Problems running/compiling root cern code after Mavericks upgrade - c++

Question

I recently upgraded my OS to Mavericks, reinstalled Xcode (upgraded to 5.0.1 from 4.6.2) and also installed xcode-select. Finally I installed root (v5.34/10) again, downloaded the source code from git, and followed the standard ./configure and make. Then source bin/thisroot.sh.
But after following all those steps, code that previously compiled and run is not working any longer.
I'm compiling my code using root libraries, to compile I use as options the output of:
root-config --cflags
root-config --glibs
getting the following:
g++ main.C -pthread -stdlib=libc++ -m64 -I/Users/user/root.git/include -L/Users/royal/root.git/lib -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lpthread -Wl,-rpath,/Users/user/root.git/lib -stdlib=libc++ -lm -ldl
I tried using both g++ and clang++ and I get the same error:
*** Break *** segmentation violation
Generating stack trace...
--
Warning: /usr/bin/atos is moving and will be removed from a future OS X release.
It is now available in the Xcode developer tools to be invoked via: `xcrun atos`
To silence this warning, pass the '-d' command-line flag to this tool.
--
0x0000000106cee8d7 in main (in a.out) + 1447
--
Warning: /usr/bin/atos is moving and will be removed from a future OS X release.
It is now available in the Xcode developer tools to be invoked via: `xcrun atos`
To silence this warning, pass the '-d' command-line flag to this tool.
--
0x00007fff8e2e95fd in start (in libdyld.dylib) + 1
0x0000000000000001 in <unknown function>
Also I've tried running the code without compiling via root main.C and in this case I get the following:
Error: Ambiguous overload resolution (10001,2) ReactorSpectrumMultiple.h:237:
Calling : getline(ifstream,string);
Match rank: file line signature
ffffffff (compiled) 0 istream& getline(istream&,string&,char);
* 10001 (compiled) 0 istream& getline(istream&,string&);
ffffffff (compiled) 0 basic_istream<char,char_traits<char> >& getline(basic_istream<char,char_traits<char> >&,string&,char);
* 10001 (compiled) 0 basic_istream<char,char_traits<char> >& getline(basic_istream<char,char_traits<char> >&,string&);
*** Interpreter error recovered ***
what is puzzling me even more, as I said before I haven't changed any line of code and this was working perfectly before. I write the lines that trigger the last error in case you see something obvious:
std::string line;
std::ifstream input(IsotopeName);
std::getline(input,line);// This line produces the error
I also tried using getline(input,line); without std::, same error.
Last trial was to write istream::getline(input,line); instead. In that case I get something similar to the first error:
*** Break *** segmentation violation
Generating stack trace...
--
Warning: /usr/bin/atos is moving and will be removed from a future OS X release.
It is now available in the Xcode developer tools to be invoked via: `xcrun atos`
To silence this warning, pass the '-d' command-line flag to this tool.
--
0x000000010e6401d9 in G__getfunction (in libCint.so) + 5929
--
Warning: /usr/bin/atos is moving and will be removed from a future OS X release.
It is now available in the Xcode developer tools to be invoked via: `xcrun atos`
To silence this warning, pass the '-d' command-line flag to this tool.
--
0x000000010e63561b in G__getitem (in libCint.so) + 507
--
I don't copy the whole output since it keeps on printing that warning but triggered by different sources (libCint.so, libCore.so, libRint.so,root.exe and libdyld.dylib)
Thank you for your time.