Trouble installing python library, cyvcf2, using both pip and anaconda
Question
I am trying to install cyvcf2.
The github instruction recommends pip install cyvcf2 or bioconda. I am on a windows 10 PC with Anaconda 1.9.7 and PyCharm. I first tried conda install -c bioconda cyvcf2 but it could not find the package even though it is the suggested location on Anaconda. Then I tried pip and that's when it said I needed Visual Studio 14. I installed it through the link it provided, but it still can't build it.
Error from conda
(base) C:\Users\Nelson\PycharmProjects\source_profiles>conda install cyvcf2
Collecting package metadata: done
Solving environment: -
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:
- defaults/win-64::dask==0.17.2=py36_0
- defaults/win-64::h5py==2.7.1=py36he54a1c3_0
- defaults/win-64::matplotlib==2.2.2=py36h153e9ff_0
- defaults/win-64::numba==0.37.0=np114py36hea3a760_0
- defaults/win-64::numexpr==2.6.4=py36h30784b8_0
- defaults/win-64::odo==0.5.1=py36h7560279_0
- defaults/win-64::patsy==0.5.0=py36_0
- defaults/win-64::pytables==3.4.2=py36h71138e3_2
- defaults/win-64::scikit-image==0.13.1=py36hfa6e2cd_1
- defaults/win-64::scikit-learn==0.19.1=py36h53aea1b_0
- defaults/win-64::scipy==1.0.1=py36hce232c7_0
- defaults/win-64::statsmodels==0.8.0=py36h6189b4c_0
failed
PackagesNotFoundError: The following packages are not available from current channels:
- cyvcf2
Current channels:
- https://conda.anaconda.org/r/win-64
- https://conda.anaconda.org/r/noarch
- https://conda.anaconda.org/bioconda/win-64
- https://conda.anaconda.org/bioconda/noarch
- https://conda.anaconda.org/conda-forge/win-64
- https://conda.anaconda.org/conda-forge/noarch
- https://repo.anaconda.com/pkgs/main/win-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/win-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/win-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/msys2/win-64
- https://repo.anaconda.com/pkgs/msys2/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Error from pip
Collecting cyvcf2
Using cached https://files.pythonhosted.org/packages/10/69/888f23e07de1364533ac666941b0e1229c7e60c1a5080b1234b849bd8b97/cyvcf2-0.10.10.tar.gz
Requirement already satisfied: numpy in c:\anaconda3\lib\site-packages (from cyvcf2) (1.15.4)
Building wheels for collected packages: cyvcf2
Building wheel for cyvcf2 (setup.py) ... error
ERROR: Complete output from command 'c:\anaconda3\python.exe' -u -c 'import setuptools, tokenize;__file__='"'"'C:\\Users\\Nelson\\AppData\\Local\\Temp\\pip-install-d8uogmra\\cyvcf2\\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 'C:\Users\Nelson\AppData\Local\Temp\pip-wheel-s8tt0cdb' --python-tag cp36:
ERROR: running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.6
creating build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\cli.py -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\__init__.py -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\__main__.py -> build\lib.win-amd64-3.6\cyvcf2
creating build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_cli.py -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_hemi.py -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_reader.py -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\__init__.py -> build\lib.win-amd64-3.6\cyvcf2\tests
running egg_info
writing cyvcf2.egg-info\PKG-INFO
writing dependency_links to cyvcf2.egg-info\dependency_links.txt
writing entry points to cyvcf2.egg-info\entry_points.txt
writing requirements to cyvcf2.egg-info\requires.txt
writing top-level names to cyvcf2.egg-info\top_level.txt
reading manifest file 'cyvcf2.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cyvcf2.egg-info\SOURCES.txt'
copying cyvcf2\cyvcf2.c -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\cyvcf2.pxd -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\cyvcf2.pyx -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\helpers.c -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\helpers.h -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\relatedness.h -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\tests\__init__.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\bug.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\decomposed.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\empty.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\issue_44.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\o.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\seg.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-alt-repr.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-diff.csi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-format-string.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-haploidX.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-hemi.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-multiallelic-homozygous-alt.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-multiallelic-homozygous-alt.vcf.gz.tbi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-strict-gt-option-flag.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-strict-gt-option-flag.vcf.gz.tbi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.comp_het.3.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.snpeff.bcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.snpeff.bcf.csi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.snpeff.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.vcf.gz.tbi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_cli.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_gt_alt_freqs.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_gt_bases.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_hemi.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_reader.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
running build_ext
skipping 'cyvcf2\cyvcf2.c' Cython extension (up-to-date)
building 'cyvcf2.cyvcf2' extension
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\cyvcf2
creating build\temp.win-amd64-3.6\Release\htslib
creating build\temp.win-amd64-3.6\Release\htslib\cram
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ihtslib -Icyvcf2 -Ic:\anaconda3\lib\site-packages\numpy\core\include -Ic:\anaconda3\include -Ic:\anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\cppwinrt" /Tccyvcf2\cyvcf2.c /Fobuild\temp.win-amd64-3.6\Release\cyvcf2\cyvcf2.obj
cyvcf2.c
c:\anaconda3\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(90): warning C4244: '=': conversion from 'int' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(98): warning C4244: '=': conversion from 'int' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(100): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(103): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(80): warning C4244: 'initializing': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(215): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(222): warning C4244: 'return': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\hts.h(810): warning C4244: 'return': conversion from 'int64_t' to 'int', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(152): warning C4267: 'return': conversion from 'size_t' to 'int', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(183): warning C4267: 'return': conversion from 'size_t' to 'int', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(191): warning C4146: unary minus operator applied to unsigned type, result still unsigned
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(220): warning C4146: unary minus operator applied to unsigned type, result still unsigned
htslib\htslib/hfile.h(123): warning C4244: 'return': conversion from '__int64' to 'off_t', possible loss of data
htslib\htslib/hfile.h(245): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(7896): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(7938): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(8454): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(8752): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(8805): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(9225): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(10510): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(12167): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(12901): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(13010): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(13010): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(13093): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(16274): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(18493): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(19538): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(20187): warning C4305: 'function': truncation from 'double' to 'float'
cyvcf2\cyvcf2.c(20605): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(20968): warning C4244: '=': conversion from 'int32_t' to 'float', possible loss of data
cyvcf2\cyvcf2.c(21014): warning C4244: '=': conversion from 'int32_t' to 'float', possible loss of data
cyvcf2\cyvcf2.c(24122): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(26133): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(28265): warning C4244: '=': conversion from 'npy_intp' to 'int', possible loss of data
cyvcf2\cyvcf2.c(28288): warning C4244: '=': conversion from 'npy_intp' to 'int', possible loss of data
cyvcf2\cyvcf2.c(29622): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
cyvcf2\cyvcf2.c(33695): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(33960): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(34174): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(36344): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(36447): warning C4244: 'function': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(39339): warning C4018: '>=': signed/unsigned mismatch
cyvcf2\cyvcf2.c(39387): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(40370): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(41024): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41052): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41120): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41292): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41330): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41389): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(68042): warning C4244: 'initializing': conversion from 'double' to 'float', possible loss of data
cyvcf2\cyvcf2.c(68048): warning C4244: 'initializing': conversion from 'double' to 'float', possible loss of data
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ihtslib -Icyvcf2 -Ic:\anaconda3\lib\site-packages\numpy\core\include -Ic:\anaconda3\include -Ic:\anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\cppwinrt" /Tchtslib\bcf_sr_sort.c /Fobuild\temp.win-amd64-3.6\Release\htslib\bcf_sr_sort.obj
bcf_sr_sort.c
htslib\bcf_sr_sort.c(27): fatal error C1083: Cannot open include file: 'strings.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\BuildTools\\VC\\Tools\\MSVC\\14.20.27508\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Failed building wheel for cyvcf2
Running setup.py clean for cyvcf2
Failed to build cyvcf2
Installing collected packages: cyvcf2
Running setup.py install for cyvcf2 ... error
ERROR: Complete output from command 'c:\anaconda3\python.exe' -u -c 'import setuptools, tokenize;__file__='"'"'C:\\Users\\Nelson\\AppData\\Local\\Temp\\pip-install-d8uogmra\\cyvcf2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\Nelson\AppData\Local\Temp\pip-record-stdp98ur\install-record.txt' --single-version-externally-managed --compile:
ERROR: running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.6
creating build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\cli.py -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\__init__.py -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\__main__.py -> build\lib.win-amd64-3.6\cyvcf2
creating build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_cli.py -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_hemi.py -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_reader.py -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\__init__.py -> build\lib.win-amd64-3.6\cyvcf2\tests
running egg_info
writing cyvcf2.egg-info\PKG-INFO
writing dependency_links to cyvcf2.egg-info\dependency_links.txt
writing entry points to cyvcf2.egg-info\entry_points.txt
writing requirements to cyvcf2.egg-info\requires.txt
writing top-level names to cyvcf2.egg-info\top_level.txt
reading manifest file 'cyvcf2.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cyvcf2.egg-info\SOURCES.txt'
copying cyvcf2\cyvcf2.c -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\cyvcf2.pxd -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\cyvcf2.pyx -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\helpers.c -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\helpers.h -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\relatedness.h -> build\lib.win-amd64-3.6\cyvcf2
copying cyvcf2\tests\__init__.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\bug.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\decomposed.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\empty.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\issue_44.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\o.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\seg.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-alt-repr.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-diff.csi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-format-string.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-haploidX.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-hemi.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-multiallelic-homozygous-alt.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-multiallelic-homozygous-alt.vcf.gz.tbi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-strict-gt-option-flag.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test-strict-gt-option-flag.vcf.gz.tbi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.comp_het.3.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.snpeff.bcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.snpeff.bcf.csi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.snpeff.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test.vcf.gz.tbi -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_cli.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_gt_alt_freqs.vcf -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_gt_bases.vcf.gz -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_hemi.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
copying cyvcf2\tests\test_reader.pyc -> build\lib.win-amd64-3.6\cyvcf2\tests
running build_ext
skipping 'cyvcf2\cyvcf2.c' Cython extension (up-to-date)
building 'cyvcf2.cyvcf2' extension
creating build\temp.win-amd64-3.6
creating build\temp.win-amd64-3.6\Release
creating build\temp.win-amd64-3.6\Release\cyvcf2
creating build\temp.win-amd64-3.6\Release\htslib
creating build\temp.win-amd64-3.6\Release\htslib\cram
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ihtslib -Icyvcf2 -Ic:\anaconda3\lib\site-packages\numpy\core\include -Ic:\anaconda3\include -Ic:\anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\cppwinrt" /Tccyvcf2\cyvcf2.c /Fobuild\temp.win-amd64-3.6\Release\cyvcf2\cyvcf2.obj
cyvcf2.c
c:\anaconda3\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(12) : Warning Msg: Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(90): warning C4244: '=': conversion from 'int' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(98): warning C4244: '=': conversion from 'int' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(100): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(103): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(80): warning C4244: 'initializing': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(215): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\cyvcf2\relatedness.h(222): warning C4244: 'return': conversion from 'double' to 'float', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\hts.h(810): warning C4244: 'return': conversion from 'int64_t' to 'int', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(152): warning C4267: 'return': conversion from 'size_t' to 'int', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(183): warning C4267: 'return': conversion from 'size_t' to 'int', possible loss of data
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(191): warning C4146: unary minus operator applied to unsigned type, result still unsigned
C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\htslib\htslib\kstring.h(220): warning C4146: unary minus operator applied to unsigned type, result still unsigned
htslib\htslib/hfile.h(123): warning C4244: 'return': conversion from '__int64' to 'off_t', possible loss of data
htslib\htslib/hfile.h(245): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(7896): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(7938): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(8454): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(8752): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(8805): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(9225): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(10510): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(12167): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(12901): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(13010): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(13010): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(13093): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(16274): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(18493): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(19538): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(20187): warning C4305: 'function': truncation from 'double' to 'float'
cyvcf2\cyvcf2.c(20605): warning C4244: '=': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(20968): warning C4244: '=': conversion from 'int32_t' to 'float', possible loss of data
cyvcf2\cyvcf2.c(21014): warning C4244: '=': conversion from 'int32_t' to 'float', possible loss of data
cyvcf2\cyvcf2.c(24122): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(26133): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(28265): warning C4244: '=': conversion from 'npy_intp' to 'int', possible loss of data
cyvcf2\cyvcf2.c(28288): warning C4244: '=': conversion from 'npy_intp' to 'int', possible loss of data
cyvcf2\cyvcf2.c(29622): warning C4244: '=': conversion from 'double' to 'float', possible loss of data
cyvcf2\cyvcf2.c(33695): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(33960): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(34174): warning C4018: '<': signed/unsigned mismatch
cyvcf2\cyvcf2.c(36344): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(36447): warning C4244: 'function': conversion from 'Py_ssize_t' to 'int', possible loss of data
cyvcf2\cyvcf2.c(39339): warning C4018: '>=': signed/unsigned mismatch
cyvcf2\cyvcf2.c(39387): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(40370): warning C4090: '=': different 'const' qualifiers
cyvcf2\cyvcf2.c(41024): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41052): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41120): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41292): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41330): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(41389): warning C4090: 'function': different 'const' qualifiers
cyvcf2\cyvcf2.c(68042): warning C4244: 'initializing': conversion from 'double' to 'float', possible loss of data
cyvcf2\cyvcf2.c(68048): warning C4244: 'initializing': conversion from 'double' to 'float', possible loss of data
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ihtslib -Icyvcf2 -Ic:\anaconda3\lib\site-packages\numpy\core\include -Ic:\anaconda3\include -Ic:\anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.20.27508\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\shared" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\um" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\winrt" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.17763.0\cppwinrt" /Tchtslib\bcf_sr_sort.c /Fobuild\temp.win-amd64-3.6\Release\htslib\bcf_sr_sort.obj
bcf_sr_sort.c
htslib\bcf_sr_sort.c(27): fatal error C1083: Cannot open include file: 'strings.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\BuildTools\\VC\\Tools\\MSVC\\14.20.27508\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Command "'c:\anaconda3\python.exe' -u -c 'import setuptools, tokenize;__file__='"'"'C:\\Users\\Nelson\\AppData\\Local\\Temp\\pip-install-d8uogmra\\cyvcf2\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\Nelson\AppData\Local\Temp\pip-record-stdp98ur\install-record.txt' --single-version-externally-managed --compile" failed with error code 1 in C:\Users\Nelson\AppData\Local\Temp\pip-install-d8uogmra\cyvcf2\
I spent all day trying to figure this out. When I did a conda install on my remote linux machine it worked just fine. I don't know what the issue is on my PC.
1 answers
solution1
0 2020-11-26 08:57:59
maybe this comment is a bit comes a bit late. I faced the same problem and I solved it using the following bioconda command:
conda install -c bioconda/label/cf201901 cyvcf2
Let me know if it works
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