Your message dated Tue, 28 Jul 2015 12:29:59 +0200
with message-id <20150728102959.gp16...@an3as.eu>
and subject line Closed upstream 1.2.1
has caused the Debian Bug report #770162,
regarding htslib: fai_build_core in faidx.c assumes char is signed
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
770162: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=770162
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: htslib
Version: 1.1-1
The code looks like this:
faidx_t *fai_build_core(BGZF *bgzf)
{
char c, *name;
...
while ( (c=bgzf_getc(bgzf))>=0 ) {
Clearly on architectures where plain char is unsigned (arm64, armhf,
...) this won't work (infinite loop).
I'd suggest changing the type of c from char to int, which is the return
type of bgzf_getc.
This bug is apparently the cause of samtools failing to build:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=762647
I can't take credit for identifying the issue as domibel seems to have
announced it here on Oct 2:
http://github.com/samtools/samtools/issues/304
--- End Message ---
--- Begin Message ---
Hi,
this bug was fixed in upstream version 1.2.1 that is now in testing/unstable.
Kind regards
Andreas.
--
http://fam-tille.de
--- End Message ---
