[Matplotlib-users] Problem building Matplotlib 1.3.1 on linux (CentOS 5.9 AMD64)
Hello, I'm having an issue building Matplotlib. In reality the build process finishes without error, but afterwards I get this error when importing pyplot: [kpi@dev-outils lib.linux-x86_64-3.3]$ python3.3 Python 3.3.2 (default, Sep 17 2013, 10:40:41) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux Type help, copyright, credits or license for more information. import matplotlib import matplotlib.pyplot as plt Traceback (most recent call last): File stdin, line 1, in module File ./matplotlib/pyplot.py, line 24, in module import matplotlib.colorbar File ./matplotlib/colorbar.py, line 27, in module import matplotlib.artist as martist File ./matplotlib/artist.py, line 8, in module from .transforms import Bbox, IdentityTransform, TransformedBbox, \ File ./matplotlib/transforms.py, line 35, in module from matplotlib._path import (affine_transform, count_bboxes_overlapping_bbox, *ImportError: ./matplotlib/_path.cpython-33m.so http://path.cpython-33m.so: undefined symbol: _ZSt16__ostream_insertIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_PKS3_l* I don't know a thing about building C extensions, but if I understood correctly some pasts posts in this list and others, this problem might be caused by a library that is compiled with an incompatible version of GCC. My first suspect was freetype, so I downloaded and compiled v2.4.12 using gcc44 (which is the same compiler I used to build python3.3 and matplotlib). But the problem persists... My question is: *how can I know wich library is causing the issue, so I could recompile it?* Or, if I am completely missing the root cause, thank you for steering me in the correct direction :-) More detailed info follows. Thank you for your help ! Nicolas Here is the information asked for in the troubleshooting FAQ: [kpi@dev-outils matplotlib]$ uname -a Linux dev-outils.admin.mt.lan 2.6.18-348.16.1.el5 #1 SMP Wed Aug 21 04:00:25 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux [kpi@dev-outils matplotlib]$ cat /etc/redhat-release CentOS release 5.9 (Final) But please, note that I am using a Python version built by myself (not the version that comes with CenOS 5.9) using gcc 4.4.7 (and not gcc 4.1.2) [kpi@dev-outils matplotlib]$ gcc44 -v Using built-in specs. Target: x86_64-redhat-linux6E Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --disable-gnu-unique-object --with-as=/usr/libexec/binutils220/as --enable-languages=c,c++,fortran --disable-libgcj --with-mpfr=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/mpfr-install/ --with-ppl=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/ppl-install --with-cloog=/builddir/build/BUILD/gcc-4.4.7-20120601/obj-x86_64-redhat-linux6E/cloog-install --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux6E Thread model: posix gcc version 4.4.7 20120313 (Red Hat 4.4.7-1) (GCC) [kpi@dev-outils lib.linux-x86_64-3.3]$ python3.3 Python 3.3.2 (default, Sep 17 2013, 10:40:41) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux matplotlib.__version__ '1.3.1' Here is what I modified in setup.cfg last time (but I also tried with an unmodified version with the same results): [gui_support] agg = True cairo = False gtk = False gtk3agg = False gtk3cairo = False gtkagg = False macosx = False pyside = False qt4agg = False tkagg = False windowing = False wxagg = False [rc_options] backend = Agg I didn't modify any other config file. Here is the output of the build process: [kpi@dev-outils matplotlib-1.3.1]$ python3.3 setup.py build Edit setup.cfg to change the build options BUILDING MATPLOTLIB matplotlib: yes [1.3.1] python: yes [3.3.2 (default, Sep 17 2013, 10:40:41) [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]] platform: yes [linux] REQUIRED DEPENDENCIES AND EXTENSIONS numpy: yes [version 1.8.0] dateutil: yes [using dateutil version 2.2] tornado: yes [using tornado version 3.1.1] pyparsing: yes [using pyparsing version 2.0.1] pycxx: yes [Official versions of PyCXX are not compatible with Python 3.x. Using local copy] libagg: yes [pkg-config information for 'libagg' could not be found. Using local copy.] freetype: yes [version 16.1.10] png: yes [version 1.2.10] OPTIONAL SUBPACKAGES sample_data: yes [installing] toolkits: yes [installing] tests: yes [using nose version 1.3.0] OPTIONAL BACKEND EXTENSIONS macosx: no [skipping due to configuration]
Re: [Matplotlib-users] problem building matplotlib
On 09/14/2010 01:36 PM, Dan Kortschak wrote: Hello, I just tried to have just tried to build matplotlib, but it fails - and is unable to find wxPython (looking under 2.8 rather than 2.6 where is lives - installed from source) or libgtk-2 headers (installed from apt repo). Can anyone suggest how to resolve these issues? If you want to use wx, you need 2.8. It looks like you don't have any of the gui dependencies. Since you you are running ubuntu, I suggest you use the installation method recently described in this thread: http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg18464.html Be careful to read down through the thread; the first try at comprehensive instructions has an error. Eric -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem building matplotlib
Thanks Eric, The gui dependencies are secondary, but I will look into that. Since they are optional, the absence of them should not be the cause of the failure, but it looks like it might be. Is that the case? cheers Dan On Tue, 2010-09-14 at 21:42 -1000, Eric Firing wrote: On 09/14/2010 01:36 PM, Dan Kortschak wrote: Hello, I just tried to have just tried to build matplotlib, but it fails - and is unable to find wxPython (looking under 2.8 rather than 2.6 where is lives - installed from source) or libgtk-2 headers (installed from apt repo). Can anyone suggest how to resolve these issues? If you want to use wx, you need 2.8. It looks like you don't have any of the gui dependencies. Since you you are running ubuntu, I suggest you use the installation method recently described in this thread: http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg18464.html Be careful to read down through the thread; the first try at comprehensive instructions has an error. Eric -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem building matplotlib
I've just has a look at that and unfortunately it does not fix the problem Is there any other suggestion that might be worth a try? I should point out that I already have numpy 1.4.1 installed and scipy 0.8.0 as dependencies for other packages. thanks Dan On Tue, 2010-09-14 at 21:42 -1000, Eric Firing wrote: Since you you are running ubuntu, I suggest you use the installation method recently described in this thread: http://www.mail-archive.com/matplotlib-users@lists.sourceforge.net/msg18464.html Be careful to read down through the thread; the first try at comprehensive instructions has an error. -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem building matplotlib
On 09/15/2010 03:50 AM, Benjamin Root wrote: On Wed, Sep 15, 2010 at 5:34 AM, Dan Kortschak dan.kortsc...@adelaide.edu.au mailto:dan.kortsc...@adelaide.edu.au wrote: I've just has a look at that and unfortunately it does not fix the problem Is there any other suggestion that might be worth a try? I should point out that I already have numpy 1.4.1 installed and scipy 0.8.0 as dependencies for other packages. thanks Dan Hmm, that shouldn't be an issue. Maybe you need to completely clean out the matplotlib build (by removing the build directory) and try again? Be sure to save the build output so we can see what happens if/when it fails. Looking again at the original build output, and at setup.py and setupext.py, it appears that there is a bug in the latter. If the wrong version of wx is found, it should be disabling the attempt to build wxagg, and reporting wxPython: no. We need to fix the bug, but the workaround for now is to use a setup.cfg file with wxagg = False Eric Ben Root -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem building matplotlib
That fixes the problem. thanks On Wed, 2010-09-15 at 07:30 -1000, Eric Firing wrote: Looking again at the original build output, and at setup.py and setupext.py, it appears that there is a bug in the latter. If the wrong version of wx is found, it should be disabling the attempt to build wxagg, and reporting wxPython: no. We need to fix the bug, but the workaround for now is to use a setup.cfg file with wxagg = False Eric -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] problem building matplotlib
On 09/15/2010 01:17 PM, Dan Kortschak wrote: That fixes the problem. thanks On Wed, 2010-09-15 at 07:30 -1000, Eric Firing wrote: Looking again at the original build output, and at setup.py and setupext.py, it appears that there is a bug in the latter. If the wrong version of wx is found, it should be disabling the attempt to build wxagg, and reporting wxPython: no. We need to fix the bug, but the workaround for now is to use a setup.cfg file with wxagg = False Eric It turns out that the _wxagg extension was specific to version 2.6, and for a long time we have required version 2.8, so there was no point in trying to build the extension. In svn 8702 I removed the extension along with related 2.6-only code, and the setup.py references to building the extension. Eric -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problem building matplotlib
On 28/10/06, Eric Firing [EMAIL PROTECTED] wrote: The error is not in matplotlib, it is in a pygtk header file, which is presumably coming from a Redhat package. I don't know why it is True. happening or what the best solution is, though. It looks like the pygobject.h that I have has typename_, not typename, so I am thinking maybe this is a pygtk bug, since fixed, in which typename is in conflict with something. C++, typename is a reserved word there. You might try editing your copy of pygobject.h, adding the trailing underscore to typename on both lines where it occurs. It can't hurt; these are just dummy variable names. That is the solution, and you say the same that was adopted by the project to solve the problem. Eric -- José Abílio - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Problem building matplotlib
Hi all, I am trying to build Matplotlib 0.87.7 on an RHEL 4.4-derived system, with Python 2.3.4. I am running into a weird problem. When I do python setup.py build, I get the following error: gcc: src/_gtkagg.cpp In file included from /usr/include/python2.3/Python.h:8, from /usr/include/pygtk-2.0/pygobject.h:5, from src/_gtkagg.cpp:11: /usr/include/python2.3/pyconfig.h:850:1: warning: _POSIX_C_SOURCE redefined In file included from /usr/include/string.h:26, from /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/cstring:51, from src/_gtkagg.cpp:2: /usr/include/features.h:150:1: warning: this is the location of the previous definition In file included from src/_gtkagg.cpp:11: /usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' before typename /usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' before typename In file included from /usr/include/python2.3/Python.h:8, from /usr/include/pygtk-2.0/pygobject.h:5, from src/_gtkagg.cpp:11: /usr/include/python2.3/pyconfig.h:850:1: warning: _POSIX_C_SOURCE redefined In file included from /usr/include/string.h:26, from /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/cstring:51, from src/_gtkagg.cpp:2: /usr/include/features.h:150:1: warning: this is the location of the previous definition In file included from src/_gtkagg.cpp:11: /usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' before typename /usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' before typename So I did a google search, and found someone recommending that #include Python.h be prepended to the offending file. I have prepended it to src/_gtkagg.cpp, did a clean, and run the build again. The error changed, and the _POSIX_C_SOURCE problem went away, but the build is still failing, at that same file: gcc: src/_gtkagg.cpp In file included from src/_gtkagg.cpp:11: /usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' before typename /usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' before typename In file included from src/_gtkagg.cpp:11: /usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' before typename /usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' before typename Does anyone have an idea of what is going wrong here? I could really use some help, as I am totally stumped. Many thanks in advance. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Problem building matplotlib
Victor Danilchenko wrote: Hi all, I am trying to build Matplotlib 0.87.7 on an RHEL 4.4-derived system, with Python 2.3.4. I am running into a weird problem. When I do python setup.py build, I get the following error: gcc: src/_gtkagg.cpp In file included from /usr/include/python2.3/Python.h:8, from /usr/include/pygtk-2.0/pygobject.h:5, from src/_gtkagg.cpp:11: /usr/include/python2.3/pyconfig.h:850:1: warning: _POSIX_C_SOURCE redefined In file included from /usr/include/string.h:26, from /usr/lib/gcc/i386-redhat-linux/3.4.6/../../../../include/c++/3.4.6/cstring:51, from src/_gtkagg.cpp:2: /usr/include/features.h:150:1: warning: this is the location of the previous definition In file included from src/_gtkagg.cpp:11: /usr/include/pygtk-2.0/pygobject.h:140: error: expected `,' or `...' before typename /usr/include/pygtk-2.0/pygobject.h:147: error: expected `,' or `...' before typename [...] The error is not in matplotlib, it is in a pygtk header file, which is presumably coming from a Redhat package. I don't know why it is happening or what the best solution is, though. It looks like the pygobject.h that I have has typename_, not typename, so I am thinking maybe this is a pygtk bug, since fixed, in which typename is in conflict with something. You might try editing your copy of pygobject.h, adding the trailing underscore to typename on both lines where it occurs. It can't hurt; these are just dummy variable names. Eric - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
