pip install fails on mojave

[RachelKarchin]

here is error output

rachels-MacBook-Pro:~ rachelk$ pip install probabilistic2020 Collecting probabilistic2020 Downloading https://files.pythonhosted.org/packages/31/27/d1769ce84e6d067a5d3bc3c3f97fd6367dbbaf21ef67678cc44bb2681778/probabilistic2020-1.2.2.tar.gz (185kB) |████████████████████████████████| 194kB 1.3MB/s Requirement already satisfied: numpy in ./anaconda/lib/python3.6/site-packages (from probabilistic2020) (1.15.0) Requirement already satisfied: scipy in ./anaconda/lib/python3.6/site-packages (from probabilistic2020) (1.1.0) Requirement already satisfied: pandas in ./anaconda/lib/python3.6/site-packages (from probabilistic2020) (0.23.3) Collecting pysam (from probabilistic2020) Downloading https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz (3.2MB) |████████████████████████████████| 3.2MB 37.3MB/s Requirement already satisfied: python-dateutil>=2.5.0 in ./anaconda/lib/python3.6/site-packages (from pandas->probabilistic2020) (2.7.3) Requirement already satisfied: pytz>=2011k in ./anaconda/lib/python3.6/site-packages (from pandas->probabilistic2020) (2018.5) Requirement already satisfied: six>=1.5 in ./anaconda/lib/python3.6/site-packages (from python-dateutil>=2.5.0->pandas->probabilistic2020) (1.11.0) Building wheels for collected packages: probabilistic2020, pysam Building wheel for probabilistic2020 (setup.py) ... error ERROR: Complete output from command /Users/rachelk/anaconda/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-install-5_ccj6kv/probabilistic2020/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/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-wheel-i_wvzay7 --python-tag cp36: ERROR: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/prob2020 copying prob2020/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020 creating build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/mymath.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/utils.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/permutation.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/indel.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/bed_line.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/scores.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/p_value.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/process_result.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python creating build/lib.macosx-10.7-x86_64-3.6/prob2020/cython copying prob2020/cython/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/cython creating build/lib.macosx-10.7-x86_64-3.6/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/cpp creating build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console running build_ext building 'prob2020.cython.cutils' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/prob2020 creating build/temp.macosx-10.7-x86_64-3.6/prob2020/cython gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rachelk/anaconda/include -arch x86_64 -I/Users/rachelk/anaconda/include -arch x86_64 -Iprob2020/cpp/ -Iprob2020/cython/ -I/Users/rachelk/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/rachelk/anaconda/include/python3.6m -c prob2020/cython/cutils.cpp -o build/temp.macosx-10.7-x86_64-3.6/prob2020/cython/cutils.o warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] prob2020/cython/cutils.cpp:628:10: fatal error: 'ios' file not found

include "ios"

       ^~~~~

1 warning and 1 error generated. error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for probabilistic2020 Running setup.py clean for probabilistic2020 Building wheel for pysam (setup.py) ... \^canceled ERROR: Operation cancelled by user ^CTraceback (most recent call last): File "/Users/rachelk/anaconda/bin/pip", line 11, in sys.exit(main()) File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_internal/init.py", line 78, in main return command.main(cmd_args) File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 227, in main timeout=min(5, options.timeout) File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 92, in _build_session insecure_hosts=options.trusted_hosts, File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_internal/download.py", line 380, in init self.headers["User-Agent"] = user_agent() File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_internal/download.py", line 160, in user_agent setuptools_version = get_installed_version("setuptools") File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_internal/utils/misc.py", line 889, in get_installed_version working_set = pkg_resources.WorkingSet() File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_vendor/pkg_resources/init.py", line 567, in init self.add_entry(entry) File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_vendor/pkg_resources/init.py", line 623, in add_entry for dist in find_distributions(entry, True): File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_vendor/pkg_resources/init.py", line 2056, in find_on_path for dist in factory(fullpath): File "/Users/rachelk/anaconda/lib/python3.6/site-packages/pip/_vendor/pkg_resources/init.py", line 2118, in distributions_from_metadata if len(os.listdir(path)) == 0: KeyboardInterrupt rachels-MacBook-Pro:~ rachelk$ pip uninstall probabilistic2020 WARNING: Skipping probabilistic2020 as it is not installed. rachels-MacBook-Pro:~ rachelk$ pip install probabilistic2020 Collecting probabilistic2020 Using cached https://files.pythonhosted.org/packages/31/27/d1769ce84e6d067a5d3bc3c3f97fd6367dbbaf21ef67678cc44bb2681778/probabilistic2020-1.2.2.tar.gz Requirement already satisfied: numpy in ./anaconda/lib/python3.6/site-packages (from probabilistic2020) (1.15.0) Requirement already satisfied: scipy in ./anaconda/lib/python3.6/site-packages (from probabilistic2020) (1.1.0) Requirement already satisfied: pandas in ./anaconda/lib/python3.6/site-packages (from probabilistic2020) (0.23.3) Collecting pysam (from probabilistic2020) Using cached https://files.pythonhosted.org/packages/15/f6/ce0611aaa1865a616f7dc164fbf046eaf38f2b17c6d404403c56250beb93/pysam-0.15.2.tar.gz Requirement already satisfied: python-dateutil>=2.5.0 in ./anaconda/lib/python3.6/site-packages (from pandas->probabilistic2020) (2.7.3) Requirement already satisfied: pytz>=2011k in ./anaconda/lib/python3.6/site-packages (from pandas->probabilistic2020) (2018.5) Requirement already satisfied: six>=1.5 in ./anaconda/lib/python3.6/site-packages (from python-dateutil>=2.5.0->pandas->probabilistic2020) (1.11.0) Building wheels for collected packages: probabilistic2020, pysam Building wheel for probabilistic2020 (setup.py) ... error ERROR: Complete output from command /Users/rachelk/anaconda/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-install-g4mcb3jg/probabilistic2020/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/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-wheel-0o27i3p1 --python-tag cp36: ERROR: running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/prob2020 copying prob2020/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020 creating build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/mymath.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/utils.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/permutation.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/indel.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/bed_line.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/scores.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/p_value.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/process_result.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python creating build/lib.macosx-10.7-x86_64-3.6/prob2020/cython copying prob2020/cython/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/cython creating build/lib.macosx-10.7-x86_64-3.6/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/cpp creating build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console running build_ext building 'prob2020.cython.cutils' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/prob2020 creating build/temp.macosx-10.7-x86_64-3.6/prob2020/cython gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rachelk/anaconda/include -arch x86_64 -I/Users/rachelk/anaconda/include -arch x86_64 -Iprob2020/cpp/ -Iprob2020/cython/ -I/Users/rachelk/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/rachelk/anaconda/include/python3.6m -c prob2020/cython/cutils.cpp -o build/temp.macosx-10.7-x86_64-3.6/prob2020/cython/cutils.o warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] prob2020/cython/cutils.cpp:628:10: fatal error: 'ios' file not found

include "ios"

       ^~~~~

1 warning and 1 error generated. error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for probabilistic2020 Running setup.py clean for probabilistic2020 Building wheel for pysam (setup.py) ... done Stored in directory: /Users/rachelk/Library/Caches/pip/wheels/34/3b/bc/f3faaba907f333632357aae7bf09a453209a8c9c3cec4cddae Successfully built pysam Failed to build probabilistic2020 Installing collected packages: pysam, probabilistic2020 Running setup.py install for probabilistic2020 ... error ERROR: Complete output from command /Users/rachelk/anaconda/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-install-g4mcb3jg/probabilistic2020/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/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-record-qzlyoh71/install-record.txt --single-version-externally-managed --compile: ERROR: running install running build running build_py creating build creating build/lib.macosx-10.7-x86_64-3.6 creating build/lib.macosx-10.7-x86_64-3.6/prob2020 copying prob2020/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020 creating build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/sequence_context.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/mymath.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/utils.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/permutation.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/indel.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/bed_line.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/count_frameshifts.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/mutation_context.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/scores.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/p_value.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/process_result.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/amino_acid.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python copying prob2020/python/gene_sequence.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/python creating build/lib.macosx-10.7-x86_64-3.6/prob2020/cython copying prob2020/cython/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/cython creating build/lib.macosx-10.7-x86_64-3.6/prob2020/cpp copying prob2020/cpp/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/cpp creating build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/probabilistic2020.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/extract_gene_seq.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/init.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/annotate.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/simulate_non_silent_ratio.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/count_frameshifts.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console copying prob2020/console/randomization_test.py -> build/lib.macosx-10.7-x86_64-3.6/prob2020/console running build_ext building 'prob2020.cython.cutils' extension creating build/temp.macosx-10.7-x86_64-3.6 creating build/temp.macosx-10.7-x86_64-3.6/prob2020 creating build/temp.macosx-10.7-x86_64-3.6/prob2020/cython gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/rachelk/anaconda/include -arch x86_64 -I/Users/rachelk/anaconda/include -arch x86_64 -Iprob2020/cpp/ -Iprob2020/cython/ -I/Users/rachelk/anaconda/lib/python3.6/site-packages/numpy/core/include -I/Users/rachelk/anaconda/include/python3.6m -c prob2020/cython/cutils.cpp -o build/temp.macosx-10.7-x86_64-3.6/prob2020/cython/cutils.o warning: include path for stdlibc++ headers not found; pass '-std=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found] prob2020/cython/cutils.cpp:628:10: fatal error: 'ios' file not found

include "ios"

         ^~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------

ERROR: Command "/Users/rachelk/anaconda/bin/python -u -c 'import setuptools, tokenize;file='"'"'/private/var/folders/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-install-g4mcb3jg/probabilistic2020/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/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-record-qzlyoh71/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/k9/cqnh8j914yl2q4mkc880nbs00000gp/T/pip-install-g4mcb3jg/probabilistic2020/