[cctbxbb] bootstrap.py build on Ubuntu

Billy Poon bkpoon at lbl.gov
Mon Jun 13 13:53:04 PDT 2016 

Hi David,

I don't have a fix yet, but here is a workaround. It seems like setup.py is
looking for libz.so instead of libz.so.1, so you can fix the issue by
making a symbolic link for libz.so in /usr/lib64.

sudo ln -s /usr/lib64/libz.so.1 /usr/lib64/libz.so

This requires root access, so that's why it's just a workaround.

--
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 5:05 PM, Billy Poon <bkpoon at lbl.gov> wrote:

> 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
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> cctbxbb mailing list
>>>>> cctbxbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>
>>>>>
>>>>
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>>
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>
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