Re: [cctbxbb] bootstrap.py build on Ubuntu

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 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 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 wrote:

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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 wrote:

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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 wrote:

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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 wrote:

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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 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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