[cctbxbb] bootstrap.py build on Ubuntu

Billy Poon bkpoon at lbl.gov
Tue Jun 14 09:34:38 PDT 2016 

Hi David,

Actually, it looks like the lib64z1-dev package provides libz.so in
/usr/lib64, so installing that package should fix your issue. It's a bit
odd that the lib64z1 package does not provide that file.

--
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 Mon, Jun 13, 2016 at 1:53 PM, Billy Poon <bkpoon at lbl.gov> wrote:

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