matplotlib - installing on CentOS - setup.py build fails

Question

trying to install matplotlib (1.1.0 with python 2.7.3 on CentOS)

python setup.py build

looks good until:

running build_ext
building 'matplotlib.ft2font' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c src/ft2font.cpp -o build/temp.linux-x86_64-2.7/src/ft2font.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c src/mplutils.cpp -o build/temp.linux-x86_64-2.7/src/mplutils.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/cxx_extensions.cxx -o build/temp.linux-x86_64-2.7/CXX/cxx_extensions.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/IndirectPythonInterface.cxx -o build/temp.linux-x86_64-2.7/CXX/IndirectPythonInterface.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/cxxsupport.cxx -o build/temp.linux-x86_64-2.7/CXX/cxxsupport.o
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1 -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/numpy-1.5.1-release/lib/python2.7/site-packages/numpy/core/include -I/usr/include/freetype2 -I/usr/local/include -I/usr/include -I. -I/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/include/python2.7 -c CXX/cxxextensions.c -o build/temp.linux-x86_64-2.7/CXX/cxxextensions.o
g++ -pthread -shared build/temp.linux-x86_64-2.7/src/ft2font.o build/temp.linux-x86_64-2.7/src/mplutils.o build/temp.linux-x86_64-2.7/CXX/cxx_extensions.o build/temp.linux-x86_64-2.7/CXX/IndirectPythonInterface.o build/temp.linux-x86_64-2.7/CXX/cxxsupport.o build/temp.linux-x86_64-2.7/CXX/cxxextensions.o -L/usr/local/lib -L/usr/lib -L/usr/local/lib64 -L/usr/lib64 -L/mnt/storage/laviniag/Tools/Qiime/qiime_software/python-2.7.3-release/lib -lfreetype -lz -lstdc++ -lm -lpython2.7 -o build/lib.linux-x86_64-2.7/matplotlib/ft2font.so
**/usr/bin/ld: /usr/local/lib/libpython2.7.a(parsetok.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
error: command 'g++' failed with exit status 1**

So I'm guessing I need to either edit the config file maybe to allow sharing? Any help appreciated, thanks.

Python 2.7 isn't installable via yum, certainly not under `/usr/local`. — Ignacio Vazquez-Abrams, Nov 27 '13 at 04:11
Sorry, yes you are right. It was installed through qiime deploy (https://github.com/qiime/qiime-deploy). — user2813132, Nov 27 '13 at 04:13
I have no clue what that does. Perhaps you should install matplotlib through it. — Ignacio Vazquez-Abrams, Nov 27 '13 at 04:23
I tried but without success, so I've been trying to install matplotlib independently. qiime-deploy just installs a number of dependencies that the program qiime depends on, including python. — user2813132, Nov 27 '13 at 04:25
and it looks like the issue is that `qiime` has installed python as static libraries, rather than shared libraries which means you can not link against them. — tacaswell, Nov 27 '13 at 05:24
and it looks like the `qiime` framework depends on matplotlib, so you should use it's magic instead of trying to fight it ;) — tacaswell, Nov 27 '13 at 05:28
Thanks tcaswell for pointing out that 1.1. is old, I just downloaded 1.3.1 and retried but same issue. I did try qiimes magic (which is pretty good for everything else) but it gave up on matplotlib as well. — user2813132, Nov 27 '13 at 20:28

score 3 · Accepted Answer · answered Nov 27 '13 at 04:41

3

matplotlib is one of the packages that can be really hard to install, there are plenty of others (ahem... lxml, pyside/pyqt4, etc).

Save yourself some trouble and checkout one of the pre-builts. Anaconda from continuum or canopy from enthought are good on cetos and will save you a log of headaches (free installs).

answered Nov 27 '13 at 04:41

Phil Cooper

5,747
1
25
41

It's not that bad to install on linux, you just need to get the correct `-dev` versions of the dependencies installed – tacaswell Nov 27 '13 at 05:21
Thanks Phil Cooper, I'll look into Anaconda. Part of the issue is that the default python on the machine is 2.6.6 and no one else wants to update, whereas qiime wants 2.7.3 hence two installations. – user2813132 Nov 27 '13 at 20:34

score 0 · Answer 2 · edited May 23 '17 at 12:12

0

Just use pip and virtualenv, it should work fine (CentOS-6.5, x86_64, python-2.6) Installing Matplotlib on CentOS 6.5

edited May 23 '17 at 12:12

Community

1
1

answered Sep 15 '14 at 12:51

Micromégas

111
5

matplotlib - installing on CentOS - setup.py build fails

2 Answers2