png error with git master, is it just me?

Hi folks,

I'm getting the following error from a clean build of master on an
ubuntu 12.10 machine:

longs[junk]> python -c 'import matplotlib._png'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:
undefined symbol: png_create_read_struct

I hadn't seen anything like this recently, nor can I find similar
reports, so I'm wondering if anyone knows what's going on, or if it's
an error on my side. I can try to bisect it but I figured I'd ask
first in case it's obvious to someone else...

Cheers,

f

Hi Fernando,

I can't recreate this on OS X with the current git master branch, which is
at 11e7ed.

Best wishes,
Damon

···

On Thu, Apr 4, 2013 at 6:41 PM, Fernando Perez <fperez.net@...149...> wrote:

Hi folks,

I'm getting the following error from a clean build of master on an
ubuntu 12.10 machine:

longs[junk]> python -c 'import matplotlib._png'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError:
/home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:
undefined symbol: png_create_read_struct

I hadn't seen anything like this recently, nor can I find similar
reports, so I'm wondering if anyone knows what's going on, or if it's
an error on my side. I can try to bisect it but I figured I'd ask
first in case it's obvious to someone else...

Cheers,

f

--
Damon McDougall
http://www.damon-is-a-geek.com
Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

Thanks, Damon, for this info.

Based on this, I’ve tested now on another, different system with the same version of linux and can’t reproduce it either. Very odd, but it looks like something is amiss on my end, so let me investigate further before anyone burns further cycles on the issue.

Cheers,

f

···

On Thu, Apr 4, 2013 at 8:06 PM, Damon McDougall <damon.mcdougall@…552…149…> wrote:

On Thu, Apr 4, 2013 at 6:41 PM, Fernando Perez <fperez.net@…149…> wrote:

Hi folks,

I’m getting the following error from a clean build of master on an

ubuntu 12.10 machine:

longs[junk]> python -c ‘import matplotlib._png’

Traceback (most recent call last):

File “”, line 1, in

ImportError: /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:

undefined symbol: png_create_read_struct

I hadn’t seen anything like this recently, nor can I find similar

reports, so I’m wondering if anyone knows what’s going on, or if it’s

an error on my side. I can try to bisect it but I figured I’d ask

first in case it’s obvious to someone else…

Cheers,

f

Hi Fernando,

I can’t recreate this on OS X with the current git master branch, which is at 11e7ed.

Best wishes,

Damon


Damon McDougall
http://www.damon-is-a-geek.com

Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

Any time, Fernando.

Out of curiosity, is the png_create_read_struct a symbol from libpng? If
so, try adding wherever your libpng lives to your LD_LIBRARY_PATH and see
what happens.

Best wishes,
Damon

···

On Thu, Apr 4, 2013 at 10:51 PM, Fernando Perez <fperez.net@...149...>wrote:

Thanks, Damon, for this info.

Based on this, I've tested now on another, different system with the same
version of linux and can't reproduce it either. Very odd, but it looks
like something is amiss on my end, so let me investigate further before
anyone burns further cycles on the issue.

Cheers,

f

On Thu, Apr 4, 2013 at 8:06 PM, Damon McDougall <damon.mcdougall@...149... > > wrote:

On Thu, Apr 4, 2013 at 6:41 PM, Fernando Perez <fperez.net@...149...>wrote:

Hi folks,

I'm getting the following error from a clean build of master on an
ubuntu 12.10 machine:

longs[junk]> python -c 'import matplotlib._png'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError:
/home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:
undefined symbol: png_create_read_struct

I hadn't seen anything like this recently, nor can I find similar
reports, so I'm wondering if anyone knows what's going on, or if it's
an error on my side. I can try to bisect it but I figured I'd ask
first in case it's obvious to someone else...

Cheers,

f

Hi Fernando,

I can't recreate this on OS X with the current git master branch, which
is at 11e7ed.

Best wishes,
Damon

--
Damon McDougall
http://www.damon-is-a-geek.com
Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

--
Damon McDougall
http://www.damon-is-a-geek.com
Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

Well, I’m using the system libpng, which is what puzzles me: there should be no need for me to modify my LD_…, and I haven’t done so in the past. I’ll have to dig into the build tomorrow to figure out exactly what’s going on there…

Will report back.

···

On Thu, Apr 4, 2013 at 9:24 PM, Damon McDougall <damon.mcdougall@…149…> wrote:

On Thu, Apr 4, 2013 at 10:51 PM, Fernando Perez <fperez.net@…149…> wrote:

Thanks, Damon, for this info.

Based on this, I’ve tested now on another, different system with the same version of linux and can’t reproduce it either. Very odd, but it looks like something is amiss on my end, so let me investigate further before anyone burns further cycles on the issue.

Cheers,

f

Any time, Fernando.

On Thu, Apr 4, 2013 at 8:06 PM, Damon McDougall <damon.mcdougall@…149…> wrote:

On Thu, Apr 4, 2013 at 6:41 PM, Fernando Perez <fperez.net@…149…> wrote:

Hi folks,

I’m getting the following error from a clean build of master on an

ubuntu 12.10 machine:

longs[junk]> python -c ‘import matplotlib._png’

Traceback (most recent call last):

File “”, line 1, in

ImportError: /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:

undefined symbol: png_create_read_struct

I hadn’t seen anything like this recently, nor can I find similar

reports, so I’m wondering if anyone knows what’s going on, or if it’s

an error on my side. I can try to bisect it but I figured I’d ask

first in case it’s obvious to someone else…

Cheers,

f

Hi Fernando,

I can’t recreate this on OS X with the current git master branch, which is at 11e7ed.

Best wishes,

Damon


Damon McDougall
http://www.damon-is-a-geek.com

Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

Out of curiosity, is the png_create_read_struct a symbol from libpng? If so, try adding wherever your libpng lives to your LD_LIBRARY_PATH and see what happens.

Best wishes,

Damon


Damon McDougall
http://www.damon-is-a-geek.com

Institute for Computational Engineering Sciences
201 E. 24th St.
Stop C0200
The University of Texas at Austin
Austin, TX 78712-1229

I've had problems like this using a git-source matplotlib and macports. This usually happens after libpng is upgraded.

Turns out a 'python setup.py install ...' in matplotlib will not solve things until you manually delete the contents of the matplotlib build/ directory. After which new go at setup.py install will link to the new libpng library. 'make clean' will not do this for you (which is probably an oversight in the matplotlib Makefile). Don't know if this will help for linux.

M

···

On 4/5/13 1:37 AM, Fernando Perez wrote:

Well, I'm using the system libpng, which is what puzzles me: there
should be no need for me to modify my LD_..., and I haven't done so in
the past. I'll have to dig into the build tomorrow to figure out
exactly what's going on there...

Will report back.

On Thu, Apr 4, 2013 at 9:24 PM, Damon McDougall > <damon.mcdougall@…149… <mailto:damon.mcdougall@…149…>> wrote:

    On Thu, Apr 4, 2013 at 10:51 PM, Fernando Perez > <fperez.net@…149… <mailto:fperez.net@…149…>> wrote:

        Thanks, Damon, for this info.

        Based on this, I've tested now on another, different system with
        the same version of linux and can't reproduce it either. Very
        odd, but it looks like something is amiss on my end, so let me
        investigate further before anyone burns further cycles on the issue.

        Cheers,

        f

        On Thu, Apr 4, 2013 at 8:06 PM, Damon McDougall > <damon.mcdougall@…149… <mailto:damon.mcdougall@…149…>> > wrote:

            On Thu, Apr 4, 2013 at 6:41 PM, Fernando Perez > <fperez.net@…149… <mailto:fperez.net@…149…>> wrote:

                Hi folks,

                I'm getting the following error from a clean build of
                master on an
                ubuntu 12.10 machine:

                longs[junk]> python -c 'import matplotlib._png'
                Traceback (most recent call last):
                   File "<string>", line 1, in <module>
                ImportError:
                /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:
                undefined symbol: png_create_read_struct

                I hadn't seen anything like this recently, nor can I
                find similar
                reports, so I'm wondering if anyone knows what's going
                on, or if it's
                an error on my side. I can try to bisect it but I
                figured I'd ask
                first in case it's obvious to someone else...

                Cheers,

                f

            Hi Fernando,

            I can't recreate this on OS X with the current git master
            branch, which is at 11e7ed.

            Best wishes,
            Damon

            --
            Damon McDougall
            http://www.damon-is-a-geek.com
            Institute for Computational Engineering Sciences
            201 E. 24th St.
            Stop C0200
            The University of Texas at Austin
            Austin, TX 78712-1229

    Any time, Fernando.

    Out of curiosity, is the png_create_read_struct a symbol from
    libpng? If so, try adding wherever your libpng lives to your
    LD_LIBRARY_PATH and see what happens.

    Best wishes,
    Damon

    --
    Damon McDougall
    http://www.damon-is-a-geek.com
    Institute for Computational Engineering Sciences
    201 E. 24th St.
    Stop C0200
    The University of Texas at Austin
    Austin, TX 78712-1229

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html

_______________________________________________
Matplotlib-devel mailing list
Matplotlib-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-devel

Well, I'm using the system libpng, which is what puzzles me: there
should be no need for me to modify my LD_..., and I haven't done so in
the past. I'll have to dig into the build tomorrow to figure out
exactly what's going on there...

whats the output of:
ldd
/home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so
apt-cache policy libpng12-dev

the system libpng in ubuntu 12.10 does have this symbol defined, maybe
you are picking up some other installation.

···

On 05.04.2013 07:37, Fernando Perez wrote:

Will report back.

On Thu, Apr 4, 2013 at 9:24 PM, Damon McDougall > <damon.mcdougall@…149… <mailto:damon.mcdougall@…149…>> wrote:

    On Thu, Apr 4, 2013 at 10:51 PM, Fernando Perez > <fperez.net@…149… <mailto:fperez.net@…149…>> wrote:

        Thanks, Damon, for this info.

        Based on this, I've tested now on another, different system with
        the same version of linux and can't reproduce it either. Very
        odd, but it looks like something is amiss on my end, so let me
        investigate further before anyone burns further cycles on the issue.

        Cheers,

        f

        On Thu, Apr 4, 2013 at 8:06 PM, Damon McDougall > <damon.mcdougall@…149… <mailto:damon.mcdougall@…149…>> > wrote:

            On Thu, Apr 4, 2013 at 6:41 PM, Fernando Perez > <fperez.net@…149… <mailto:fperez.net@…149…>> wrote:

                Hi folks,

                I'm getting the following error from a clean build of
                master on an
                ubuntu 12.10 machine:

                longs[junk]> python -c 'import matplotlib._png'
                Traceback (most recent call last):
                  File "<string>", line 1, in <module>
                ImportError:
                /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so:
                undefined symbol: png_create_read_struct

                I hadn't seen anything like this recently, nor can I
                find similar
                reports, so I'm wondering if anyone knows what's going
                on, or if it's
                an error on my side. I can try to bisect it but I
                figured I'd ask
                first in case it's obvious to someone else...

                Cheers,

                f

            Hi Fernando,

            I can't recreate this on OS X with the current git master
            branch, which is at 11e7ed.

            Best wishes,
            Damon

            --
            Damon McDougall
            http://www.damon-is-a-geek.com
            Institute for Computational Engineering Sciences
            201 E. 24th St.
            Stop C0200
            The University of Texas at Austin
            Austin, TX 78712-1229

    Any time, Fernando.

    Out of curiosity, is the png_create_read_struct a symbol from
    libpng? If so, try adding wherever your libpng lives to your
    LD_LIBRARY_PATH and see what happens.

    Best wishes,
    Damon

    --
    Damon McDougall
    http://www.damon-is-a-geek.com
    Institute for Computational Engineering Sciences
    201 E. 24th St.
    Stop C0200
    The University of Texas at Austin
    Austin, TX 78712-1229

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html

_______________________________________________
Matplotlib-devel mailing list
Matplotlib-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/matplotlib-devel

Here's what I get:

longs[~]> ldd /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so
linux-vdso.so.1 => (0x00007fff56dff000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f97ecaeb000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f97ec8d4000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f97ec6b7000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f97ec2f8000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f97ebffb000)
/lib64/ld-linux-x86-64.so.2 (0x00007f97ed04b000)

longs[~]> apt-cache policy libpng12-dev
libpng12-dev:
  Installed: 1.2.49-1ubuntu1
  Candidate: 1.2.49-1ubuntu1
  Version table:
*** 1.2.49-1ubuntu1 0
        500 http://ubuntu.cs.utah.edu/ubuntu/ quantal/main amd64 Packages
        100 /var/lib/dpkg/status

Thanks for any insights you may provide...

f

···

On Fri, Apr 5, 2013 at 10:06 AM, Julian Taylor <jtaylor.debian@...564...> wrote:

whats the output of:
ldd
/home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so
apt-cache policy libpng12-dev

the system libpng in ubuntu 12.10 does have this symbol defined, maybe
you are picking up some other installation.

strange, it isn't linked against libpng at all. I can't reproduce that
on my Ubuntu machine with git head.

Do you still have a buildlog?
Maybe do a new build from a clean folder (and save the log).

···

On 05.04.2013 22:32, Fernando Perez wrote:

On Fri, Apr 5, 2013 at 10:06 AM, Julian Taylor > <jtaylor.debian@...564...> wrote:

whats the output of:
ldd
/home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so
apt-cache policy libpng12-dev

the system libpng in ubuntu 12.10 does have this symbol defined, maybe
you are picking up some other installation.

Here's what I get:

longs[~]> ldd /home/fperez/usr/opt/lib/python2.7/site-packages/matplotlib-1.3.x-py2.7-linux-x86_64.egg/matplotlib/_png.so
linux-vdso.so.1 => (0x00007fff56dff000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f97ecaeb000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f97ec8d4000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f97ec6b7000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f97ec2f8000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f97ebffb000)
/lib64/ld-linux-x86-64.so.2 (0x00007f97ed04b000)

longs[~]> apt-cache policy libpng12-dev
libpng12-dev:
  Installed: 1.2.49-1ubuntu1
  Candidate: 1.2.49-1ubuntu1
  Version table:
*** 1.2.49-1ubuntu1 0
        500 http://ubuntu.cs.utah.edu/ubuntu/ quantal/main amd64 Packages
        100 /var/lib/dpkg/status

Thanks for any insights you may provide...

f

I just did a fully clean rebuild in a fresh clone, and the same thing
happens. Build log here:

http://pastebin.com/eCGbEvKb

The only thing that jumpts at me is:

Package PyCXX was not found in the pkg-config search path.
Perhaps you should add the directory containing `PyCXX.pc'
to the PKG_CONFIG_PATH environment variable
No package 'PyCXX' found

which I don't understand, as pycxx is clearly installed:

(master)longs[matplotlib]> apt-cache policy python-cxx
python-cxx:
  Installed: 6.2.4-1
  Candidate: 6.2.4-1
  Version table:
*** 6.2.4-1 0
        500 http://ubuntu.cs.utah.edu/ubuntu/ quantal/universe amd64 Packages
        100 /var/lib/dpkg/status

Puzzled...

f

···

On Fri, Apr 5, 2013 at 1:49 PM, Julian Taylor <jtaylor.debian@...564...> wrote:

strange, it isn't linked against libpng at all. I can't reproduce that
on my Ubuntu machine with git head.

Do you still have a buildlog?
Maybe do a new build from a clean folder (and save the log).

actually the presence of the PyCXX package seems to be the problem. If I
have it installed it fails, if not it works. Looks like some weird bug
in the build system.
Why is it looking for a pkg-config file? PyCXX does not provide one.

I though system PyCXX could not be used because it needed unmerged patches?
Btw. I could merge the patches into the Debian package if they are
forwarded to me.

···

On 05.04.2013 23:16, Fernando Perez wrote:

On Fri, Apr 5, 2013 at 1:49 PM, Julian Taylor > <jtaylor.debian@...564...> wrote:

strange, it isn't linked against libpng at all. I can't reproduce that
on my Ubuntu machine with git head.

Do you still have a buildlog?
Maybe do a new build from a clean folder (and save the log).

I just did a fully clean rebuild in a fresh clone, and the same thing
happens. Build log here:

http://pastebin.com/eCGbEvKb

The only thing that jumpts at me is:

Package PyCXX was not found in the pkg-config search path.
Perhaps you should add the directory containing `PyCXX.pc'
to the PKG_CONFIG_PATH environment variable
No package 'PyCXX' found

which I don't understand, as pycxx is clearly installed:

(master)longs[matplotlib]> apt-cache policy python-cxx
python-cxx:
  Installed: 6.2.4-1
  Candidate: 6.2.4-1
  Version table:
*** 6.2.4-1 0
        500 http://ubuntu.cs.utah.edu/ubuntu/ quantal/universe amd64 Packages
        100 /var/lib/dpkg/status

Puzzled...

I filed an issue:
https://github.com/matplotlib/matplotlib/issues/1884

···

On 05.04.2013 23:35, Julian Taylor wrote:

On 05.04.2013 23:16, Fernando Perez wrote:

On Fri, Apr 5, 2013 at 1:49 PM, Julian Taylor >> <jtaylor.debian@...564...> wrote:

strange, it isn't linked against libpng at all. I can't reproduce that
on my Ubuntu machine with git head.

Do you still have a buildlog?
Maybe do a new build from a clean folder (and save the log).

I just did a fully clean rebuild in a fresh clone, and the same thing
happens. Build log here:

http://pastebin.com/eCGbEvKb

The only thing that jumpts at me is:

Package PyCXX was not found in the pkg-config search path.
Perhaps you should add the directory containing `PyCXX.pc'
to the PKG_CONFIG_PATH environment variable
No package 'PyCXX' found

which I don't understand, as pycxx is clearly installed:

(master)longs[matplotlib]> apt-cache policy python-cxx
python-cxx:
  Installed: 6.2.4-1
  Candidate: 6.2.4-1
  Version table:
*** 6.2.4-1 0
        500 http://ubuntu.cs.utah.edu/ubuntu/ quantal/universe amd64 Packages
        100 /var/lib/dpkg/status

Puzzled...

actually the presence of the PyCXX package seems to be the problem. If I
have it installed it fails, if not it works. Looks like some weird bug
in the build system.
Why is it looking for a pkg-config file? PyCXX does not provide one.

I though system PyCXX could not be used because it needed unmerged patches?
Btw. I could merge the patches into the Debian package if they are
forwarded to me.

Go figure, it was an actual bug! Well, thanks a lot for tracking it down :slight_smile:

I guess for now I'll just remove pycxx-dev from my system.
Fortunately I don't need it for anything else. But it means that
right now, mpl can't be built on a system with the matplotlib
build-deps loaded, which is a bummer.

Cheers,

f

···

On Fri, Apr 5, 2013 at 2:51 PM, Julian Taylor <jtaylor.debian@...564...> wrote:

I filed an issue:
https://github.com/matplotlib/matplotlib/issues/1884

Hey there,

Just getting to this after a vacation. I think I was stymied by the fact that the Fedora package for pycxx provides a pkg-config file, whereas, as you point out, it is not upstream.

I'll put my further comments on the issue.

Cheers,
Mike

···

On 04/05/2013 11:23 PM, Fernando Perez wrote:

On Fri, Apr 5, 2013 at 2:51 PM, Julian Taylor > <jtaylor.debian@...564...> wrote:

I filed an issue:
https://github.com/matplotlib/matplotlib/issues/1884

Go figure, it was an actual bug! Well, thanks a lot for tracking it down :slight_smile:

I guess for now I'll just remove pycxx-dev from my system.
Fortunately I don't need it for anything else. But it means that
right now, mpl can't be built on a system with the matplotlib
build-deps loaded, which is a bummer.

Cheers,

f

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
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