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pip installlifelines - failure (solved: missing fortran)
See original GitHub issueUsing Anaconda in both Linux Mint abd Mac OS. pip install lifelines results in:
Downloading/unpacking lifelines
Downloading lifelines-0.4.3.tar.gz (628kB): 628kB downloaded
Running setup.py (path:/tmp/pip_build_root/lifelines/setup.py) egg_info for package lifelines
build_src
building extension "lifelines._statistics" sources
f2py options: []
f2py:> build/src.linux-i686-2.7/lifelines/_statisticsmodule.c
Reading fortran codes...
Reading file 'lifelines/_statistics.f90' (format:free)
Post-processing...
Block: _statistics
Block: concordance_index
Post-processing (stage 2)...
Building modules...
Building module "_statistics"...
Creating wrapper for Fortran function "concordance_index"("concordance_index")...
Constructing wrapper function "concordance_index"...
cindex = concordance_index(event_times,predictions,event_observed,[rows])
Wrote C/API module "_statistics" to file "build/src.linux-i686-2.7/lifelines/_statisticsmodule.c"
Fortran 77 wrappers are saved to "build/src.linux-i686-2.7/lifelines/_statistics-f2pywrappers.f"
adding 'build/src.linux-i686-2.7/fortranobject.c' to sources.
adding 'build/src.linux-i686-2.7' to include_dirs.
adding 'build/src.linux-i686-2.7/lifelines/_statistics-f2pywrappers.f' to sources.
build_src: building npy-pkg config files
warning: no files found matching '*' under directory 'styles'
warning: no previously-included files matching '*.py[co]' found under directory '*'
Requirement already satisfied (use --upgrade to upgrade): numpy in /usr/lib/python2.7/dist-packages (from lifelines)
Requirement already satisfied (use --upgrade to upgrade): scipy in /usr/lib/python2.7/dist-packages (from lifelines)
Requirement already satisfied (use --upgrade to upgrade): matplotlib in /usr/lib/pymodules/python2.7 (from lifelines)
Downloading/unpacking pandas>=0.14 (from lifelines)
Downloading pandas-0.14.1.tar.gz (6.7MB): 6.7MB downloaded
Running setup.py (path:/tmp/pip_build_root/pandas/setup.py) egg_info for package pandas
warning: no files found matching 'README.rst'
no previously-included directories found matching 'doc/build'
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.git*' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no previously-included files matching '*.png' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /usr/lib/python2.7/dist-packages (from matplotlib->lifelines)
Requirement already satisfied (use --upgrade to upgrade): tornado in /usr/lib/python2.7/dist-packages (from matplotlib->lifelines)
Requirement already satisfied (use --upgrade to upgrade): pyparsing>=1.5.6 in /usr/lib/python2.7/dist-packages (from matplotlib->lifelines)
Downloading/unpacking nose (from matplotlib->lifelines)
Downloading nose-1.3.4.tar.gz (277kB): 277kB downloaded
Running setup.py (path:/tmp/pip_build_root/nose/setup.py) egg_info for package nose
no previously-included directories found matching 'doc/.build'
Requirement already satisfied (use --upgrade to upgrade): pytz>=2011k in /usr/lib/python2.7/dist-packages (from pandas>=0.14->lifelines)
Installing collected packages: lifelines, pandas, nose
Running setup.py install for lifelines
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
build_src
building extension "lifelines._statistics" sources
f2py options: []
adding 'build/src.linux-i686-2.7/fortranobject.c' to sources.
adding 'build/src.linux-i686-2.7' to include_dirs.
adding 'build/src.linux-i686-2.7/lifelines/_statistics-f2pywrappers.f' to sources.
build_src: building npy-pkg config files
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'lifelines._statistics' extension
compiling C sources
C compiler: i686-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
compile options: '-Ibuild/src.linux-i686-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
i686-linux-gnu-gcc: build/src.linux-i686-2.7/fortranobject.c
In file included from build/src.linux-i686-2.7/fortranobject.c:2:0:
build/src.linux-i686-2.7/fortranobject.h:7:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
In file included from build/src.linux-i686-2.7/fortranobject.c:2:0:
build/src.linux-i686-2.7/fortranobject.h:7:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: Command "i686-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Ibuild/src.linux-i686-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c build/src.linux-i686-2.7/fortranobject.c -o build/temp.linux-i686-2.7/build/src.linux-i686-2.7/fortranobject.o" failed with exit status 1
Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/lifelines/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-xn95nq-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building extension "lifelines._statistics" sources
f2py options: []
adding 'build/src.linux-i686-2.7/fortranobject.c' to sources.
adding 'build/src.linux-i686-2.7' to include_dirs.
adding 'build/src.linux-i686-2.7/lifelines/_statistics-f2pywrappers.f' to sources.
build_src: building npy-pkg config files
running build_py
creating build/lib.linux-i686-2.7
creating build/lib.linux-i686-2.7/lifelines
copying lifelines/_cox_regression.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/generate_datasets.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/__init__.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/estimation.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/plotting.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/progress_bar.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/datasets.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/statistics.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/utils.py -> build/lib.linux-i686-2.7/lifelines
copying lifelines/_statistics.f90 -> build/lib.linux-i686-2.7/lifelines
copying lifelines/../README.md -> build/lib.linux-i686-2.7/lifelines/..
copying lifelines/../README.txt -> build/lib.linux-i686-2.7/lifelines/..
copying lifelines/../LICENSE -> build/lib.linux-i686-2.7/lifelines/..
copying lifelines/../MANIFEST.in -> build/lib.linux-i686-2.7/lifelines/..
copying lifelines/../Untitled0.ipynb -> build/lib.linux-i686-2.7/lifelines/..
creating build/lib.linux-i686-2.7/datasets
copying lifelines/../datasets/static_test.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/psychiatric_patients.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/gehan.dat -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/dd.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/divorce.dat -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/Divorces Rates.ipynb -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/The Gehan Survival Data.ipynb -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/panel_test.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/canadian_senators.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/lung.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
copying lifelines/../datasets/2002FemResp.csv -> build/lib.linux-i686-2.7/lifelines/../datasets
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /usr/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using build_ext
building 'lifelines._statistics' extension
compiling C sources
C compiler: i686-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-i686-2.7
creating build/temp.linux-i686-2.7/build
creating build/temp.linux-i686-2.7/build/src.linux-i686-2.7
creating build/temp.linux-i686-2.7/build/src.linux-i686-2.7/lifelines
compile options: '-Ibuild/src.linux-i686-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
i686-linux-gnu-gcc: build/src.linux-i686-2.7/fortranobject.c
In file included from build/src.linux-i686-2.7/fortranobject.c:2:0:
build/src.linux-i686-2.7/fortranobject.h:7:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
In file included from build/src.linux-i686-2.7/fortranobject.c:2:0:
build/src.linux-i686-2.7/fortranobject.h:7:20: fatal error: Python.h: No such file or directory
#include "Python.h"
^
compilation terminated.
error: Command "i686-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Ibuild/src.linux-i686-2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c build/src.linux-i686-2.7/fortranobject.c -o build/temp.linux-i686-2.7/build/src.linux-i686-2.7/fortranobject.o" failed with exit status 1
----------------------------------------
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/lifelines/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-xn95nq-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/lifelines
Storing debug log for failure in /home/juan/.pip/pip.log
Issue Analytics
- State:
- Created 9 years ago
- Comments:8 (2 by maintainers)
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Created a fresh VM with Linux Mint “Debian” - 201403 Cinnamon 64-bit, and here are the steps I took from a fresh install to get lifelines installed and working:
@spacecowboy you rock!