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

[Wei Shi]

Hi Alex,

We have tested subread on both 32-bit and 64-bit Intel and AMD platforms and it works fine (the gcc flags you mentioned were all included). So I do not know what caused the installation failure. Maybe you can show us the errors you have encountered?

Currently, Subread only supports AMD and Intel architectures and we do not have a plan to support other platforms such as ARM.

Best regards,
Wei

On May 11, 2015, at 5:34 PM, Alex Mestiashvili wrote:

> 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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> Debian-med-packaging at lists.alioth.debian.org
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> 
> 


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