compilation problem on brand new Mac running the latest Xcode

[UnixJunkie]

---------- Forwarded message ---------- From: terwill Date: Tue, Sep 4, 2012 at 2:10 PM Subject: durandal To: nechols, terwilliger

Hi Nat,

I got my compilation working using a mac-osx version (even though my computer is 64-bit I couldn't get that to work; it installed and then libraries were missing).

however there is one thing that didn't work. When compiling Durandal/:

In file included from /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/DistMatrix.cc:33: /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/Singleton.h:101:8: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup os << v[i] << '\n'; ^

Is this directory needed? And have you seen an error like that? seems weird that << would not be recognized.

All the best, Tom T

[UnixJunkie]

Here is more context...

---------- Forwarded message ---------- From: terwill Date: Tue, Sep 4, 2012 at 2:17 PM Subject: Re: durandal To: Nathaniel Echols

Hi Nat, Maybe the entire error message will be more helpful...here it is:

c++ -o Durandal/src/DistMatrix.o -c -DBOOST_ALL_NO_LIB -arch i386 -fPIC -fno-strict-aliasing -w -no-cpp-precomp -arch i386 -DNDEBUG -O1 -ffast-math /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/DistMatrix.cc c++ -o Durandal/src/rmsd.o -c -DBOOST_ALL_NO_LIB -arch i386 -fPIC -fno-strict-aliasing -w -no-cpp-precomp -arch i386 -DNDEBUG -O1 -ffast-math /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/rmsd.cc c++ -o Durandal/src/ranker.o -c -DBOOST_ALL_NO_LIB -arch i386 -fPIC -fno-strict-aliasing -w -no-cpp-precomp -arch i386 -DNDEBUG -O1 -ffast-math /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/ranker.cc

In file included from /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/DistMatrix.cc:33: /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/Singleton.h:101:8: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup os << v[i] << '\n'; ^ /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/DistMatrix.cc:844:12: note: in instantiation of function template specialization 'operator<<<std::pair<float, int> >' requested here cerr << bins; ^ /Users/terwill/unix/PHENIX/phenix-dev-1148/Durandal/src/Singleton.h:117:10: note: 'operator<<' should be declared prior to the call site ostream& operator<<(ostream& os, const pair<T, U>& p) { ^ 1 error generated.

All the best, Tom T

[UnixJunkie]

Hello,

I registered the bug under github's bugtracker here: https://github.com/HappyCrow/Durandal/issues?state=open

It would be nice if follow-ups go there.

I could not reproduce the problem at home on my mac.

Please provide the commands you ran to observe the bug.

I untared Durandal, ran make and it went fine.

Did you compile phenix using the install script?

What options did you give to this script?

Thanks, F.

[terwill]

The problem only appears to be with clang. Here is compilation with g++ and then clang:

terwill% mkdir -p build terwill% g++ -o build/DistMatrix.o -c -g -O3 -DNDEBUG -W -Wall src/DistMatrix.cc terwill% clang -o build/DistMatrix.o -c -g -O3 -DNDEBUG -W -Wall src/DistMatrix.cc In file included from src/DistMatrix.cc:33: src/Singleton.h:101:8: error: call to function 'operator<<' that is neither visible in the template definition nor found by argument-dependent lookup os << v[i] << '\n'; ^ src/DistMatrix.cc:844:12: note: in instantiation of function template specialization 'operator<<<std::pair<float, int> >' requested here cerr << bins; ^ src/Singleton.h:117:10: note: 'operator<<' should be declared prior to the call site ostream& operator<<(ostream& os, const pair<T, U>& p) { ^ 1 error generated.

[UnixJunkie]

I created a branch for fixes here: https://github.com/HappyCrow/Durandal/tree/fix_for_clang

Compilation goes further than before. I have binding of executable failing on Ubuntu but you should give it a try on a Mac.

[UnixJunkie]

I got until here: make find . -name "_.cc" > srcfiles find . -name ".h" >> src_files cat src_files | xargs etags -a -o src/TAGS rm -f src_files scons opt=true scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... clang -o build/DistMatrix.o -c -g -O3 -DNDEBUG -W -Wall src/DistMatrix.cc clang -o build/DistRange.o -c -g -O3 -DNDEBUG -W -Wall src/DistRange.cc clang -o build/SimpPDB.o -c -g -O3 -DNDEBUG -W -Wall src/SimpPDB.cc clang -o build/Singleton.o -c -g -O3 -DNDEBUG -W -Wall src/Singleton.cc clang -o build/Stru.o -c -g -O3 -DNDEBUG -W -Wall src/Stru.cc clang -o build/durandal.o -c -g -O3 -DNDEBUG -W -Wall src/durandal.cc clang -o build/ranker.o -c -g -O3 -DNDEBUG -W -Wall src/ranker.cc clang -o build/rmsd.o -c -g -O3 -DNDEBUG -W -Wall src/rmsd.cc clang -o durandal.cluster_pdbs build/durandal.o build/DistMatrix.o build/DistRange.o build/Stru.o build/SimpPDB.o build/rmsd.o build/Singleton.o Undefined symbols for architecture x86_64: "std::basic_string<char, std::char_traits, std::allocator >::basicstring(char const, std::allocator const&)", referenced from: contains(int, char, std::string) in durandal.o contains(int, char, std::string, std::string) in durandal.o get_option(int, char, std::string) in durandal.o main in durandal.o DistMatrix::DistMatrix(char const, float) in DistMatrix.o SimPDB::read(int, bool) in SimpPDB.o cstring_tostrategy(char const) in Singleton.o ... "std::string::_Rep::_S_empty_rep_storage", referenced from: contains(int, char, std::string) in durandal.o contains(int, char, std::string, std::string) in durandal.o get_option(int, char__, std::string) in durandal.o get_option(int, char, std::string, std::string) in durandal.o main in durandal.o DistMatrix::DistMatrix(char const, float) in DistMatrix.o DistMatrix::~DistMatrix() in DistMatrix.o ... "std::string::_Rep::_M_destroy(std::allocator const&)", referenced from: contains(int, char, std::string) in durandal.o contains(int, char, std::string, std::string) in durandal.o get_option(int, char, std::string) in durandal.o get_option(int, char, std::string, std::string) in durandal.o _main in durandal.o DistMatrix::DistMatrix(char const*, float) in DistMatrix.o DistMatrix::~DistMatrix() in DistMatrix.o ...

And I have no idea of what clang is missing.

[UnixJunkie]

Corrections were merged into the master branch. Thanks to Thomas Terwilliger for having confirmed the fixes are OK.