<div dir="ltr">Ludovic<div><br></div><div>Can you move to Rosetta 3.7 and let me know if it still fails?</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 Thu, Nov 3, 2016 at 9:16 AM, ludovic Pecqueur <span dir="ltr"><<a href="mailto:ludovic.pecqueur@college-de-france.fr" target="_blank">ludovic.pecqueur@college-de-france.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Phenix developers,<br>
<br>
I installed the latest phenix version today (1.11.1-2575) on Centos 7.2<br>
I have rosetta_2016.13.58602<br>
<br>
When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors).<br>
<br>
When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors.<br>
<br>
If you have any idea of the change between the two versions leading to this issue.<br>
<br>
Thank you for your help,<br>
<br>
Ludovic.<br>
<br>
########################<br>
Error message:<br>
<br>
Substituting phenix.python into build shell scripts<br>
update_options.sh<br>
update_ResidueType_enum_files.<wbr>sh<br>
/usr/local/PROGRAMS/ROSETTA/<wbr>PHENIX_Rosetta_refine/rosetta_<wbr>src_2016.13.58602_bundle/main/<wbr>source<br>
<br>
~> phenix.python scons.py bin mode=release extras=python -j 8<br>
<br>
scons: Reading SConscript files ...<br>
Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local)<br>
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_<wbr>FILESYSTEM not set).<br>
Done. (0.0 seconds)<br>
file ./options.dox being updated<br>
file ./<a href="http://full-options-list.md" rel="noreferrer" target="_blank">full-options-list.md</a> being updated<br>
Number of option files updated: 2<br>
Total 3657 options.<br>
Finished updating ResidueProperty code -- no changes needed<br>
Finished updating VariantType code -- no changes needed<br>
scons: done reading SConscript files.<br>
scons: Building targets ...<br>
g++ -o build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/<wbr>protocols/hybridization/<wbr>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>MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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>CartesianSampler.cc<br>
In file included from src/protocols/hybridization/<wbr>CartesianSampler.cc:17:0:<br>
src/core/scoring/cryst/<wbr>PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
g++ -o build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/<wbr>protocols/cryst/cryst_movers.<wbr>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>MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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>movers.cc<br>
In file included from src/protocols/cryst/cryst_<wbr>movers.cc:16:0:<br>
src/core/scoring/cryst/<wbr>PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
gcc -o build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>libsqlite3.so -shared build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil<br>
g++ -o build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>libcifparse.so -Wl,-rpath=/usr/local/<wbr>PROGRAMS/ROSETTA/PHENIX_<wbr>Rosetta_refine/rosetta_src_<wbr>2016.13.58602_bundle/main/<wbr>source/build/external/release/<wbr>linux/3.10/64/x86/gcc/4.8/<wbr>python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/BlockIO.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifDataInfo.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifExcept.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifFile.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifFileReadDef.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifParentChild.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifParserBase.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifScannerBase.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifString.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/DataInfo.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/DicFile.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/DICParserBase.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/DICScannerBase.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/Exceptions.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/GenCont.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/GenString.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/ISTable.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/ITTable.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/mapped_ptr_vector.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/mapped_vector.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/ParentChild.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/RcsbFile.!<br>
os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/RcsbPlatform.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/Serializer.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/TableFile.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/TTable.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifParser.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/CifScanner.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/DICParser.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/DICScanner.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/regcomp.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/regerror.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/regexec.os build/external/release/linux/<wbr>3.10/64/x86/gcc/4.8/python/<wbr>cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/<wbr>linux/3.10/64/x86/gcc/4.8/<wbr>python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil<br>
g++ -o build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/core/<wbr>scoring/cryst/PhenixInterface.<wbr>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>MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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>PhenixInterface.cc<br>
In file included from src/core/scoring/cryst/<wbr>PhenixInterface.cc:15:0:<br>
src/core/scoring/cryst/<wbr>PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
g++ -o build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/core/<wbr>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>MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.<wbr>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>XtalMLEnergy.cc<br>
In file included from src/core/scoring/cryst/<wbr>XtalMLEnergy.cc:16:0:<br>
src/core/scoring/cryst/<wbr>PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory<br>
#include "Python.h"<br>
^<br>
compilation terminated.<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/<wbr>protocols/hybridization/<wbr>CartesianSampler.os] Error 1<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/<wbr>protocols/cryst/cryst_movers.<wbr>os] Error 1<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/core/<wbr>scoring/cryst/PhenixInterface.<wbr>os] Error 1<br>
scons: *** [build/src/release/linux/3.10/<wbr>64/x86/gcc/4.8/python/core/<wbr>scoring/cryst/XtalMLEnergy.os] Error 1<br>
scons: building terminated because of errors.<br>
<br>
<br>
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</blockquote></div><br></div>