[phenixbb] rosetta.build_phenix_interface errors

[Gerhard Fischer]

I am having some trouble setting up phenix.rosetta_refine on my Kubuntu
16.04 LTS-system.

I've been following the instructions found here:
https://www.phenix-online.org/documentation/reference/rosetta_install.html

The installation/compilation of Rosetta as such
(rosetta_src_2016.37.58930_bundle.tgz) worked fine, and so did installing
the latest version of Phenix - here, I've tried both the binary available
for download (phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6)
and a self-compiled version (phenix-installer-1.11-2567-source).

But when running

rosetta.build_phenix_interface

(both with nproc=6 or no multiple processor options set), the compilation
crashes at some point. This takes quite a while, and I suspect most parts
get compiled, but it does not run to completion.

Any ideas? I attach the output of the error message below.


Best wishes,

Gerhard



------ stdout ----
g++ -o
build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os
-c -std=c++11 -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_MATH_FUNCTIONS -DPTR_STD -DNDEBUG
-DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/5.4
-Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux
-Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal
-Iexternal/dbio -I/usr/include -I/usr/local/include
-Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void
core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:253:34: error: no matching
function for call to 'core::pose::Pose::dump_pdb(char [256], const char
[2])'
  pose_asu.dump_pdb( pdbout , "1" );
                                  ^
In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0:
src/core/pose/Pose.hh:1518:2: note: candidate: bool
core::pose::Pose::dump_pdb(const string&) const
  dump_pdb(std::string const & file_name) const;
  ^
src/core/pose/Pose.hh:1518:2: note:   candidate expects 1 argument, 2
provided
src/core/pose/Pose.hh:1521:2: note: candidate: void
core::pose::Pose::dump_pdb(std::ostream&) const
  dump_pdb(std::ostream & out) const;
  ^
src/core/pose/Pose.hh:1521:2: note:   candidate expects 1 argument, 2
provided
src/core/pose/Pose.hh:1525:2: note: candidate: void
core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long
unsigned int>&) const
  dump_pdb(
  ^
src/core/pose/Pose.hh:1525:2: note:   no known conversion for argument 1
from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}'
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void
core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const
core::pose::Pose&, std::__cxx11::string)':
src/core/scoring/cryst/PhenixInterface.cc:916:34: error: no matching
function for call to 'core::pose::Pose::dump_pdb(char [256], const char
[2])'
  pose_asu.dump_pdb( buffer , "1" );
                                  ^
In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0:
src/core/pose/Pose.hh:1518:2: note: candidate: bool
core::pose::Pose::dump_pdb(const string&) const
  dump_pdb(std::string const & file_name) const;
  ^
src/core/pose/Pose.hh:1518:2: note:   candidate expects 1 argument, 2
provided
src/core/pose/Pose.hh:1521:2: note: candidate: void
core::pose::Pose::dump_pdb(std::ostream&) const
  dump_pdb(std::ostream & out) const;
  ^
src/core/pose/Pose.hh:1521:2: note:   candidate expects 1 argument, 2
provided
src/core/pose/Pose.hh:1525:2: note: candidate: void
core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long
unsigned int>&) const
  dump_pdb(
  ^
src/core/pose/Pose.hh:1525:2: note:   no known conversion for argument 1
from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}'
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void
core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)':
src/core/scoring/cryst/PhenixInterface.cc:244:25: warning: ignoring return
value of 'int chdir(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
  chdir(tempdir_.c_str());
                         ^
src/core/scoring/cryst/PhenixInterface.cc:375:13: warning: ignoring return
value of 'int chdir(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
  chdir("..");
             ^
src/core/scoring/cryst/PhenixInterface.cc: In member function 'void
core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const
core::pose::Pose&, std::__cxx11::string)':
src/core/scoring/cryst/PhenixInterface.cc:914:25: warning: ignoring return
value of 'int chdir(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
  chdir(tempdir_.c_str());
                         ^
src/core/scoring/cryst/PhenixInterface.cc:1080:13: warning: ignoring return
value of 'int chdir(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
  chdir("..");
             ^
src/core/scoring/cryst/PhenixInterface.cc: In member function
'std::__cxx11::string
core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&,
bool)':
src/core/scoring/cryst/PhenixInterface.cc:1100:25: warning: ignoring return
value of 'int chdir(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
  chdir(tempdir_.c_str());
                         ^
src/core/scoring/cryst/PhenixInterface.cc:1109:13: warning: ignoring return
value of 'int chdir(const char*)', declared with attribute
warn_unused_result [-Wunused-result]
  chdir("..");
             ^
scons: ***
[build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os]
Error 1
scons: building terminated because of errors.
--------- stdout end ------


--
Gerhard Fischer, PhD
Postdoctoral Research Associate

University of Cambridge
Department of Biochemistry
80 Tennis Court Road
CB2 1GA Cambridge
United Kingdom

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