[cctbxbb] bz2 support on Ubuntu

[David Waterman]

Great, all working now. It seemed I didn't need to mess with
libtbx.list_modules after all, I could just rebuild the foundations without
the house falling down. So, for reference I did this:

rm -rf base
cd base_tmp
find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm -rf
cd ..
python bootstrap.py --builder=dials base
cd build
source setpaths.sh
make reconf

-- David

On 8 June 2017 at 14:15, David Waterman <dgwaterman at gmail.com> wrote:

> Thanks, I did this, currently churning through the base build. Checking
> the latest Python_install_log I see hopeful-looking things like "building
> 'bz2' extension". I can only assume I've installed a few more packages
> since I did the original build. Will report back if there are any new
> problems, otherwise I think this might be fixed :)
>
> Cheers
>
> -- David
>
> On 8 June 2017 at 13:08, <markus.gerstel at diamond.ac.uk> wrote:
>
>> Hi David,
>>
>>
>>
>> You’ll have to look into the python setup.py script to figure that one
>> out.
>>
>> https://github.com/python/cpython/blob/2.7/setup.py#L1463
>>
>> Python expects the library to be in some fixed place, and If it’s not
>> there support is disabled.
>>
>>
>>
>> Regarding your rebuild question. I would keep the base_tmp directory, you
>> then don’t have to redownload and recompile everything. Stuff should still
>> recompile if anything changed, and if versions are updated etc.
>>
>> If you definitely want to recompile everything you can still save time by
>> running  this **in the base_tmp directory**:
>>
>>     find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm
>> –rf
>>
>> This removes all subdirectories, leaving the files intact, so you don’t
>> have to redownload everything.
>>
>>
>>
>> I would expect the steps *export, rm -rf base, python bootstrap.py base,
>> cd build, setpaths, libtbx.configure, make* to suffice.
>>
>>
>>
>> -Markus
>>
>>
>>
>> *From:* cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix
>> -online.org] *On Behalf Of *David Waterman
>> *Sent:* 08 June 2017 12:58
>> *To:* cctbx mailing list <cctbxbb at phenix-online.org>
>> *Subject:* [cctbxbb] bz2 support on Ubuntu
>>
>>
>>
>> Hi folks,
>>
>>
>>
>> My bootstrap build of cctbx/DIALS on Ubuntu 16.04.2 LTS produces a base
>> Python that does not have bz2 support. This is despite the fact that the
>> package "libbz2-dev is already the newest version (1.0.6-8)." Looking in
>> Python_install_log I see
>>
>>
>>
>> Python build finished, but the necessary bits to build these modules were
>> not found:
>>
>> _bsddb             _curses            _curses_panel
>>
>> _sqlite3           _tkinter           bsddb185
>>
>> bz2                dbm                dl
>>
>> gdbm               imageop            readline
>>
>> sunaudiodev
>>
>>
>>
>> Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where
>> bz2 can be imported in Python?
>>
>>
>>
>> Also, what's the procedure to rebuild from base, recovering all the
>> currently configured modules? My guess is that something like this would do
>> it, but is there a better way?
>>
>>
>>
>> export MYMODULES=$(libtbx.list_modules | tr '\n' ' ')
>>
>> rm -rf base_tmp/ base/ build/
>>
>> python bootstrap.py --builder=dials base
>>
>> python bootstrap.py --builder=dials build
>>
>> cd build
>>
>> source setpaths.sh
>>
>> libtbx.configure $MYMODULES
>>
>> make
>>
>>
>>
>> Cheers
>>
>>
>> -- David
>>
>>
>>
>> --
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