[phenixbb] rosetta.build_phenix_interface errors

Fri Oct 28 07:52:39 PDT 2016

I think you may want to try build using clang instead of g++. I had the
similar problem with g++ but clang is fine.

Regards,
Wei

On Fri, Oct 28, 2016 at 6:08 AM, Gerhard Fischer <gf288 at cam.ac.uk> wrote:

> 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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