<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Nigel,<div class=""><br class=""></div><div class="">Switching to rosetta 3.7 did the trick.</div><div class=""><br class=""></div><div class="">Thanks a lot for the tip.</div><div class=""><br class=""></div><div class="">Ludovic.</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 07 Nov 2016, at 18:39, Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" class="">nwmoriarty@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Ludovic<div class=""><br class=""></div><div class="">Can you move to Rosetta 3.7 and let me know if it still fails?</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class="">Cheers<div class=""><br class=""></div><div class="">Nigel<div class=""><br class=""></div><div class="">---</div><div class="">Nigel W. Moriarty<br class="">Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div><div class="">Lawrence Berkeley National Laboratory<br class="">Berkeley, CA 94720-8235<br class="">Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@lbl.gov" class="">NWMoriarty@LBL.gov</a><br class="">Fax : 510-486-5909 Web : <a href="http://cci.lbl.gov/" target="_blank" class="">CCI.LBL.gov</a></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur <span dir="ltr" class=""><<a href="mailto:ludovic.pecqueur@college-de-france.fr" target="_blank" class="">ludovic.pecqueur@college-de-france.fr</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Phenix developers,<br class="">
<br class="">
I installed the latest phenix version today (1.11.1-2575) on Centos 7.2<br class="">
I have rosetta_2016.13.58602<br class="">
<br class="">
When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).<br class="">
<br class="">
When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.<br class="">
<br class="">
If you have any idea of the change between the two versions leading to this issue.<br class="">
<br class="">
Thank you for your help,<br class="">
<br class="">
Ludovic.<br class="">
<br class="">
########################<br class="">
Error message:<br class="">
<br class="">
Substituting phenix.python into build shell scripts<br class="">
update_options.sh<br class="">
update_ResidueType_enum_files.<wbr class="">sh<br class="">
/usr/local/PROGRAMS/ROSETTA/<wbr class="">PHENIX_Rosetta_refine/rosetta_<wbr class="">src_2016.13.58602_bundle/main/<wbr class="">source<br class="">
<br class="">
~> phenix.python scons.py bin mode=release extras=python -j 8<br class="">
<br class="">
scons: Reading SConscript files ...<br class="">
Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local)<br class="">
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_<wbr class="">FILESYSTEM not set).<br class="">
Done. (0.0 seconds)<br class="">
file ./options.dox being updated<br class="">
file ./<a href="http://full-options-list.md/" rel="noreferrer" target="_blank" class="">full-options-list.md</a> being updated<br class="">
Number of option files updated: 2<br class="">
Total 3657 options.<br class="">
Finished updating ResidueProperty code -- no changes needed<br class="">
Finished updating VariantType code -- no changes needed<br class="">
scons: done reading SConscript files.<br class="">
scons: Building targets ...<br class="">
g++ -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/hybridization/<wbr class="">CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/<wbr class=""><a href="http://cartesiansampler.cc" class="">CartesianSampler.cc</a><br class="">
In file included from src/protocols/hybridization/<wbr class="">CartesianSampler.cc:17:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
#include "Python.h"<br class="">
^<br class="">
compilation terminated.<br class="">
g++ -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/cryst/cryst_movers.<wbr class="">os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_<wbr class="">movers.cc<br class="">
In file included from src/protocols/cryst/cryst_<wbr class="">movers.cc:16:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
#include "Python.h"<br class="">
^<br class="">
compilation terminated.<br class="">
gcc -o build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">libsqlite3.so -shared build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil<br class="">
g++ -o build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">libcifparse.so -Wl,-rpath=/usr/local/<wbr class="">PROGRAMS/ROSETTA/PHENIX_<wbr class="">Rosetta_refine/rosetta_src_<wbr class="">2016.13.58602_bundle/main/<wbr class="">source/build/external/release/<wbr class="">linux/3.10/64/x86/gcc/4.8/<wbr class="">python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/BlockIO.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifDataInfo.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifExcept.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifFile.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifFileReadDef.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifParentChild.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifParserBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifScannerBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifString.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DataInfo.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DicFile.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICParserBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICScannerBase.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/Exceptions.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/GenCont.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/GenString.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/ISTable.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/ITTable.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/mapped_ptr_vector.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/mapped_vector.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/ParentChild.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/RcsbFile.!<br class="">
os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/RcsbPlatform.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/Serializer.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/TableFile.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/TTable.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifParser.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/CifScanner.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICParser.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/DICScanner.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regcomp.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regerror.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regexec.os build/external/release/linux/<wbr class="">3.10/64/x86/gcc/4.8/python/<wbr class="">cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/<wbr class="">linux/3.10/64/x86/gcc/4.8/<wbr class="">python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil<br class="">
g++ -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/PhenixInterface.<wbr class="">os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/<wbr class="">PhenixInterface.cc<br class="">
In file included from src/core/scoring/cryst/<wbr class="">PhenixInterface.cc:15:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
#include "Python.h"<br class="">
^<br class="">
compilation terminated.<br class="">
g++ -o build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_<wbr class="">MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr class="">8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/<wbr class="">XtalMLEnergy.cc<br class="">
In file included from src/core/scoring/cryst/<wbr class="">XtalMLEnergy.cc:16:0:<br class="">
src/core/scoring/cryst/<wbr class="">PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br class="">
#include "Python.h"<br class="">
^<br class="">
compilation terminated.<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/hybridization/<wbr class="">CartesianSampler.os] Error 1<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/<wbr class="">protocols/cryst/cryst_movers.<wbr class="">os] Error 1<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/PhenixInterface.<wbr class="">os] Error 1<br class="">
scons: *** [build/src/release/linux/3.10/<wbr class="">64/x86/gcc/4.8/python/core/<wbr class="">scoring/cryst/XtalMLEnergy.os] Error 1<br class="">
scons: building terminated because of errors.<br class="">
<br class="">
<br class="">
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