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<div class="moz-cite-prefix">Hi Wei, <br>
<br>
On 05/20/2015 01:09 AM, Wei Shi wrote:<br>
</div>
<blockquote
cite="mid:CED5503E-3372-40D1-ADEC-100C1424B17F@wehi.edu.au"
type="cite">Hi Alex,
<div><br>
</div>
<div>Thanks for testing our package and providing us the feedback.</div>
<div><br>
</div>
<div>We will look into the getopt issue. If that is the only issue
that caused problem for running Subread on ARM, I think we can
fix it.</div>
</blockquote>
<br>
The good news - ARM issues are solved by adding -fsigned-char to
CCFLAGS.<br>
In this case subread works on architectures where char is by default
unsigned such as armel, armhf and so on.<br>
And in this case there is no need to patch getopt.<br>
<br>
Though there are still problems on powerpc, mips and s390x:<br>
- subjunc test return Segmentation fault, <br>
- exactSNP test complains that it can not read the file <br>
<br>
here is the output:<br>
exactSNP FEOF 0!<br>
SAM file does not exist or is not accessible: 'data/test-in.BAM'<br>
<br>
<blockquote
cite="mid:CED5503E-3372-40D1-ADEC-100C1424B17F@wehi.edu.au"
type="cite"><br>
<div>Could you also please provide us your cppcheck results? We
would like to know where memory leaks occur in the code and we
can then fix them.</div>
</blockquote>
<br>
Please see the attachment for the cppcheck output.<br>
<br>
Thank you, <br>
Alex<br>
<br>
<blockquote
cite="mid:CED5503E-3372-40D1-ADEC-100C1424B17F@wehi.edu.au"
type="cite">
<div>Best regards,</div>
<div><br>
</div>
<div>Wei</div>
</blockquote>
<br>
<blockquote
cite="mid:CED5503E-3372-40D1-ADEC-100C1424B17F@wehi.edu.au"
type="cite">
<div><br>
<div>
<div>On May 15, 2015, at 10:59 PM, Alex Mestiashvili wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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<div class="moz-cite-prefix">Dear Wei, <br>
<br>
thank you for the quick answer.<br>
<br>
On 05/12/2015 01:59 AM, Wei Shi wrote:<br>
</div>
<blockquote
cite="mid:F0200EB6-835B-4F01-AFAA-1D2BF4E9048E@wehi.edu.au"
type="cite">Hi Alex,
<div><br>
</div>
<div>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?</div>
</blockquote>
<br>
I was not correct in the last email, the failure on i386
was related to the debian specific part of the build
process.<br>
So both AMD64 and i386 are fine.<br>
The full build logs are located here: <a
moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://buildd.debian.org/status/logs.php?pkg=subread">https://buildd.debian.org/status/logs.php?pkg=subread</a><br>
<br>
Regarding the -mtune option, My understanding is that
tuning for a specific CPU shouldn't be used for a <br>
binary package which can be used on a wide range of CPUs.<br>
Currently I removed -mtune completely, but maybe
-mtune=generic should be used instead of -mtune=core2.<br>
<br>
"generic" <br>
Produce code optimized for the most common
IA32/AMD64/EM64T processors.<br>
If you know the CPU on which your code will run, then you
should use the <br>
corresponding <samp><span class="option">-mtune</span></samp>
or <samp><span class="option">-march</span></samp> option
instead of <samp><span class="option">-mtune=generic</span></samp>.
<br>
But, if you do not know exactly what CPU users of your
application will have, <br>
then you should use this option. <br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html">https://gcc.gnu.org/onlinedocs/gcc/x86-Options.html</a><br>
<br>
The -msse and -msse2 flags are enabled by default for
x86-64 compiler, so it should be no problem to strip them,
<br>
and AFAIK SSE also implies support for MMX, so -mmmx flag
is not needed too.<br>
<br>
<blockquote
cite="mid:F0200EB6-835B-4F01-AFAA-1D2BF4E9048E@wehi.edu.au"
type="cite">
<div>Currently, Subread only supports AMD and Intel
architectures and we do not have a plan to support
other platforms such as ARM.</div>
</blockquote>
<br>
I see, In such case I'll limit the architectures for the
package to the ones where it builds successfully and
passes the tests.<br>
<br>
Just for your information, I tried to fix the getopt issue
by defining "c" as int instead of char.<br>
The binaries were build successfully on ARM and other
architectures, but the tests fail, you can see the results
here:<br>
<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://buildd.debian.org/status/logs.php?pkg=subread&ver=1.4.6-p2%2Bdfsg-3&suite=experimental">https://buildd.debian.org/status/logs.php?pkg=subread&ver=1.4.6-p2%2Bdfsg-3&suite=experimental</a><br>
<br>
Also the cppcheck reveals a lot of memory leaks in the
code.<br>
<br>
Best regards, <br>
Alex<br>
<br>
<blockquote
cite="mid:F0200EB6-835B-4F01-AFAA-1D2BF4E9048E@wehi.edu.au"
type="cite">
<div><br>
<div>
<div>On May 11, 2015, at 5:34 PM, Alex Mestiashvili
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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content="text/html; charset=windows-1252">
<div 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 moz-do-not-send="true"
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>
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<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
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class="moz-txt-link-rfc2396E"
href="mailto:edmund.grimley.evans@gmail.com"><edmund.grimley.evans@gmail.com></a></td>
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<td>Debian Med Packaging Team <a
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href="mailto:debian-med-packaging@lists.alioth.debian.org"><debian-med-packaging@lists.alioth.debian.org></a></td>
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<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
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:edmund.grimley.evans@gmail.com"><edmund.grimley.evans@gmail.com></a></td>
</tr>
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<th nowrap="nowrap" valign="BASELINE"
align="RIGHT">Reply-To: </th>
<td>Edmund Grimley Evans <a
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:edmund.grimley.evans@gmail.com"><edmund.grimley.evans@gmail.com></a>,
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:784929@bugs.debian.org">784929@bugs.debian.org</a></td>
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<th nowrap="nowrap" valign="BASELINE"
align="RIGHT">To: </th>
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class="moz-txt-link-abbreviated"
href="mailto:submit@bugs.debian.org">submit@bugs.debian.org</a></td>
</tr>
</tbody>
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<br>
<br>
<pre>Source: subread
Version: 1.4.6-p2+dfsg-2
It failed to build on several architectures:
<a moz-do-not-send="true" 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 moz-do-not-send="true" 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
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<a moz-do-not-send="true" 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>
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<br>
</div>
</blockquote>
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