<div dir="ltr"><div dir="ltr">Hi Luc,<div><br></div><div>I would recommend using conda for building with Python 3. Just add the &quot;--use-conda&quot; flag to your bootstrap command so that it looks like</div><div><br></div><div><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(54,97,247)">python</span><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0);background-color:rgb(209,209,209)"><b>boots</b></span><span style="color:rgb(36,36,36);font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures">trap.py</span><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="color:rgb(36,36,36);font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures">--git-ssh</span><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="color:rgb(36,36,36);font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures">--python3</span><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="color:rgb(36,36,36);font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures">--builder</span><span style="font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures;color:rgb(0,0,0)"> </span><span style="color:rgb(36,36,36);font-family:Menlo;font-size:12px;font-variant-ligatures:no-common-ligatures">cctbxlite <b>--use-conda</b></span><br></div><div><br></div><div>The builds on Azure pipelines are being run with conda environments and are built with different versions of Xcode (supposed to be nightly, but the scheduling is not behaving as expect.</div><div><br></div><div>When you do use the &quot;--use-conda&quot; flag, make sure that you&#39;re not in an active conda environment. Otherwise, that one will be used instead of a new one being created. That behavior will be changed so that the active environment is not always used.</div><div><br></div><div>Also, the default Python 3 currently is Python 3.6 and the default environment has a bunch of extra dependencies not in cctbxlite. That will also be changed so that a minimal set of dependencies will be installed for the cctbxlite builder.</div><div><br></div><div><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 13, 2019 at 7:30 AM Luc Bourhis &lt;<a href="mailto:luc_j_bourhis@mac.com">luc_j_bourhis@mac.com</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space">Fails later. As can be seen below, the symlinks are bogus: python3 ends up being a link to ../../python3.7 and then of course, kaboom!<div><br></div><div>Oh, my!</div><div><br></div><div>Trying conda…<br><div><br><div><div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Installing wxPython 4.0.3...</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Cross platform GUI toolkit for Python, &quot;Phoenix&quot; version</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  log file is /Users/luc/Developer/cctbx/base_tmp/wxPython_install_log</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  verifying wxPython installation in /Users/luc/Developer/cctbx/base/bin/python3 OK</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  package wxpython took 7.5s to install</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Dependencies finished building.</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Regenerating symlinks with relative paths...</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../2to3-3.7</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../python3.7</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../python3.7m-config</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../libpng16-config</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../idle3.7</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../python3.7m-config</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../pyvenv-3.7</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  creating symlink to ../../pydoc3.7</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">===== Running in build: run configure.py</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Traceback (most recent call last):</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  File &quot;bootstrap.py&quot;, line 2695, in &lt;module&gt;</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">    run()</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  File &quot;bootstrap.py&quot;, line 2690, in run</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">    use_conda=options.use_conda,</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  File &quot;bootstrap.py&quot;, line 1166, in run</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">    i.run()</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">  File &quot;bootstrap.py&quot;, line 189, in run</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">    raise RuntimeError(&quot;Could not run %s: File not found&quot; % executable)</span></div><div style="margin:0px;font-stretch:normal;font-size:12px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">RuntimeError: Could not run base/bin/python3: File not found</span></div><div><span style="font-variant-ligatures:no-common-ligatures"><br></span></div><div><br><blockquote type="cite"><div>On 13 Aug 2019, at 15:58, Luc Bourhis &lt;<a href="mailto:luc_j_bourhis@mac.com" target="_blank">luc_j_bourhis@mac.com</a>&gt; wrote:</div><br class="gmail-m_-3405746641763947837Apple-interchange-newline"><div><div style="word-wrap:break-word;line-break:after-white-space">I see a message should have been printed to advise me to do that but it was not. Buffering maybe? In any case, yes, it helps! <div>Sorry, I missed that closed issue…<br><div><br><blockquote type="cite"><div>On 13 Aug 2019, at 15:40, <a href="mailto:richard.gildea@diamond.ac.uk" target="_blank">richard.gildea@diamond.ac.uk</a> wrote:</div><br class="gmail-m_-3405746641763947837Apple-interchange-newline"><div><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Hi Luc,</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Does this help?<span class="gmail-m_-3405746641763947837Apple-converted-space"> </span></span><a href="https://github.com/cctbx/cctbx_project/issues/333" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">https://github.com/cctbx/cctbx_project/issues/333</a><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">I.e. have you also run:</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">See also:<span class="gmail-m_-3405746641763947837Apple-converted-space"> </span></span><a href="https://github.com/cctbx/cctbx_project/issues/240" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">https://github.com/cctbx/cctbx_project/issues/240</a><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><span class="gmail-m_-3405746641763947837Apple-converted-space"> </span>and<span class="gmail-m_-3405746641763947837Apple-converted-space"> </span></span><a href="https://github.com/cctbx/cctbx_project/pull/334" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">https://github.com/cctbx/cctbx_project/pull/334</a><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Cheers,</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Richard</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Dr Richard Gildea</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Data Analysis Scientist</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Tel: +441235 77 8078</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Diamond Light Source Ltd.</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Diamond House</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Harwell Science &amp; Innovation Campus</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Didcot</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Oxfordshire</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">OX11 0DE</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">________________________________</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">From:<span class="gmail-m_-3405746641763947837Apple-converted-space"> </span></span><a href="mailto:cctbxbb-bounces@phenix-online.org" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">cctbxbb-bounces@phenix-online.org</a><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"><span class="gmail-m_-3405746641763947837Apple-converted-space"> </span>&lt;</span><a href="mailto:cctbxbb-bounces@phenix-online.org" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">cctbxbb-bounces@phenix-online.org</a><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">&gt; on behalf of Luc Bourhis &lt;</span><a href="mailto:luc_j_bourhis@mac.com" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">luc_j_bourhis@mac.com</a><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">&gt;</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Sent: 13 August 2019 14:28:05</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">To: cctbx mailing list</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Subject: [cctbxbb] Booststrap fails: zlib.h missing on Mojave with Xcode 10.3</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Hi,</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">I am trying to setup a Python 3 cctbx. I did</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">python bootstrap.py --git-ssh --python3 --builder cctbxlite</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">But it fails at the installation of OpenSSL. Clang version is &quot;Apple LLVM version 10.0.1 (clang-1001.0.46.4)”. I attached the OpenSSL install log but I don’t see any error in it. And the advice to run xcode-select is bogus: I have it already setup.</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Best wishes,</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Luc</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Installing OpenSSL...</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"> log file is /Users/luc/Developer/cctbx/base_tmp/OpenSSL_install_log</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"> getting package openssl-1.0.2r.tar.gz...</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">   downloading from <a href="https://gitcdn.link/repo/dials/dependencies/master/openssl-1.0.2r.tar.gz" target="_blank">https://gitcdn.link/repo/dials/dependencies/master/openssl-1.0.2r.tar.gz</a> : 5223 kB</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"> installing openssl-1.0.2r.tar.gz...</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline"> package openssl took 219.5s to install</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">--------------------------------------------------------------------------------</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">zlib.h missing -- try running &#39;xcode-select --install&#39; first</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Process failed with return code 1</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-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al;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">cctbxbb mailing list</span><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="mailto:cctbxbb@phenix-online.org" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">cctbxbb@phenix-online.org</a><br style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="http://phenix-online.org/mailman/listinfo/cctbxbb" style="font-family:Helvetica;font-size:14px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a></div></blockquote></div><br></div></div></div></blockquote></div><br></div></div></div></div></div>_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org" target="_blank">cctbxbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
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