Installing NumPy with pip fails on Ubuntu
34,870
Solution 1
It seems like your system does not have gcc.
Install build tools using following command:
apt-get install build-essential python-dev
Solution 2
Some of these packages may not be required (don't have time to check in detail) but in a setup script of mine to install the NumPy stack I install the following Ubuntu packages first:
- build-essential
- gfortran
- libatlas-base-dev
- libatlas3gf-base
- python-dev
- libjpeg-dev
- libxml2-dev
- libfreetype6-dev
- libpng-dev
Otherwise you could simply use the Anaconda Python distribution, which works great.
Author by
Eric Wilson
Software developer, experienced in Java and Python in Linux environments, formerly a professor of mathematics. I'm a father of five children, and a husband of one wife.
Updated on July 20, 2022Comments
-
Eric Wilson almost 2 years
When I try:
$ sudo pip install numpyon my Ubuntu 12.04 server, I get:
------------------------------------------------------------ /usr/local/bin/pip run on Tue Dec 10 18:25:54 2013 Downloading/unpacking numpy Getting page https://pypi.python.org/simple/numpy/ URLs to search for versions for numpy: * https://pypi.python.org/simple/numpy/ Analyzing links from page https://pypi.python.org/simple/numpy/ Skipping link https://pypi.python.org/packages/2.4/n/numpy/numpy-1.0.1.dev3460.win32-py2.4.exe#md5=a55b13b1f141de2aa965d5c5554c4ad8 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/2.5/n/numpy/numpy-1.3.0.win32-py2.5.exe#md5=28ee6681b04beb5bfc4bc056417ff087 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/2.5/n/numpy/numpy-1.5.1.win32-py2.5-nosse.exe#md5=bfcb66706ebdece6a9680f79f2b643ca (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/2.5/n/numpy/numpy-1.6.0.win32-py2.5.exe#md5=539782c7311d4a3379f66a964159ef11 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe [ ...SNIP...] Skipping link https://pypi.python.org/packages/3.2/n/numpy/numpy-1.6.1.win32-py3.2.exe#md5=a6b66602e72436db37e6edbbce269fdf (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/3.2/n/numpy/numpy-1.6.2.win32-py3.2.exe#md5=b98cc04b20347127e297a99b6114b514 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/3.2/n/numpy/numpy-1.7.0.win32-py3.2.exe#md5=1b12834a53d3ba543d41399c40b5b791 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/3.2/n/numpy/numpy-1.7.1.win32-py3.2.exe#md5=651465cacf107d254ddcefcebb47064d (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/3.3/n/numpy/numpy-1.7.0.win32-py3.3.exe#md5=4f20740e7e9d31a9d4c1636a931bc3f9 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Skipping link https://pypi.python.org/packages/3.3/n/numpy/numpy-1.7.1.win32-py3.3.exe#md5=6519c7bb198d0caf2913469883a63be9 (from https://pypi.python.org/simple/numpy/); unknown archive format: .exe Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.3.0.tar.gz#md5=3f7773ff0971a5ebb8591536d8ec7bd6 (from https://pypi.python.org/simple/numpy/), version: 1.3.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.4.1.tar.gz#md5=89b8a56e018b634f7d05c56f17bc4943 (from https://pypi.python.org/simple/numpy/), version: 1.4.1 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.5.0.tar.gz#md5=3a8bfdc434df782d647161c48943ee09 (from https://pypi.python.org/simple/numpy/), version: 1.5.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.5.1.tar.gz#md5=376ef150df41b5353944ab742145352d (from https://pypi.python.org/simple/numpy/), version: 1.5.1 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.6.0.tar.gz#md5=e0993c74cb8e83292e560eac1a9be8e9 (from https://pypi.python.org/simple/numpy/), version: 1.6.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.6.0.zip#md5=f0ce7ea1a12b3b3480571980af243e48 (from https://pypi.python.org/simple/numpy/), version: 1.6.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.6.1.tar.gz#md5=2bce18c08fc4fce461656f0f4dd9103e (from https://pypi.python.org/simple/numpy/), version: 1.6.1 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.6.1.zip#md5=462c22b8eb221c78ddd51de98fbb5979 (from https://pypi.python.org/simple/numpy/), version: 1.6.1 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.tar.gz#md5=95ed6c9dcc94af1fc1642ea2a33c1bba (from https://pypi.python.org/simple/numpy/), version: 1.6.2 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.6.2.zip#md5=7e13c931985f90efcfa0408f845d6fee (from https://pypi.python.org/simple/numpy/), version: 1.6.2 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.7.0.tar.gz#md5=4fa54e40b6a243416f0248123b6ec332 (from https://pypi.python.org/simple/numpy/), version: 1.7.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.7.0.zip#md5=ca27913c59393940e880fab420f985b4 (from https://pypi.python.org/simple/numpy/), version: 1.7.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz#md5=0ab72b3b83528a7ae79c6df9042d61c6 (from https://pypi.python.org/simple/numpy/), version: 1.7.1 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.zip#md5=9a72db3cad7a6286c0d22ee43ad9bc6c (from https://pypi.python.org/simple/numpy/), version: 1.7.1 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.8.0.tar.gz#md5=2a4b0423a758706d592abb6721ec8dcd (from https://pypi.python.org/simple/numpy/), version: 1.8.0 Found link https://pypi.python.org/packages/source/n/numpy/numpy-1.8.0.zip#md5=6c918bb91c0cfa055b16b13850cfcd6e (from https://pypi.python.org/simple/numpy/), version: 1.8.0 Using version 1.8.0 (newest of versions: 1.8.0, 1.8.0, 1.7.1, 1.7.1, 1.7.0, 1.7.0, 1.6.2, 1.6.2, 1.6.1, 1.6.1, 1.6.0, 1.6.0, 1.5.1, 1.5.0, 1.4.1, 1.3.0) Downloading from URL https://pypi.python.org/packages/source/n/numpy/numpy-1.8.0.tar.gz#md5=2a4b0423a758706d592abb6721ec8dcd (from https://pypi.python.org/simple/numpy/) Running setup.py egg_info for package numpy Running from numpy source directory. /bin/sh: 1: svnversion: not found non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE openblas_info: libraries openblas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1522: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1531: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1534: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE /bin/sh: 1: svnversion: not found non-existing path in 'numpy/lib': 'benchmarks' lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1428: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1439: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) lapack_src_info: NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1442: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) NOT AVAILABLE /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) running egg_info running build_src build_src building py_modules sources creating build creating build/src.linux-x86_64-2.7 creating build/src.linux-x86_64-2.7/numpy creating build/src.linux-x86_64-2.7/numpy/distutils building library "npymath" sources customize Gnu95FCompiler Could not locate executable gfortran Could not locate executable f95 customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize LaheyFCompiler Could not locate executable lf95 customize PGroupFCompiler Could not locate executable pgfortran customize AbsoftFCompiler Could not locate executable f90 Could not locate executable f77 customize NAGFCompiler customize VastFCompiler customize CompaqFCompiler Could not locate executable fort customize IntelItaniumFCompiler Could not locate executable efort Could not locate executable efc customize IntelEM64TFCompiler customize GnuFCompiler Could not locate executable g77 customize G95FCompiler Could not locate executable g95 customize PathScaleFCompiler Could not locate executable pathf95 don't know how to compile Fortran code on platform 'posix' C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC compile options: '-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 -Inumpy/core/include -I/usr/include/python2.7 -c' gcc: _configtest.c sh: 1: gcc: not found sh: 1: gcc: not found failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "<string>", line 16, in <module> File "/tmp/pip_build_root/numpy/setup.py", line 192, in <module> setup_package() File "/tmp/pip_build_root/numpy/setup.py", line 185, in setup_package configuration=configuration ) File "/tmp/pip_build_root/numpy/numpy/distutils/core.py", line 169, in setup return old_setup(**new_attr) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip_build_root/numpy/numpy/distutils/command/egg_info.py", line 10, in run self.run_command("build_src") File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 153, in run self.build_sources() File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 164, in build_sources self.build_library_sources(*libname_info) File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 299, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 386, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 674, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program") RuntimeError: Broken toolchain: cannot link a simple C program Complete output from command python setup.py egg_info: Running from numpy source directory. /bin/sh: 1: svnversion: not found non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE openblas_info: libraries openblas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1522: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1531: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1534: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) NOT AVAILABLE /bin/sh: 1: svnversion: not found non-existing path in 'numpy/lib': 'benchmarks' lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib libraries lapack_atlas not found in /usr/lib numpy.distutils.system_info.atlas_info NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1428: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in ['/usr/local/lib', '/usr/lib'] NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1439: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) lapack_src_info: NOT AVAILABLE /tmp/pip_build_root/numpy/numpy/distutils/system_info.py:1442: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) NOT AVAILABLE /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) running egg_info running build_src build_src building py_modules sources creating build creating build/src.linux-x86_64-2.7 creating build/src.linux-x86_64-2.7/numpy creating build/src.linux-x86_64-2.7/numpy/distutils building library "npymath" sources customize Gnu95FCompiler Could not locate executable gfortran Could not locate executable f95 customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize LaheyFCompiler Could not locate executable lf95 customize PGroupFCompiler Could not locate executable pgfortran customize AbsoftFCompiler Could not locate executable f90 Could not locate executable f77 customize NAGFCompiler customize VastFCompiler customize CompaqFCompiler Could not locate executable fort customize IntelItaniumFCompiler Could not locate executable efort Could not locate executable efc customize IntelEM64TFCompiler customize GnuFCompiler Could not locate executable g77 customize G95FCompiler Could not locate executable g95 customize PathScaleFCompiler Could not locate executable pathf95 don't know how to compile Fortran code on platform 'posix' C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC compile options: '-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 -Inumpy/core/include -I/usr/include/python2.7 -c' gcc: _configtest.c sh: 1: gcc: not found sh: 1: gcc: not found failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "<string>", line 16, in <module> File "/tmp/pip_build_root/numpy/setup.py", line 192, in <module> setup_package() File "/tmp/pip_build_root/numpy/setup.py", line 185, in setup_package configuration=configuration ) File "/tmp/pip_build_root/numpy/numpy/distutils/core.py", line 169, in setup return old_setup(**new_attr) File "/usr/lib/python2.7/distutils/core.py", line 152, in setup dist.run_commands() File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands self.run_command(cmd) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip_build_root/numpy/numpy/distutils/command/egg_info.py", line 10, in run self.run_command("build_src") File "/usr/lib/python2.7/distutils/cmd.py", line 326, in run_command self.distribution.run_command(command) File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command cmd_obj.run() File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 153, in run self.build_sources() File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 164, in build_sources self.build_library_sources(*libname_info) File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 299, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/tmp/pip_build_root/numpy/numpy/distutils/command/build_src.py", line 386, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 674, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program") RuntimeError: Broken toolchain: cannot link a simple C program ---------------------------------------- Cleaning up... Removing temporary dir /tmp/pip_build_root... Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/numpy Exception information: Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/pip/basecommand.py", line 134, in main status = self.run(options, args) File "/usr/local/lib/python2.7/dist-packages/pip/commands/install.py", line 236, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) File "/usr/local/lib/python2.7/dist-packages/pip/req.py", line 1134, in prepare_files req_to_install.run_egg_info() File "/usr/local/lib/python2.7/dist-packages/pip/req.py", line 259, in run_egg_info command_desc='python setup.py egg_info') File "/usr/local/lib/python2.7/dist-packages/pip/util.py", line 670, in call_subprocess % (command_desc, proc.returncode, cwd)) InstallationError: Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/numpyI have no idea what I need to do to fix this. Eventually I would be able to put all dependencies that I need in a
requirements.txtfile, so that I can install devendencies in avirtualenv. With that in mind, I would prefer a solution that usespipas opposed toapt-getor installing from source.