: warning: will never be executed
clipper/src/readsToWiggle.c:2030: warning: will never be executed
clipper/src/readsToWiggle.c:2030: warning: will never be executed
clipper/src/readsToWiggle.c:2030: warning: will never be executed
clipper/src/readsToWiggle.c:2030: warning: will never be executed
clipper/src/readsToWiggle.c:2030: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_PyInt_As_int’:
clipper/src/readsToWiggle.c:3147: warning: will never be executed
clipper/src/readsToWiggle.c:2695: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_SetItemInt_Fast.clone.0’:
clipper/src/readsToWiggle.c:2391: warning: will never be executed
clipper/src/readsToWiggle.c:2388: warning: will never be executed
clipper/src/readsToWiggle.c:2390: warning: will never be executed
clipper/src/readsToWiggle.c:2386: warning: will never be executed
clipper/src/readsToWiggle.c:2385: warning: will never be executed
clipper/src/readsToWiggle.c:2385: warning: will never be executed
clipper/src/readsToWiggle.c:2396: warning: will never be executed
clipper/src/readsToWiggle.c:2385: warning: will never be executed
clipper/src/readsToWiggle.c:2384: warning: will never be executed
clipper/src/readsToWiggle.c:2383: warning: will never be executed
clipper/src/readsToWiggle.c:2373: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__Pyx_AddTraceback’:
clipper/src/readsToWiggle.c:3005: warning: will never be executed
clipper/src/readsToWiggle.c:3005: warning: will never be executed
clipper/src/readsToWiggle.c:2901: warning: will never be executed
clipper/src/readsToWiggle.c:3004: warning: will never be executed
clipper/src/readsToWiggle.c:2927: warning: will never be executed
clipper/src/readsToWiggle.c:3013: warning: will never be executed
clipper/src/readsToWiggle.c:3005: warning: will never be executed
clipper/src/readsToWiggle.c:3032: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘PyInit_readsToWiggle’:
clipper/src/readsToWiggle.c:1971: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__pyx_pf_7clipper_3src_13readsToWiggle_readsToWiggle_pysam’:
clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2340: warning: will never be executed
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clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2391: warning: will never be executed
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clipper/src/readsToWiggle.c:2390: warning: will never be executed
clipper/src/readsToWiggle.c:2386: warning: will never be executed
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clipper/src/readsToWiggle.c:2383: warning: will never be executed
clipper/src/readsToWiggle.c:2373: warning: will never be executed
clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2391: warning: will never be executed
clipper/src/readsToWiggle.c:2388: warning: will never be executed
clipper/src/readsToWiggle.c:2390: warning: will never be executed
clipper/src/readsToWiggle.c:2386: warning: will never be executed
clipper/src/readsToWiggle.c:2385: warning: will never be executed
clipper/src/readsToWiggle.c:2385: warning: will never be executed
clipper/src/readsToWiggle.c:2396: warning: will never be executed
clipper/src/readsToWiggle.c:2385: warning: will never be executed
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clipper/src/readsToWiggle.c:2383: warning: will never be executed
clipper/src/readsToWiggle.c:2373: warning: will never be executed
clipper/src/readsToWiggle.c:2391: warning: will never be executed
clipper/src/readsToWiggle.c:2388: warning: will never be executed
clipper/src/readsToWiggle.c:2390: warning: will never be executed
clipper/src/readsToWiggle.c:2386: warning: will never be executed
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clipper/src/readsToWiggle.c:2385: warning: will never be executed
clipper/src/readsToWiggle.c:2396: warning: will never be executed
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clipper/src/readsToWiggle.c:2373: warning: will never be executed
clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2250: warning: will never be executed
clipper/src/readsToWiggle.c:2391: warning: will never be executed
clipper/src/readsToWiggle.c:2388: warning: will never be executed
clipper/src/readsToWiggle.c:2390: warning: will never be executed
clipper/src/readsToWiggle.c:2386: warning: will never be executed
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clipper/src/readsToWiggle.c:2396: warning: will never be executed
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clipper/src/readsToWiggle.c:3147: warning: will never be executed
clipper/src/readsToWiggle.c:3147: warning: will never be executed
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clipper/src/readsToWiggle.c:1140: warning: will never be executed
clipper/src/readsToWiggle.c:1169: warning: will never be executed
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clipper/src/readsToWiggle.c:2695: warning: will never be executed
clipper/src/readsToWiggle.c:2695: warning: will never be executed
clipper/src/readsToWiggle.c:2695: warning: will never be executed
clipper/src/readsToWiggle.c:2695: warning: will never be executed
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clipper/src/readsToWiggle.c:1173: warning: will never be executed
clipper/src/readsToWiggle.c:1202: warning: will never be executed
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clipper/src/readsToWiggle.c:1280: warning: will never be executed
clipper/src/readsToWiggle.c:1308: warning: will never be executed
clipper/src/readsToWiggle.c:1318: warning: will never be executed
clipper/src/readsToWiggle.c:1367: warning: will never be executed
clipper/src/readsToWiggle.c:1377: warning: will never be executed
clipper/src/readsToWiggle.c:1571: warning: will never be executed
clipper/src/readsToWiggle.c:1573: warning: will never be executed
clipper/src/readsToWiggle.c:1482: warning: will never be executed
clipper/src/readsToWiggle.c:1280: warning: will never be executed
clipper/src/readsToWiggle.c:1308: warning: will never be executed
clipper/src/readsToWiggle.c:1318: warning: will never be executed
clipper/src/readsToWiggle.c:1367: warning: will never be executed
clipper/src/readsToWiggle.c:1377: warning: will never be executed
clipper/src/readsToWiggle.c: In function ‘__pyx_pw_7clipper_3src_13readsToWiggle_1readsToWiggle_pysam’:
clipper/src/readsToWiggle.c:2130: warning: will never be executed
clipper/src/readsToWiggle.c:3147: warning: will never be executed
clipper/src/readsToWiggle.c:3147: warning: will never be executed
clipper/src/readsToWiggle.c:953: warning: will never be executed
clipper/src/readsToWiggle.c:2695: warning: will never be executed
clipper/src/readsToWiggle.c:2695: warning: will never be executed
clipper/src/readsToWiggle.c:2105: warning: will never be executed
clipper/src/readsToWiggle.c:2121: warning: will never be executed
clipper/src/readsToWiggle.c:949: warning: will never be executed
clipper/src/readsToWiggle.c:950: warning: will never be executed
gcc -pthread -shared -L/home/ecwheele/anaconda3/envs/ecwheele/lib -Wl,-rpath=/home/ecwheele/anaconda3/envs/ecwheele/lib,--no-as-needed build/temp.linux-x86_64-3.5/clipper/src/readsToWiggle.o -L/home/ecwheele/anaconda3/envs/ecwheele/lib -lpython3.5m -o build/lib.linux-x86_64-3.5/clipper/src/readsToWiggle.cpython-35m-x86_64-linux-gnu.so
building 'clipper.src.peaks' extension
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/ecwheele/anaconda3/envs/ecwheele/include/python3.5m -c clipper/src/peaksmodule.cc -o build/temp.linux-x86_64-3.5/clipper/src/peaksmodule.o
cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++
clipper/src/peaksmodule.cc: In function ‘int main(int, char**)’:
clipper/src/peaksmodule.cc:26: error: cannot convert ‘char*’ to ‘wchar_t*’ for argument ‘1’ to ‘void Py_SetProgramName(wchar_t*)’
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_shuffle(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:86: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc:92: error: ‘PyInt_AsLong’ was not declared in this scope
clipper/src/peaksmodule.cc:123: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc:193: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc:202: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc:203: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_find_sections(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:261: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc:271: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc:281: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc: In function ‘PyObject* peaks_readsToWiggle_pysam(PyObject*, PyObject*)’:
clipper/src/peaksmodule.cc:329: warning: suggest parentheses around assignment used as truth value
clipper/src/peaksmodule.cc:390: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc:421: error: ‘PyInt_AsLong’ was not declared in this scope
clipper/src/peaksmodule.cc:455: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc:456: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc:464: warning: comparison between signed and unsigned integer expressions
clipper/src/peaksmodule.cc:468: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc:471: error: ‘PyInt_FromLong’ was not declared in this scope
clipper/src/peaksmodule.cc: In function ‘PyObject* initpeaks()’:
clipper/src/peaksmodule.cc:501: error: ‘Py_InitModule’ was not declared in this scope
clipper/src/peaksmodule.cc:502: warning: no return statement in function returning non-void
error: command 'gcc' failed with exit status 1