Hi,
I'm having trouble building 3.14 from the release 371 source on RHEL8 using gcc 8.5.0 following the instructions at https://phenix-online.org/documentation/reference/rosetta_install.html. I realize this is a newer compiler / glibc, but that doesn't seem to be the issue. Instead I seem to be seeing missing / incompatible header issues. Specifically, I get:
g++ -o build/src/release/linux/4.18/64/x86/gcc/8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -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_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc
src/core/scoring/cryst/PhenixInterface.cc: In constructor 'core::scoring::cryst::PhenixInterface::PhenixInterface()':
src/core/scoring/cryst/PhenixInterface.cc:66:20: error: 'basic::options' has not been declared
mtzfile_ = basic::options::option[ basic::options::OptionKeys::cryst::mtzfile ]();
^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:66:44: error: 'basic::options' has not been declared
followed by many more errors all indicative of missing namespaces-names or incomplete / incorrect declarations, and ultimately terminating in a sizeof failure due to application to an incomplete type. (I've attached the complete error log). I tried explicitly including src/basic/basic.hh from PhenixInterface.cc, but that doesn't seem to help. Suggestions would be greatly appreciated.
Thanks!
-jh-
| Attachment | Size |
|---|---|
 error.log | 63.79 KB |
Hi,
I am facing the same problem trying to install 3.14 release 371 in both Ubuntu 20.04 and 24.04, with gcc 9.4.0. Specifically:
[...]
g++ -o build/src/release/linux/5.15/64/x86/gcc/9/python/core/scoring/methods/dfire/DFIRE_Potential.os -c -std=c++0x -ffor-scope -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -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_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/9 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/include/python2.7 src/core/scoring/methods/dfire/DFIRE_Potential.cc
g++: warning: switch '-ffor-scope' is no longer supported
src/core/scoring/cryst/PhenixInterface.cc: In constructor 'core::scoring::cryst::PhenixInterface::PhenixInterface()':
src/core/scoring/cryst/PhenixInterface.cc:66:20: error: 'basic::options' has not been declared
66 | mtzfile_ = basic::options::option[ basic::options::OptionKeys::cryst::mtzfile ]();
| ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc:66:44: error: 'basic::options' has not been declared
66 | mtzfile_ = basic::options::option[ basic::options::OptionKeys::cryst::mtzfile ]();
| ^~~~~~~
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:215:14: error: 'initialize_disulfide_bonds' is not a member of 'core::pose'
215 | core::pose::initialize_disulfide_bonds( pose );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
[...]
I would love to here if there is any update for this situation. Also, are you able to compile other releases/versions with no errors?
Cheers,
Lucas S
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