<div dir="ltr">Hi all,<div><br></div><div>I just checked in an update that should fix the gdk-pixbuf issue. I enabled a flag called --enable-relocations in the configure step. I've created a new installer on our CentOS 6 machine and a new installation does not generate the error message. I'm running builds on the other Linux distributions, but I don't expect any issues from this flag.</div><div><br></div><div>Let me know if the updated packages are causing any other issues. Thanks!</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Jun 22, 2016 at 10:42 AM, Marcin Wojdyr <span dir="ltr"><<a href="mailto:wojdyr@gmail.com" target="_blank">wojdyr@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">FWIW we also needed gdk-pixbuf in ccp4, because of coot.<br>
A few years ago I patched it to use $COOT_PREFIX to find loaders.cache:<br>
<br>
<a href="http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/devtools/trunk/view/head:/patches/gdk-pixbuf-hack.patch" rel="noreferrer" target="_blank">http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/devtools/trunk/view/head:/patches/gdk-pixbuf-hack.patch</a><br>
<br>
I don't remember it well, but I think the second part of the patch is<br>
to make regeneration of the cache file not necessary.<br>
The only plugin that we have is for svg. Other formats can be included<br>
in the library, not as plugins. The configure command we use is:<br>
<br>
./configure --prefix=$PREFIX \<br>
--enable-shared --disable-static \<br>
--disable-introspection --without-libtiff --disable-rpath \<br>
--disable-glibtest --disable-nls --disable-gio-sniffing \<br>
--with-included-loaders=png<br>
<br>
(some of this may not be necessary, the last line is to make png<br>
built-in rather than a plugin)<br>
<span class="HOEnZb"><font color="#888888"><br>
Marcin<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Wed, Jun 22, 2016 at 6:00 PM, Billy Poon <<a href="mailto:bkpoon@lbl.gov">bkpoon@lbl.gov</a>> wrote:<br>
> Hi all,<br>
><br>
> I haven't found the place where the loaders.cache directory is hard-coded,<br>
> but I'll keep looking. In the meantime, there is a workaround for the GTK<br>
> message. You can export the GDK_PIXBUF_MODULE_FILE environment variable to<br>
> point to <installation directory>/base/lib. That will tell gdk-pixbuf where<br>
> to look for the loaders.cache file.<br>
><br>
> <a href="https://developer.gnome.org/gdk-pixbuf/unstable//gdk-pixbuf-query-loaders.html" rel="noreferrer" target="_blank">https://developer.gnome.org/gdk-pixbuf/unstable//gdk-pixbuf-query-loaders.html</a><br>
><br>
> The loaders.cache file is updated during the installation. It's a text file,<br>
> so if you look at it, the directories for the loaders should be updated with<br>
> the installation directory. But for some reason, the directory for the<br>
> loaders.cache file is hard-coded somewhere.<br>
><br>
> I was planning on updating the rest of the packages (numpy, matplotlib, PIL<br>
> -> Pillow, etc.) after the Phenix release, so the segmentation fault issue<br>
> should go away if a newer version matplotlib works.<br>
><br>
> Hi James,<br>
><br>
> What is the error message that you're getting?<br>
><br>
><br>
> --<br>
> Billy K. Poon<br>
> Research Scientist, Molecular Biophysics and Integrated Bioimaging<br>
> Lawrence Berkeley National Laboratory<br>
> 1 Cyclotron Road, M/S 33R0345<br>
> Berkeley, CA 94720<br>
> Tel: <a href="tel:%28510%29%20486-5709" value="+15104865709">(510) 486-5709</a><br>
> Fax: <a href="tel:%28510%29%20486-5909" value="+15104865909">(510) 486-5909</a><br>
> Web: <a href="https://phenix-online.org" rel="noreferrer" target="_blank">https://phenix-online.org</a><br>
><br>
> On Wed, Jun 22, 2016 at 3:38 AM, <<a href="mailto:markus.gerstel@diamond.ac.uk">markus.gerstel@diamond.ac.uk</a>> wrote:<br>
>><br>
>> James followed up that once he installed libjpeg he got the same error<br>
>> message.<br>
>><br>
>><br>
>><br>
>> I ran one build with the current stable version of matplotlib 1.5.1, and<br>
>> that did not segfault. However I’m not going to change that dependency at<br>
>> this time with the phenix release looming.<br>
>><br>
>> Anyone have an idea for a less intrusive fix, or should we just wait until<br>
>> after phenix?<br>
>><br>
>><br>
>><br>
>> Markus Gerstel MBCS<br>
>><br>
>> Postdoctoral Research Associate<br>
>><br>
>> Tel: <a href="tel:%2B44%201235%20778698" value="+441235778698">+44 1235 778698</a><br>
>><br>
>><br>
>><br>
>> Diamond Light Source Ltd.<br>
>><br>
>> Diamond House<br>
>><br>
>> Harwell Science & Innovation Campus<br>
>><br>
>> Didcot<br>
>><br>
>> Oxfordshire<br>
>><br>
>> OX11 0DE<br>
>><br>
>><br>
>><br>
>> From: Parkhurst, James (DLSLtd,RAL,LSCI)<br>
>> Sent: 22 June 2016 10:37<br>
>> To: Gerstel, Markus (DLSLtd,RAL,LSCI)<br>
>><br>
>><br>
>> Cc: <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
>> Subject: RE: error<br>
>><br>
>><br>
>><br>
>> Hi Markus,<br>
>><br>
>> I tried this on my machine and I think I needed to install numpy - it was<br>
>> picking up the system numpy. However, I then get the following message:<br>
>><br>
>> fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat<br>
>> fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat<br>
>> Plotting image failed: Matplotlib backend_wx and backend_wxagg require<br>
>> wxPython >=2.8<br>
>><br>
>> Presumably wxPython is distributed with DIALS, so do we need to have a<br>
>> newer version or something?<br>
>><br>
>> Thanks,<br>
>><br>
>> James<br>
>><br>
>> ________________________________<br>
>><br>
>> From: Gerstel, Markus (DLSLtd,RAL,LSCI)<br>
>> Sent: 22 June 2016 10:17<br>
>> To: Parkhurst, James (DLSLtd,RAL,LSCI)<br>
>> Cc: <a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
>> Subject: RE: error<br>
>><br>
>> Hi James,<br>
>><br>
>> CCing cctbxbb for further support<br>
>><br>
>><br>
>><br>
>> I can reproduce at least similar errors with both DIALS 1.2.5 and current<br>
>> nightly builds.<br>
>><br>
>> I think this may be a matplotlib 1.3.1 problem.<br>
>><br>
>> A minimal reproducer is:<br>
>><br>
>><br>
>><br>
>> $ dials.python<br>
>><br>
>> > import matplotlib.pyplot as plt<br>
>><br>
>> > plt.imshow([[1]])<br>
>><br>
>> Gtk-Message…<br>
>><br>
>> > (press ctrl+D)<br>
>><br>
>> Segmentation fault<br>
>><br>
>><br>
>><br>
>> When compiled on the same machine I do not get the Gtk-Messages, but I do<br>
>> get the segmentation fault.<br>
>><br>
>><br>
>><br>
>> Markus Gerstel MBCS<br>
>><br>
>> Postdoctoral Research Associate<br>
>><br>
>> Tel: +44 1235 778698<br>
>><br>
>><br>
>><br>
>> Diamond Light Source Ltd.<br>
>><br>
>> Diamond House<br>
>><br>
>> Harwell Science & Innovation Campus<br>
>><br>
>> Didcot<br>
>><br>
>> Oxfordshire<br>
>><br>
>> OX11 0DE<br>
>><br>
>><br>
>><br>
>> From: Parkhurst, James (DLSLtd,RAL,LSCI)<br>
>> Sent: 21 June 2016 16:58<br>
>> To: Gerstel, Markus (DLSLtd,RAL,LSCI)<br>
>> Subject: FW: error<br>
>><br>
>><br>
>><br>
>> Hi Markus,<br>
>><br>
>> I've been getting my summer student to do the cctbx_introduction tutorials<br>
>> in dials_scratch. He's using a version of dials downloaded from the website<br>
>> and when he runs the introduction script he gets errors about gdk-pixbuf<br>
>> giving paths to /scratch/jenkins_slave/workspace/. This seems like there is<br>
>> a jenkins path being set in the distributed installers. Would you have any<br>
>> idea how I can fix this? I'm downloading the linux installer of DIALS now so<br>
>> I can test this myself.<br>
>><br>
>> Thanks,<br>
>><br>
>> James<br>
>><br>
>> ________________________________<br>
>><br>
>> [sse87232@ws188 cctbx_introduction_1]$ dials.python<br>
>> cctbx_introduction_1_test.py ximg2701_00001.cbf<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>><br>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open<br>
>> pixbuf loader module file<br>
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':<br>
>> No such file or directory<br>
>> Segmentation fault (core dumped)<br>
>> [sse87232@ws188 cctbx_introduction_1]$ which dials.python<br>
>> /dls/science/users/sse87232/dials/dials-v1-2-4/build/bin/dials.python<br>
>><br>
>><br>
>><br>
>> --<br>
>><br>
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</div></div></blockquote></div><br></div>