Hi, On 07/12/17 15:28, Andreas Tille wrote: > On Thu, Dec 07, 2017 at 02:40:36PM +0000, James Bonfield wrote: >> On Tue, Dec 05, 2017 at 08:02:18AM +0100, Andreas Tille wrote: >>> this is a kind ping since as I wrote below the issue seems not be solved. >> >> I'm not sure I can easily debug this as it only fails on systems I >> have no access to; it's like trying to debug your grandmother's >> windows desktop over the phone... >> >> I'm still convinced it's something to do with large file support not >> working correctly, likely with off_t being the wrong size. Especially >> given the 64-bit mips build works while the 32-bit one does not. I >> assume everything else about these architectures are the same. >> >> We don't have any 32-bit build systems any more though. >> >>>>> Does adding that fix the fseeko call to start working again? >>>> >>>> Unfortunately not - see here the build logs: >>>> >>>> https://buildd.debian.org/status/package.php?p=staden-io-lib >> >> James >> -- >> James Bonfield (j...@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia >> Tova > > > I'm just forwarding this to debian-arm and debian-mips. I see no other > chance to deal with this bug rather than removing these architectures > from the architectures field. > > Do you have any better suggestion?
The bug is here: https://sources.debian.org/src/staden-io-lib/1.14.9-3/io_lib/bgzip.c/#L47 Unlike most packages (although there are quite a few that do this), staden-io-lib defines _FILE_OFFSET_BITS in a config header instead of passing it as a -D argument to the compiler. Since this flag affects the behavior of standard headers, you *must* include this header before any others. In the bgzip.c file above, stdio.h is included before the io_lib_config.h header. This causes bgzip.c to have a different opinion of what sizeof(off_t) compared to other files, so all external calls to bzi_seek invoke undefined behavior. To fix, move the "#ifdef HAVE_CONFIG_H...#endif" block above all the other includes in that file. Thanks, James
signature.asc
Description: OpenPGP digital signature
