<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=windows-1252">
</head>
<body text="#000000" bgcolor="#FFFFFF">
Dear Dr. Wei Shi, <br>
<br>
Debian supports many CPU architectures and building of subread
failed on some of these architectures.<br>
<br>
1. Due to quite specific -mtune and -mmmx -msse* gcc flags, subread
failed to build almost on any architecture except amd64.<br>
This issue was fixed by removing -mtune and -mmmx -msse* flags from
the src/Makefile.Linux. <br>
<a class="moz-txt-link-freetext" href="http://anonscm.debian.org/cgit/debian-med/subread.git/tree/debian/patches/gcc_flags_cleanup.patch">http://anonscm.debian.org/cgit/debian-med/subread.git/tree/debian/patches/gcc_flags_cleanup.patch</a><br>
<br>
2. We still have an issue, now with exactSNP, please see the bug
report below.<br>
<br>
Thank you, <br>
Alex<br>
<div class="moz-forward-container"><br>
<br>
-------- Forwarded Message --------
<table class="moz-email-headers-table" border="0" cellpadding="0"
cellspacing="0">
<tbody>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Subject:
</th>
<td>[Debian-med-packaging] Bug#784929: subread: FTBFS on
arm64, armel, armhf, ...</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Resent-Date:
</th>
<td>Sun, 10 May 2015 19:54:01 +0000</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Resent-From:
</th>
<td>Edmund Grimley Evans
<a class="moz-txt-link-rfc2396E" href="mailto:edmund.grimley.evans@gmail.com"><edmund.grimley.evans@gmail.com></a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Resent-To:
</th>
<td><a class="moz-txt-link-abbreviated" href="mailto:debian-bugs-dist@lists.debian.org">debian-bugs-dist@lists.debian.org</a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Resent-CC:
</th>
<td>Debian Med Packaging Team
<a class="moz-txt-link-rfc2396E" href="mailto:debian-med-packaging@lists.alioth.debian.org"><debian-med-packaging@lists.alioth.debian.org></a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Date: </th>
<td>Sun, 10 May 2015 20:51:41 +0100</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">From: </th>
<td>Edmund Grimley Evans
<a class="moz-txt-link-rfc2396E" href="mailto:edmund.grimley.evans@gmail.com"><edmund.grimley.evans@gmail.com></a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Reply-To:
</th>
<td>Edmund Grimley Evans
<a class="moz-txt-link-rfc2396E" href="mailto:edmund.grimley.evans@gmail.com"><edmund.grimley.evans@gmail.com></a>,
<a class="moz-txt-link-abbreviated" href="mailto:784929@bugs.debian.org">784929@bugs.debian.org</a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">To: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:submit@bugs.debian.org">submit@bugs.debian.org</a></td>
</tr>
</tbody>
</table>
<br>
<br>
<pre>Source: subread
Version: 1.4.6-p2+dfsg-2
It failed to build on several architectures:
<a class="moz-txt-link-freetext" href="https://buildd.debian.org/status/package.php?p=subread&suite=sid">https://buildd.debian.org/status/package.php?p=subread&suite=sid</a>
There seems to be a problem with (unsigned) char. See this file, for
example:
<a class="moz-txt-link-freetext" href="https://sources.debian.net/src/subread/1.4.6-p2%2Bdfsg-2/src/SNPCalling.c/">https://sources.debian.net/src/subread/1.4.6-p2%2Bdfsg-2/src/SNPCalling.c/</a>
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).
_______________________________________________
Debian-med-packaging mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Debian-med-packaging@lists.alioth.debian.org">Debian-med-packaging@lists.alioth.debian.org</a>
<a class="moz-txt-link-freetext" href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging</a>
</pre>
<br>
</div>
<br>
</body>
</html>