<div dir="ltr">Thanks for providing patch. I will merge it to our code base. We do have unit tests internally but we didn't include it the package. I will include it in the new version. <div><br></div><div>Thanks,</div>
<div>Yu Peng</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jun 20, 2014 at 4:39 AM, Andreas Tille <span dir="ltr"><<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
the Debian Med team has packaged your program idba for Debian.<br>
Currently there is an effort in Debian to build the distribution with<br>
the clang compiler that is a bit more strict about syntax. A patch was<br>
provided to solve this problem which can be found here:<br>
<br>
<a href="http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/debian/patches/clang.patch?view=markup" target="_blank">http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/debian/patches/clang.patch?view=markup</a><br>
<br>
BTW, we also have applied another patch for some architectures. Fell<br>
free to apply also this<br>
<br>
<a href="http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/debian/patches/use-atomic-for-mips.patch?view=markup" target="_blank">http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/debian/patches/use-atomic-for-mips.patch?view=markup</a><br>
<br>
to your code (I forgot whether I just reported this to you - sorry if<br>
it is a duplicate). Finally our sanity check has found a misspelling:<br>
<br>
I: idba: spelling-error-in-binary usr/bin/idba_hybrid unkown unknown<br>
<br>
What I'm also wondering is: You are providing a test directory which<br>
unfortunately only contains an empty Makefile.am (and the according<br>
Makefile.in). We would be really interested to run some unit tests to<br>
prove the proper function of idba.<br>
<br>
Kind regards and thanks for providing idba as free software<br>
<br>
Andreas.<br>
<br>
<br>
On Thu, Jun 19, 2014 at 05:12:39PM -0400, Alexander Ovchinnikov wrote:<br>
> Package: idba<br>
> Severity: minor<br>
> Tags: patch<br>
> User: <a href="mailto:pkg-llvm-team@lists.alioth.debian.org">pkg-llvm-team@lists.alioth.debian.org</a><br>
> Usertags: clang-ftbfs<br>
><br>
> Hello,<br>
><br>
> Using the rebuild infrastructure, your package fails to build with clang<br>
> (instead of gcc).<br>
><br>
> We detected this kinf of error:<br>
> <a href="http://clang.debian.net/status.php?version=3.4.2&key=NON-POD" target="_blank">http://clang.debian.net/status.php?version=3.4.2&key=NON-POD</a><br>
><br>
> Full build log is available here:<br>
> <a href="http://clang.debian.net/logs/2014-06-16/idba_1.1.1-2_unstable_clang.log" target="_blank">http://clang.debian.net/logs/2014-06-16/idba_1.1.1-2_unstable_clang.log</a><br>
><br>
> Thanks,<br>
> Alexander<br>
><br>
> -- System Information:<br>
> Debian Release: jessie/sid<br>
> APT prefers unstable<br>
> APT policy: (500, 'unstable')<br>
> Architecture: amd64 (x86_64)<br>
><br>
> Kernel: Linux 3.13-1-amd64 (SMP w/1 CPU core)<br>
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)<br>
> Shell: /bin/sh linked to /bin/dash<br>
<br>
> --- idba-1.1.1/src/tools/parallel_rna_blat.cpp 2013-07-23 14:27:57.000000000 -0400<br>
> +++ idba-1.1.1-my/src/tools/parallel_rna_blat.cpp 2014-06-19 17:08:02.373666423 -0400<br>
> @@ -61,7 +61,7 @@<br>
><br>
> void SplitSequenceFile()<br>
> {<br>
> - FastaWriter writers[num_threads];<br>
> + FastaWriter *writers = static_cast<FastaWriter *>(alloca(sizeof(FastaWriter) * num_threads));<br>
> for (int i = 0; i < num_threads; ++i)<br>
> writers[i].Open(split_files[i]);<br>
><br>
> --- idba-1.1.1/src/release/parallel_blat.cpp 2013-07-23 14:27:57.000000000 -0400<br>
> +++ idba-1.1.1-my/src/release/parallel_blat.cpp 2014-06-19 17:09:06.758253507 -0400<br>
> @@ -61,7 +61,7 @@<br>
><br>
> void SplitSequenceFile()<br>
> {<br>
> - FastaWriter writers[num_threads];<br>
> + FastaWriter *writers = static_cast<FastaWriter *>(alloca(sizeof(FastaWriter) * num_threads));<br>
> for (int i = 0; i < num_threads; ++i)<br>
> writers[i].Open(split_files[i]);<br>
><br>
<br>
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<br>
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<br>
</font></span></blockquote></div><br></div>