Fresh install of kwant on OS X failed
I’ve completely reinstalled my OS and am now encountering issues that I’ve heard other talk about, I’ve followed the instructions on the website word by word, except that I forked Michael’s repo and changed to kwant version 1.0.3. This has worked before for me. This is the error message: brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC. If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.3.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.3.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.3 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1 READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues Best Bas
Can you try to run brew install -vd kwant to get a more detailed error? Best, Michael
Am 23 jun. 2015 um 02:00 schrieb Bas Nijholt <basnijholt@gmail.com>:
I’ve completely reinstalled my OS and am now encountering issues that I’ve heard other talk about, I’ve followed the instructions on the website word by word, except that I forked Michael’s repo and changed to kwant version 1.0.3. This has worked before for me.
This is the error message: brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC.
If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.3.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.3.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.3 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1
READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues
Best Bas
I get: brew install -vd kwant /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/basnijholt/homebrew-kwant/kwant.rb ==> Installing kwant from basnijholt/homebrew-kwant /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/basnijholt/homebrew-kwant/tinyarray.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/basnijholt/homebrew-kwant/mumps_seq.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/homebrew/homebrew-science/scotch5.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/homebrew/homebrew-science/metis4.rb /usr/bin/env python -c import numpy /usr/bin/env python -c import scipy /usr/local/bin/mpicc --version /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/open-mpi.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/libevent.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/pkg-config.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/openssl.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/makedepend.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/gcc.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/gmp.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/libmpc.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/mpfr.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/isl.rb /usr/local/Library/brew.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/xz.rb /usr/local/Library/Homebrew/build.rb (Formulary::FromPathLoader): loading /usr/local/Library/Taps/basnijholt/homebrew-kwant/kwant.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/basnijholt/homebrew-kwant/tinyarray.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/basnijholt/homebrew-kwant/mumps_seq.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/homebrew/homebrew-science/scotch5.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Taps/homebrew/homebrew-science/metis4.rb /usr/bin/env python -c import numpy /usr/bin/env python -c import scipy /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/gcc.rb /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/python.rb /usr/local/bin/mpicc --version /usr/local/Library/Homebrew/build.rb (Formulary::FormulaLoader): loading /usr/local/Library/Formula/open-mpi.rb ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC. If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.3.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.3.tar.gz ==> Verifying kwant-1.0.3.tar.gz checksum tar xf /Library/Caches/Homebrew/kwant-1.0.3.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.3 running install running build running build_tut running build_py creating build creating build/lib.macosx-10.10-x86_64-2.7 creating build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/_static_version.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/builder.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/digest.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/lattice.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/plotter.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/rmt.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/system.py -> build/lib.macosx-10.10-x86_64-2.7/kwant copying kwant/version.py -> build/lib.macosx-10.10-x86_64-2.7/kwant creating build/lib.macosx-10.10-x86_64-2.7/kwant/graph copying kwant/graph/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph copying kwant/graph/defs.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph copying kwant/graph/dissection.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph creating build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests copying kwant/graph/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests copying kwant/graph/tests/test_core.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests copying kwant/graph/tests/test_dissection.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests copying kwant/graph/tests/test_scotch.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests copying kwant/graph/tests/test_slicer.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests copying kwant/graph/tests/test_utils.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/graph/tests creating build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/cmumps.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/decomp_ev.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/decomp_lu.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/decomp_schur.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/f_lapack.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/fortran_helpers.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/lll.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg copying kwant/linalg/mumps.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg creating build/lib.macosx-10.10-x86_64-2.7/kwant/linalg/tests copying kwant/linalg/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg/tests copying kwant/linalg/tests/_test_utils.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg/tests copying kwant/linalg/tests/test_linalg.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg/tests copying kwant/linalg/tests/test_lll.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg/tests copying kwant/linalg/tests/test_mumps.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/linalg/tests creating build/lib.macosx-10.10-x86_64-2.7/kwant/physics copying kwant/physics/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics copying kwant/physics/dispersion.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics copying kwant/physics/leads.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics copying kwant/physics/noise.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics creating build/lib.macosx-10.10-x86_64-2.7/kwant/physics/tests copying kwant/physics/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics/tests copying kwant/physics/tests/test_dispersion.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics/tests copying kwant/physics/tests/test_leads.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics/tests copying kwant/physics/tests/test_noise.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/physics/tests creating build/lib.macosx-10.10-x86_64-2.7/kwant/solvers copying kwant/solvers/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers copying kwant/solvers/common.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers copying kwant/solvers/default.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers copying kwant/solvers/mumps.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers copying kwant/solvers/sparse.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers creating build/lib.macosx-10.10-x86_64-2.7/kwant/solvers/tests copying kwant/solvers/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers/tests copying kwant/solvers/tests/_test_sparse.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers/tests copying kwant/solvers/tests/test_mumps.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers/tests copying kwant/solvers/tests/test_sparse.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/solvers/tests creating build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/__init__.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/test_builder.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/test_comprehensive.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/test_lattice.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/test_plotter.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/test_rmt.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests copying kwant/tests/test_system.py -> build/lib.macosx-10.10-x86_64-2.7/kwant/tests running build_ext skipping 'kwant/_system.c' Cython extension (up-to-date) building 'kwant._system' extension creating build/temp.macosx-10.10-x86_64-2.7 creating build/temp.macosx-10.10-x86_64-2.7/kwant clang -fno-strict-aliasing -fno-common -dynamic -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Ikwant/graph -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/2.7.10/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c kwant/_system.c -o build/temp.macosx-10.10-x86_64-2.7/kwant/_system.o kwant/_system.c:303:10: fatal error: 'numpy/arrayobject.h' file not found #include "numpy/arrayobject.h" ^ 1 error generated. ********************************************************************** The compilation of Kwant has failed. Please examine the error message above and consult the installation instructions in README.rst. You might have to customize build.conf. ********************************************************************** Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1 /usr/local/Library/Homebrew/debrew.rb:11:in `raise' BuildError: Failed executing: python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.3 1. raise 2. ignore 3. backtrace 4. irb 5. shell Choose an action: 1 ==> Formula Tap: basnijholt/homebrew-kwant Path: /usr/local/Library/Taps/basnijholt/homebrew-kwant/kwant.rb ==> Configuration HOMEBREW_VERSION: 0.9.5 ORIGIN: https://github.com/Homebrew/homebrew HEAD: cea7b94a0b7c96ed5b90af366634e96ba27620a8 Last commit: 11 hours ago HOMEBREW_PREFIX: /usr/local HOMEBREW_CELLAR: /usr/local/Cellar CPU: quad-core 64-bit haswell OS X: 10.10.3-x86_64 Xcode: 6.3.2 CLT: 6.3.2.0.1.1431401888 Clang: 6.1 build 602 X11: N/A System Ruby: 2.0.0-p481 Perl: /usr/bin/perl Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.10/Frameworks/Python.framework/Versions/2.7/bin/python2.7 Ruby: /usr/bin/ruby Java: 1.8.0_45 ==> ENV HOMEBREW_CC: clang HOMEBREW_CXX: clang++ MAKEFLAGS: -j4 CMAKE_PREFIX_PATH: /usr/local/opt/scotch5:/usr/local/opt/metis4:/usr/local/opt/mumps_seq:/usr/local CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries CMAKE_FRAMEWORK_PATH: /usr/local/opt/python/Frameworks PKG_CONFIG_PATH: /usr/local/opt/python/lib/pkgconfig:/usr/local/opt/open-mpi/lib/pkgconfig PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.10 ACLOCAL_PATH: /usr/local/share/aclocal PATH: /usr/local/opt/python/bin:/usr/local/Library/ENV/4.3:/usr/local/opt/scotch5/bin:/usr/local/opt/metis4/bin:/usr/local/opt/gcc/bin:/usr/local/opt/python/bin:/usr/local/opt/open-mpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin Error: basnijholt/kwant/kwant 1.0.3 did not build Logs: /Users/bnijholt/Library/Logs/Homebrew/kwant/01.python /Users/bnijholt/Library/Logs/Homebrew/kwant/01.python.cc On Tue, Jun 23, 2015 at 8:32 AM, Michael Wimmer <wimmer@lorentz.leidenuniv.nl> wrote:
Can you try to run brew install -vd kwant to get a more detailed error? Best, Michael
Am 23 jun. 2015 um 02:00 schrieb Bas Nijholt <basnijholt@gmail.com>:
I’ve completely reinstalled my OS and am now encountering issues that I’ve heard other talk about, I’ve followed the instructions on the website word by word, except that I forked Michael’s repo and changed to kwant version 1.0.3. This has worked before for me.
This is the error message: brew install kwant ==> Installing kwant from basnijholt/homebrew-kwant ==> Using Homebrew-provided fortran compiler. This may be changed by setting the FC environment variable. ==> Building with an alternative Fortran compiler This is unsupported. Warning: No Fortran optimization information was provided. You may want to consider setting FCFLAGS and FFLAGS or pass the `--default-fortran-flags` option to `brew install` if your compiler is compatible with GCC.
If you like the default optimization level of your compiler, ignore this warning. ==> Downloading pypi.python.org/packages/source/k/kwant/kwant-1.0.3.tar.gz Already downloaded: /Library/Caches/Homebrew/kwant-1.0.3.tar.gz ==> Patching patching file build.conf ==> python setup.py install --prefix=/usr/local/Cellar/kwant/1.0.3 Build configuration was: User-configured LAPACK and BLAS User-configured MUMPS ********************************************************************** error: command 'clang' failed with exit status 1
READ THIS: https://git.io/brew-troubleshooting If reporting this issue please do so at (not Homebrew/homebrew): https://github.com/basnijholt/homebrew-kwant/issues
Best Bas
Hi, I get exactly the same errors. How did you resolve this? I'm running on my Mac. I checked Xcode, updates, Python and whatever I knew. They are apparently installed OK. I even used "brew install kwant --force" but not working! thanks, Jason
Hi everyone It is solved? For mac users, kwant works on OSX 10 (Yosemite)? Best Regards César 2015-07-01 12:59 GMT-04:00 Jason <ataffice@gmail.com>:
Hi, I get exactly the same errors. How did you resolve this? I'm running on my Mac. I checked Xcode, updates, Python and whatever I knew. They are apparently installed OK.
I even used "brew install kwant --force" but not working!
thanks, Jason
-- César Núñez Ramírez Doctor(C) Física U.T.F.S.M.
Hi César, I'm a mac user (Yosemite); I have installed kwant 1.02 via Homebrew, where works fine by now. The reason why I use Homebrew is that I don't know how to install MUMPS without using Homebrew. A direct setup.py way of kwant installation also works except for no MUMPS support. Best, Xin 2015-07-24 23:01 GMT+08:00 cesar nunez <cesar.nunez@postgrado.usm.cl>:
Hi everyone It is solved? For mac users, kwant works on OSX 10 (Yosemite)? Best Regards César
2015-07-01 12:59 GMT-04:00 Jason <ataffice@gmail.com>:
Hi, I get exactly the same errors. How did you resolve this? I'm running on my Mac. I checked Xcode, updates, Python and whatever I knew. They are apparently installed OK.
I even used "brew install kwant --force" but not working!
thanks, Jason
-- César Núñez Ramírez Doctor(C) Física U.T.F.S.M.
Hi, the Mac installation should work again, with kwant 1.0.3 being installed. The problem was actually a bug of python in homebrew/MacOSX itself - a include path is not properly registered in distutils. I have created a workaround and updated the kwant formula. I actually intended to announce this a while ago, but accidentally only sent to a single user, instead of the list. Please check if the problem is solved for all! Best, Michael On 24-07-15 17:01, cesar nunez wrote:
Hi everyone It is solved? For mac users, kwant works on OSX 10 (Yosemite)? Best Regards César
2015-07-01 12:59 GMT-04:00 Jason <ataffice@gmail.com <mailto:ataffice@gmail.com>>:
Hi, I get exactly the same errors. How did you resolve this? I'm running on my Mac. I checked Xcode, updates, Python and whatever I knew. They are apparently installed OK.
I even used "brew install kwant --force" but not working!
thanks, Jason
-- César Núñez Ramírez Doctor(C) Física U.T.F.S.M.
participants (5)
-
Bas Nijholt -
cesar nunez -
Jason -
Michael Wimmer -
Xin Dai