<div dir="ltr">Sebastiano<div><br></div><div>It's not a bother and I'm glad you find the solution. Can you email me directly with the version of XCode you have and whether </div><div><br></div><div>rosetta.run_tests</div><div><br></div><div>succeeds.</div><div><div><br></div><div><br></div></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Sep 12, 2016 at 7:39 AM, Sebastiano Pasqualato <span dir="ltr"><<a href="mailto:sebastiano.pasqualato@gmail.com" target="_blank">sebastiano.pasqualato@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><br></div><div>OK the problem seems to be solved by running:</div><div><br></div><div>xcode-select —install</div><div><br></div><div>thanks anyway,</div><div>sorry for bothering,</div><div>ciao,</div><div>S</div><div><div class="h5"><br><div><blockquote type="cite"><div>On 12 Sep 2016, at 16:22, Sebastiano Pasqualato <<a href="mailto:sebastiano.pasqualato@gmail.com" target="_blank">sebastiano.pasqualato@GMAIL.<wbr>COM</a>> wrote:</div><br><div><div style="word-wrap:break-word"><div><br></div><div>Hi there,</div><div>I am trying to run Phenix Rosetta Refinement on my laptop, which is running MacOSX 10.11.6 (El Capitan) with XQuartz 2.7.9.</div><div>I have followed the instructions on this page:</div><div><br></div><div><a href="https://www.phenix-online.org/documentation/reference/rosetta_refine.html" target="_blank">https://www.phenix-online.org/<wbr>documentation/reference/<wbr>rosetta_refine.html</a></div><div><br></div><div>and specifically </div><div><br></div><font color="#0433ff">Once you have both a Phenix installation and a Rosetta source distribution, you can build the hybrid system with this command (located in the Phenix tree):<br><br></font><div><font color="#0433ff">rosetta.build_phenix_interface nproc=X</font></div><br>Unfortunately, when I do that, the building does not proceed flawlessly, but instead stops with the message the I report below.<div>Has someone gone through the same and can tell me how to set up Rosetta to be used with Phenix?</div><div><br></div><div>Thanks in advance for the help,</div><div>Sebastiano</div><div><br></div><div><div><font face="Courier New" style="font-size:11px"><b>Seba@host028:</b>~> </font><span style="font-size:11px;font-family:'Courier New'">rosetta.build_<wbr>phenix_interface nproc=8</span></div><div><font face="Courier New" style="font-size:11px">False</font></div><div><font face="Courier New" style="font-size:11px">scons: Reading SConscript files ...</font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">Running versioning script ... xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">Done. (0.0 seconds)</font></div><div><font face="Courier New" style="font-size:11px">Number of option files updated: 0</font></div><div><font face="Courier New" style="font-size:11px">Total 3741 options.</font></div><div><font face="Courier New" style="font-size:11px">Finished updating ResidueProperty code -- no changes needed</font></div><div><font face="Courier New" style="font-size:11px">Finished updating VariantType code -- no changes needed</font></div><div><font face="Courier New" style="font-size:11px">scons: done reading SConscript files.</font></div><div><font face="Courier New" style="font-size:11px">scons: Building targets ...</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/apps/<wbr>public/AbinitioRelax.o -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/apps/public/<a href="http://abinitiorelax.cc/" target="_blank">AbinitioRelax.<wbr>cc</a></font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/devel/<wbr>init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/<a href="http://init.cc/" target="_blank">init.cc</a></font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/devel/svn_<wbr>version.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/devel/svn_version.cc</font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>init/init.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/init/<a href="http://init.cc/" target="_blank">init.cc</a></font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/<wbr>DownstreamRMSEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/<a href="http://downstreamrmsevaluator.cc/" target="_blank">Dow<wbr>nstreamRMSEvaluator.cc</a></font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/<wbr>LimitHitsPerRotamerFilter.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/<a href="http://limithitsperrotamerfilter.cc/" target="_blank">Lim<wbr>itHitsPerRotamerFilter.cc</a></font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/<wbr>MatchConsolidator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/<a href="http://matchconsolidator.cc/" target="_blank">Mat<wbr>chConsolidator.cc</a></font></div><div><font face="Courier New" style="font-size:11px">xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun</font></div><div><font face="Courier New" style="font-size:11px">scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/apps/<wbr>public/AbinitioRelax.o] Error 1</font></div><div><font face="Courier New" style="font-size:11px">clang++ -o build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/MatchEvaluator.os -c -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -std=c++11 -march=core2 -mtune=generic -pipe -Qunused-arguments -DUNUSUAL_ALLOCATOR_<wbr>DECLARATION -ftemplate-depth-256 -stdlib=libstdc++ -W -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -march=native -mtune=native -stdlib=libc++ -Wno-unused-variable -O3 -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr>MATH_FUNCTIONS -DCXX11 -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/macos/64/clang -Isrc/platform/macos/64 -Isrc/platform/macos -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/match/output/<a href="http://matchevaluator.cc/" target="_blank">Mat<wbr>chEvaluator.cc</a></font></div><div><font face="Courier New"><span style="font-size:11px">scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/devel/<wbr>init.os] Error 1<br>scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/devel/svn_<wbr>version.os] Error 1<br>scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>init/init.os] Error 1<br>scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/<wbr>DownstreamRMSEvaluator.os] Error 1<br>scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/<wbr>LimitHitsPerRotamerFilter.os] Error 1<br>scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/<wbr>MatchConsolidator.os] Error 1<br>xcrun: error: invalid active developer path (/Library/Developer/<wbr>CommandLineTools), missing xcrun at: /Library/Developer/<wbr>CommandLineTools/usr/bin/xcrun<br>scons: *** [build/src/release/macos/15.6/<wbr>64/x86/clang/python/protocols/<wbr>match/output/MatchEvaluator.<wbr>os] Error 1<br>scons: building terminated because of errors.<br><b>Seba@host028</b>:~> </span></font></div>
<br><div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div><div style="text-align:-webkit-auto;word-wrap:break-word">-- <br><b>Sebastiano Pasqualato, PhD</b><br>Crystallography Unit<br>Department of Experimental Oncology<br>European Institute of Oncology<br>IFOM-IEO Campus<br>via Adamello, 16<br>20139 - Milano<br>Italy<br><br>tel <a href="tel:%2B39%2002%209437%205167" value="+390294375167" target="_blank">+39 02 9437 5167</a><br>fax <a href="tel:%2B39%2002%209437%205990" value="+390294375990" target="_blank">+39 02 9437 5990</a></div><div style="text-align:-webkit-auto;word-wrap:break-word">web <a href="http://is.gd/IEOXtalUnit" target="_blank">http://is.gd/IEOXtalUnit</a></div></div></div></div>
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