[cctbxbb] bootstrap.py build on Ubuntu

David Waterman dgwaterman at gmail.com
Sat Jun 11 02:04:41 PDT 2016


Hi Billy,

I'm replying on this old thread because I have finally got round to trying
a bootstrap build for DIALS out again on Ubuntu, having waited for updates
to the dependencies and updating the OS to 16.04.

The good news is, the build ran through fine. This is the first time I've
had a bootstrap build complete without error on Ubuntu, so thanks to you
and the others who have worked on improving the build in the last few
months!

The bad news is I'm getting two failures in the DIALS tests:

dials/test/command_line/tst_export_bitmaps.py
dials_regression/test.py

Both are from PIL

      File
"/home/fcx32934/dials_test_build/base/lib/python2.7/site-packages/PIL/Image.py",
line 401, in _getencoder
        raise IOError("encoder %s not available" % encoder_name)
    IOError: encoder zip not available

Indeed, from base_tmp/imaging_install_log it looks like PIL is not
configured properly

--------------------------------------------------------------------
PIL 1.1.7 SETUP SUMMARY
--------------------------------------------------------------------
version       1.1.7
platform      linux2 2.7.8 (default_cci, Jun 10 2016, 16:04:32)
              [GCC 5.3.1 20160413]
--------------------------------------------------------------------
*** TKINTER support not available
*** JPEG support not available
*** ZLIB (PNG/ZIP) support not available
*** FREETYPE2 support not available
*** LITTLECMS support not available
--------------------------------------------------------------------

Any ideas? I have zlib headers but perhaps PIL can't find them.

On a related note, the free version of PIL has not been updated for years.
The replacement Pillow has started to diverge. I first noticed this when
Ubuntu 16.04 gave me Pillow 3.1.2 and my cctbx build with the system python
produced failures because it no longer supports certain deprecated methods
from PIL. I worked around that in r24587, but these things are a losing
battle. Is it time to switch cctbx over to Pillow instead of PIL?

Cheers

-- David

On 7 January 2016 at 18:12, Billy Poon <bkpoon at lbl.gov> wrote:

> Hi all,
>
> Since wxPython was updated to 3.0.2, I have been thinking about updating
> the other GUI-related packages to more recent versions. I would probably
> update to the latest, stable version that does not involve major changes to
> the API so that backwards compatibility is preserved. Let me know if that
> would be helpful and I can prioritize the migration and testing.
>
> --
> 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 Thu, Jan 7, 2016 at 9:30 AM, Nicholas Sauter <nksauter at lbl.gov> wrote:
>
>> David,
>>
>> I notice that the Pango version, 1.16.1, was released in 2007, so perhaps
>> it is no surprise that the latest Ubuntu does not support it.  Maybe this
>> calls for stepping forward the Pango version until you find one that works.
>> I see that the latest stable release is 1.39.
>>
>> This would be valuable information for us..Billy Poon in the Phenix group
>> is supporting the Phenix GUI, so it might be advisable for him to update
>> the Pango version in the base installer.
>>
>> Nick
>>
>> Nicholas K. Sauter, Ph. D.
>> Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging
>> Division
>> Lawrence Berkeley National Laboratory
>> 1 Cyclotron Rd., Bldg. 33R0345
>> Berkeley, CA 94720
>> (510) 486-5713
>>
>> On Thu, Jan 7, 2016 at 8:54 AM, David Waterman <dgwaterman at gmail.com>
>> wrote:
>>
>>> Hi again
>>>
>>> Another data point: I just tried this on a different Ubuntu machine,
>>> this time running 14.04. In this case pango installed just fine. In fact
>>> all other packages installed too and the machine is now compiling cctbx.
>>>
>>> I might have enough for comparison between the potentially working 14.04
>>> and failed 15.04 builds to figure out what is wrong in the second case.
>>>
>>> Cheers
>>>
>>> -- David
>>>
>>> On 7 January 2016 at 09:56, David Waterman <dgwaterman at gmail.com> wrote:
>>>
>>>> Hi folks
>>>>
>>>> I recently tried building cctbx+dials on Ubuntu 15.04 following the
>>>> instructions here:
>>>> http://dials.github.io/documentation/installation_developer.html
>>>>
>>>> This failed during installation of pango-1.16.1. Looking
>>>> at pango_install_log, I see the command that failed was as follows:
>>>>
>>>> gcc -DHAVE_CONFIG_H -I. -I. -I../..
>>>> -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\"
>>>> -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\"
>>>> -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED
>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include
>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2
>>>> -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c  -fPIC
>>>> -DPIC -o .libs/fribidi.o
>>>> In file included from fribidi.h:31:0,
>>>>                  from fribidi.c:28:
>>>> fribidi_config.h:1:18: fatal error: glib.h: No such file or directory
>>>>
>>>> The file glib.h appears to be in base/include/glib-2.0/, however this
>>>> directory was not explicitly included in the command above, only its
>>>> parent. This suggests a configuration failure in pango to me. Taking a look
>>>> at base_tmp/pango-1.16.1/config.log, I see what look like the relevant
>>>> lines:
>>>>
>>>> configure:22227: checking for GLIB
>>>> configure:22235: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES"
>>>> configure:22238: $? = 0
>>>> configure:22253: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES"
>>>> configure:22256: $? = 0
>>>> configure:22304: result: yes
>>>>
>>>> but this doesn't tell me very much. Does anyone have any suggestions as
>>>> to how I might proceed?
>>>>
>>>> Many thanks
>>>>
>>>> -- David
>>>>
>>>
>>>
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>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>
>>>
>>
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>
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