Hello,

I believe I have found a bug in GCC, but I am unable to report it for
lack of a bugzilla account. I'm including below the text of the bug
report that I'd like to add. At minimum, this issue needs to be
discussed or documented.

Would you please create a GCC bugzilla account for me?

-Alex


istream::seekg should not reset eofbit if -std=c++98

According to N3168 [1], as recently as 2010 the C++ standards did not
permit istream::seekg to reset istream::eof. When the change to the
standard was approved, libstdc++ started using the new behavior, even
for programs compiled with -std=c++98. This caused the bioinformatics
program GERMLINE [2] to break. In PEDIndividualsExtractor.cpp [3] we
see:

void PEDIndividualsExtractor::loadInput()
{
    ...

    while (!stream.eof() )
    {
        getIndividuals();
        stream.seekg(numberOfMarkers*4 + 1,ios::cur);
    }

    ...
}

void PEDIndividualsExtractor::getIndividuals()
{
    string discard, ID, famID;
    stream >> famID >> ID >> discard >> discard >> discard >> discard;
    if(!stream.good()) return;

    ...
}

This code stopped working sometime between GCC 4.4.5 / libstdc++
6.0.13 and GCC 4.6.3 / libstdc++ 6.0.16. With the change to libstdc++,
stream.eof() is always false, so loadInput() goes into an infinite
loop. An simple test program is attached.

I realize that I could petition the GERMLINE authors to change the
loop condition (and I eventually will), but the fact that you can't
get the old behavior even with -std=c++98 is a bug in GCC.

[1] http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2010/n3168.htm
[2] http://www.cs.columbia.edu/~gusev/germline/
[3] http://www.cs.columbia.edu/~gusev/germline/germline-1-5-1.tar.gz