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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi David,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">You’ll have to look into the python setup.py script to figure that one out.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><a href="https://github.com/python/cpython/blob/2.7/setup.py#L1463">https://github.com/python/cpython/blob/2.7/setup.py#L1463</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Python expects the library to be in some fixed place, and If it’s not there support is disabled.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">If you definitely want to recompile everything you can still save time by running this *<b>in the base_tmp directory</b>*:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> find . -maxdepth 1 -mindepth 1 -type d -print0 | xargs -0 -n 1 -- rm –rf<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">This removes all subdirectories, leaving the files intact, so you don’t have to redownload everything.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I would expect the steps
<i>export, rm -rf base, python bootstrap.py base, cd build, setpaths, libtbx.configure, make</i> to suffice.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">-Markus<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
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<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"> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>David Waterman<br>
<b>Sent:</b> 08 June 2017 12:58<br>
<b>To:</b> cctbx mailing list <cctbxbb@phenix-online.org><br>
<b>Subject:</b> [cctbxbb] bz2 support on Ubuntu<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi folks,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">Python build finished, but the necessary bits to build these modules were not found:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">_bsddb _curses _curses_panel </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">_sqlite3 _tkinter bsddb185 </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">bz2 dbm dl </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">gdbm imageop readline </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">sunaudiodev </span>
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Has anyone got any ideas? Anyone done a boostrap build on Ubuntu where bz2 can be imported in Python?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">export MYMODULES=$(libtbx.list_modules | tr '\n' ' ')</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">rm -rf base_tmp/ base/ build/</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">python bootstrap.py --builder=dials base</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">python bootstrap.py --builder=dials build</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">cd build</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">source setpaths.sh</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">libtbx.configure $MYMODULES</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">make</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers<o:p></o:p></p>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<p class="MsoNormal">-- David<o:p></o:p></p>
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<p align="justify"> </p>
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