[cctbxbb] bootstrap.py build on Ubuntu

Sat Jun 11 17:05:21 PDT 2016

Hi David,

Sorry it look so long! Setting up all the virtual machines was a time sink
and getting things to work on 32-bit CentOS 5 and Ubuntu 12.04 was a little
tricky.

It looks like Ubuntu 16.04 moved its libraries around. I used apt-get to
install libz-dev and lib64z1 (the 64-bit library). There is a libz.so.1
file in /lib/x86_64-linux-gnu and in /usr/lib64.

I have not gotten it to work yet, but I'm pretty sure this is the issue.
I'll have to double-check 12.04 and 14.04.

As for Pillow, I did test it a few months ago, but I remember there being
API changes that will need to fixed.

--
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 Sat, Jun 11, 2016 at 2:04 AM, David Waterman <dgwaterman at gmail.com>
wrote:

> 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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>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>
>>>>
>>>
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>>
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