pip install fails on mojave #8
Description
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/