[cctbxbb] error

[Billy Poon]

Hi all,

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.

Let me know if the updated packages are causing any other issues. Thanks!

--
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 10:42 AM, Marcin Wojdyr <wojdyr at gmail.com> wrote:

> 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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