Re: Bug#269643: readseq: segfaults when command line arguments are provided

[Michael Schmitz <schmitz@opal.biophys.uni-duesseldorf.de>]

> > >  On gcc-3.4 AMD64 (from
> > > deb http://debian-amd64.alioth.debian.org/gcc-3.4 testing main contrib non-free)
> > > on a dual Opteron, readseq segfaults when it gets command line arguments
> > > (even --help).  It seems to work when everything is specified interactively.
> > [...]
> > > Versions of packages readseq depends on:
> > > ii  libc6           2.3.2.ds1-16.0.0.1.amd64 GNU C Library: Shared libraries an
> > > ii  libncbi6        6.1.20040616-1           NCBI libraries for biology applica
> >
> > I cannot reproduce this on powerpc - package versions are pretty much the
> > same here. In order to investigate the bug, I'd need ncbi-tools-dev
> > installed in the sid-amd64-pure chroot on pergolesi, please.
>
> Done.

OK, found the bug:

readseq retrieves its argc and argv via the ncbi libs' interface
(Nlm_GetArgc() and Nlm_GetArgv()) instead of declaring a main(). On amd64,
we get

DEBUG: argc=2 org argv=0xffffffffbffffaa8

while compiling without ncbi support I see

DEBUG: argc=2 org argv=0x7fbffffa98

The first argv pointer segfaults, the second is just fine, so the ncbi libs
seem to generate an invalid argv pointer somewhere.

Hacking a workaround (just masking off the offending high bits of the
pointer) I get to:

DEBUG: argc=2 org argv=0xffffffffbffffaa8
DEBUG: argc=2 new argv=0x7fbffffaa8
readSeq (1Feb93), multi-format molbio sequence reader.
usage: readseq [-options] in.seq > out.seq
 options
    -a[ll]         select All sequences
    -c[aselower]   change to lower case
 ....

which is fine again. I suspect libncbi6 is broken on amd64 and will at
least need a recompile. I might be missing some subtle 64bit trick here,
though: CC goes to debian-amd64 (please CC me, I'm not subscribed there).

Unless someone convinces me to the contrary, I will reassign the bug to
libncbi6 in a few days.

	Michael