[Debian-med-packaging] Fwd: Bug#784929: subread: FTBFS on arm64, armel, armhf, ...

[Alex Mestiashvili]

Dear Dr. Wei Shi,

Debian supports many CPU architectures and building of subread failed on 
some of these architectures.

1. Due to quite specific -mtune and -mmmx -msse* gcc flags, subread 
failed to build almost on any architecture except amd64.
This issue was fixed by removing -mtune and -mmmx -msse* flags from the 
src/Makefile.Linux.
http://anonscm.debian.org/cgit/debian-med/subread.git/tree/debian/patches/gcc_flags_cleanup.patch

2. We still have an issue, now with exactSNP, please see the bug report 
below.

Thank you,
Alex


-------- Forwarded Message --------
Subject: 	[Debian-med-packaging] Bug#784929: subread: FTBFS on arm64, 
armel, armhf, ...
Resent-Date: 	Sun, 10 May 2015 19:54:01 +0000
Resent-From: 	Edmund Grimley Evans <edmund.grimley.evans at gmail.com>
Resent-To: 	debian-bugs-dist at lists.debian.org
Resent-CC: 	Debian Med Packaging Team 
<debian-med-packaging at lists.alioth.debian.org>
Date: 	Sun, 10 May 2015 20:51:41 +0100
From: 	Edmund Grimley Evans <edmund.grimley.evans at gmail.com>
Reply-To: 	Edmund Grimley Evans <edmund.grimley.evans at gmail.com>, 
784929 at bugs.debian.org
To: 	submit at bugs.debian.org



Source: subread
Version: 1.4.6-p2+dfsg-2

It failed to build on several architectures:

https://buildd.debian.org/status/package.php?p=subread&suite=sid

There seems to be a problem with (unsigned) char. See this file, for
example:

https://sources.debian.net/src/subread/1.4.6-p2%2Bdfsg-2/src/SNPCalling.c/

This line:

while ((c = getopt_long (argc, argv, "7:N:a:i:g:o:bQ:p:f:n:r:x:w:s:t:T:v4",snp_long_options, &optindex))!=-1)

The function getopt_long returns int, but the value is assigned to a
char c, which is unsigned on ARM architectures, so it will never be
equal to -1. That is probably the immediate cause of the failure.
However, there may be other char-related problems in there. I noticed,
for example, that mask_snp_bitmap may be incorrect according to the C
standard (signed overflow).

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