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biobakery / homebrew-biobakery

Biobakery formulae for the Homebrew package manager
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Installation failed #20

Closed SK-N-BE closed 6 years ago

SK-N-BE commented 6 years ago

Hei, to install metaphlan2, I was using the command

$ brew tap biobakery/biobakery followed by $ brew install metaphlan2

everything seems to work correctly; but at the end , I get the following error messages:

Last 15 lines from /home/SKNBE/.cache/Homebrew/Logs/metaphlan2/02.python2: gcc-7: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/nditer_templ.c gcc-7: numpy/core/src/multiarray/python_xerbla.c gcc-7: numpy/core/src/multiarray/ucsnarrow.c gcc-7: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/einsum.c gcc-7: numpy/core/src/multiarray/number.c gcc-7: numpy/core/src/multiarray/numpyos.c numpy/core/src/multiarray/numpyos.c:18:10: fatal error: xlocale.h: No such file or directory

include

compilation terminated. numpy/core/src/multiarray/numpyos.c:18:10: fatal error: xlocale.h: No such file or directory

include

compilation terminated. error: Command "gcc-7 -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/linuxbrew/.linuxbrew/include -I/home/linuxbrew/.linuxbrew/opt/openssl/include -I/home/linuxbrew/.linuxbrew/opt/sqlite/include -I/home/linuxbrew/.linuxbrew/opt/python@2/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c numpy/core/src/multiarray/numpyos.c -o build/temp.linux-x86_64-2.7/numpy/core/src/multiarray/numpyos.o" failed with exit status 1

ljmciver commented 6 years ago

Hello - It looks like the error is from trying to install numpy (a dependency of metaphlan2). If you try installing metaphlan2 again, adding the option "--without-dependencies" it will bypass the numpy install. This should resolve the error you are seeing. Then install numpy with "brew install numpy". This way you can use a pre-complied bottle if available for your OS instead of having to install numpy from source. Please reopen this ticket if you have any issues.

Thanks, Lauren

SK-N-BE commented 6 years ago

Thank you Lauren!