[cctbxbb] error

Marcin Wojdyr wojdyr at gmail.com
Wed Jun 22 10:42:11 PDT 2016


FWIW we also needed gdk-pixbuf in ccp4, because of coot.
A few years ago I patched it to use $COOT_PREFIX to find loaders.cache:

http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/devtools/trunk/view/head:/patches/gdk-pixbuf-hack.patch

I don't remember it well, but I think the second part of the patch is
to make regeneration of the cache file not necessary.
The only plugin that we have is for svg. Other formats can be included
in the library, not as plugins. The configure command we use is:

./configure --prefix=$PREFIX \
            --enable-shared --disable-static \
            --disable-introspection --without-libtiff --disable-rpath \
            --disable-glibtest --disable-nls --disable-gio-sniffing \
            --with-included-loaders=png

(some of this may not be necessary, the last line is to make png
built-in rather than a plugin)

Marcin

On Wed, Jun 22, 2016 at 6:00 PM, Billy Poon <bkpoon at lbl.gov> wrote:
> Hi all,
>
> I haven't found the place where the loaders.cache directory is hard-coded,
> but I'll keep looking. In the meantime, there is a workaround for the GTK
> message. You can export the GDK_PIXBUF_MODULE_FILE environment variable to
> point to <installation directory>/base/lib. That will tell gdk-pixbuf where
> to look for the loaders.cache file.
>
> https://developer.gnome.org/gdk-pixbuf/unstable//gdk-pixbuf-query-loaders.html
>
> The loaders.cache file is updated during the installation. It's a text file,
> so if you look at it, the directories for the loaders should be updated with
> the installation directory. But for some reason, the directory for the
> loaders.cache file is hard-coded somewhere.
>
> I was planning on updating the rest of the packages (numpy, matplotlib, PIL
> -> Pillow, etc.) after the Phenix release, so the segmentation fault issue
> should go away if a newer version matplotlib works.
>
> Hi James,
>
> What is the error message that you're getting?
>
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
> On Wed, Jun 22, 2016 at 3:38 AM, <markus.gerstel at diamond.ac.uk> wrote:
>>
>> James followed up that once he installed libjpeg he got the same error
>> message.
>>
>>
>>
>> I ran one build with the current stable version of matplotlib 1.5.1, and
>> that did not segfault. However I’m not going to change that dependency at
>> this time with the phenix release looming.
>>
>> Anyone have an idea for a less intrusive fix, or should we just wait until
>> after phenix?
>>
>>
>>
>> Markus Gerstel MBCS
>>
>> Postdoctoral Research Associate
>>
>> Tel: +44 1235 778698
>>
>>
>>
>> Diamond Light Source Ltd.
>>
>> Diamond House
>>
>> Harwell Science & Innovation Campus
>>
>> Didcot
>>
>> Oxfordshire
>>
>> OX11 0DE
>>
>>
>>
>> From: Parkhurst, James (DLSLtd,RAL,LSCI)
>> Sent: 22 June 2016 10:37
>> To: Gerstel, Markus (DLSLtd,RAL,LSCI)
>>
>>
>> Cc: cctbxbb at phenix-online.org
>> Subject: RE: error
>>
>>
>>
>> Hi Markus,
>>
>> I tried this on my machine and I think I needed to install numpy - it was
>> picking up the system numpy. However, I then get the following message:
>>
>> fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat
>> fc-list: symbol lookup error: fc-list: undefined symbol: FcPatternFormat
>> Plotting image failed: Matplotlib backend_wx and backend_wxagg require
>> wxPython >=2.8
>>
>> Presumably wxPython is distributed with DIALS, so do we need to have a
>> newer version or something?
>>
>> Thanks,
>>
>> James
>>
>> ________________________________
>>
>> From: Gerstel, Markus (DLSLtd,RAL,LSCI)
>> Sent: 22 June 2016 10:17
>> To: Parkhurst, James (DLSLtd,RAL,LSCI)
>> Cc: cctbxbb at phenix-online.org
>> Subject: RE: error
>>
>> Hi James,
>>
>> CCing cctbxbb for further support
>>
>>
>>
>> I can reproduce at least similar errors with both DIALS 1.2.5 and current
>> nightly builds.
>>
>> I think this may be a matplotlib 1.3.1 problem.
>>
>> A minimal reproducer is:
>>
>>
>>
>> $ dials.python
>>
>> > import matplotlib.pyplot as plt
>>
>> > plt.imshow([[1]])
>>
>> Gtk-Message…
>>
>> > (press ctrl+D)
>>
>> Segmentation fault
>>
>>
>>
>> When compiled on the same machine I do not get the Gtk-Messages, but I do
>> get the segmentation fault.
>>
>>
>>
>> Markus Gerstel MBCS
>>
>> Postdoctoral Research Associate
>>
>> Tel: +44 1235 778698
>>
>>
>>
>> Diamond Light Source Ltd.
>>
>> Diamond House
>>
>> Harwell Science & Innovation Campus
>>
>> Didcot
>>
>> Oxfordshire
>>
>> OX11 0DE
>>
>>
>>
>> From: Parkhurst, James (DLSLtd,RAL,LSCI)
>> Sent: 21 June 2016 16:58
>> To: Gerstel, Markus (DLSLtd,RAL,LSCI)
>> Subject: FW: error
>>
>>
>>
>> Hi Markus,
>>
>> I've been getting my summer student to do the cctbx_introduction tutorials
>> in dials_scratch. He's using a version of dials downloaded from the website
>> and when he runs the introduction script he gets errors about gdk-pixbuf
>> giving paths to /scratch/jenkins_slave/workspace/. This seems like there is
>> a jenkins path being set in the distributed installers. Would you have any
>> idea how I can fix this? I'm downloading the linux installer of DIALS now so
>> I can test this myself.
>>
>> Thanks,
>>
>> James
>>
>> ________________________________
>>
>> [sse87232 at ws188 cctbx_introduction_1]$ dials.python
>> cctbx_introduction_1_test.py ximg2701_00001.cbf
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>>
>> (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open
>> pixbuf loader module file
>> '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders':
>> No such file or directory
>> Segmentation fault (core dumped)
>> [sse87232 at ws188 cctbx_introduction_1]$ which dials.python
>> /dls/science/users/sse87232/dials/dials-v1-2-4/build/bin/dials.python
>>
>>
>>
>> --
>>
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