<div dir="ltr">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 :)<div><br></div><div>Cheers</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature">-- David<br></div></div>
<br><div class="gmail_quote">On 8 June 2017 at 13:08, <span dir="ltr"><<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-GB" link="#0563C1" vlink="#954F72">
<div class="m_-7646054687096516679WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi David,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">You’ll have to look into the python setup.py script to figure that one out.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><a href="https://github.com/python/cpython/blob/2.7/setup.py#L1463" target="_blank">https://github.com/python/<wbr>cpython/blob/2.7/setup.py#<wbr>L1463</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Python expects the library to be in some fixed place, and If it’s not there support is disabled.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">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.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">If you definitely want to recompile everything you can still save time by running this *<b>in the base_tmp directory</b>*:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"> find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm –rf<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">This removes all subdirectories, leaving the files intact, so you don’t have to redownload everything.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">I would expect the steps
<i>export, rm -rf base, python bootstrap.py base, cd build, setpaths, libtbx.configure, make</i> to suffice.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">-Markus<u></u><u></u></span></p>
<p class="MsoNormal"><a name="m_-7646054687096516679__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></a></p>
<span></span>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@phenix-online.<wbr>org</a> [mailto:<a href="mailto:cctbxbb-bounces@phenix-online.org" target="_blank">cctbxbb-bounces@<wbr>phenix-online.org</a>]
<b>On Behalf Of </b>David Waterman<br>
<b>Sent:</b> 08 June 2017 12:58<br>
<b>To:</b> cctbx mailing list <<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a>><br>
<b>Subject:</b> [cctbxbb] bz2 support on Ubuntu<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi folks,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">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<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">Python build finished, but the necessary bits to build these modules were not found:</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">_bsddb _curses _curses_panel </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">_sqlite3 _tkinter bsddb185 </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">bz2 dbm dl </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">gdbm imageop readline </span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">sunaudiodev </span>
<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where bz2 can be imported in Python?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">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?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">export MYMODULES=$(libtbx.list_<wbr>modules | tr '\n' ' ')</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">rm -rf base_tmp/ base/ build/</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">python bootstrap.py --builder=dials base</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">python bootstrap.py --builder=dials build</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">cd build</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">source setpaths.sh</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">libtbx.configure $MYMODULES</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New"">make</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Cheers<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">-- David<u></u><u></u></p>
</div>
</div>
</div>
</div>
</div></div></div><span class="HOEnZb"><font color="#888888">
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