[cctbxbb] bootstrap.py build on Ubuntu

David Waterman dgwaterman at gmail.com
Tue Jun 14 11:29:36 PDT 2016 

Hey Billy,

Thanks. I'm travelling at the moment, but once I'm back I'll give that a go.

Cheers
David

On Tue, 14 Jun 2016, 17:34 Billy Poon, <bkpoon at lbl.gov> wrote:

> 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
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> cctbxbb mailing list
>>>>>>> cctbxbb at phenix-online.org
>>>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> cctbxbb mailing list
>>>>>> cctbxbb at phenix-online.org
>>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> cctbxbb mailing list
>>>>> cctbxbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> cctbxbb mailing list
>>>> cctbxbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>
>>>>
>>>
>>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20160614/d33a1184/attachment-0001.htm>

More information about the cctbxbb mailing list