<div dir="ltr">I migrated idba code to github and applied the patches. (<a href="https://github.com/loneknightpy/idba/tree/idba-1.1.2">https://github.com/loneknightpy/idba/tree/idba-1.1.2</a>) You can find the binary package here (<a href="https://github.com/loneknightpy/idba/blob/idba-1.1.2/idba-1.1.2.tar.gz?raw=true">https://github.com/loneknightpy/idba/blob/idba-1.1.2/idba-1.1.2.tar.gz?raw=true</a>). <div>
<br></div><div>Thanks, </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jun 20, 2014 at 9:19 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">Hi,<br>
<br>
thanks for the quick and helpful reply. Feel free to ping me once your<br>
next release is ready.<br>
<br>
Kind regards<br>
<br>
Andreas.<br>
<div class="HOEnZb"><div class="h5"><br>
On Fri, Jun 20, 2014 at 08:54:25AM -0700, Yu PENG wrote:<br>
> Thanks for providing patch. I will merge it to our code base. We do have<br>
> unit tests internally but we didn't include it the package. I will include<br>
> it in the new version.<br>
><br>
> Thanks,<br>
> Yu Peng<br>
><br>
><br>
> On Fri, Jun 20, 2014 at 4:39 AM, Andreas Tille <<a href="mailto:andreas@an3as.eu">andreas@an3as.eu</a>> wrote:<br>
><br>
> > 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>
> ><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>
> ><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<br>
> > 14:27:57.000000000 -0400<br>
> > > +++ idba-1.1.1-my/src/tools/parallel_rna_blat.cpp 2014-06-19<br>
> > 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<br>
> > *>(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<br>
> > 14:27:57.000000000 -0400<br>
> > > +++ idba-1.1.1-my/src/release/parallel_blat.cpp 2014-06-19<br>
> > 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<br>
> > *>(alloca(sizeof(FastaWriter) * num_threads));<br>
> > > for (int i = 0; i < num_threads; ++i)<br>
> > > writers[i].Open(split_files[i]);<br>
> > ><br>
> ><br>
> > > _______________________________________________<br>
> > > Debian-med-packaging mailing list<br>
> > > <a href="mailto:Debian-med-packaging@lists.alioth.debian.org">Debian-med-packaging@lists.alioth.debian.org</a><br>
> > ><br>
> > <a href="http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging" target="_blank">http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging</a><br>
> ><br>
> ><br>
> > --<br>
> > <a href="http://fam-tille.de" target="_blank">http://fam-tille.de</a><br>
> ><br>
> ><br>
<br>
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<a href="http://fam-tille.de" target="_blank">http://fam-tille.de</a><br>
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