[Debian-med-packaging] Bug#752122: Patch for idba to build with clang compiler (Was: Bug#752122: idba: FTBFS with clang instead of gcc)

[Yu PENG]

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.

Thanks,
Yu Peng


On Fri, Jun 20, 2014 at 4:39 AM, Andreas Tille <andreas at an3as.eu> wrote:

> Hello,
>
> the Debian Med team has packaged your program idba for Debian.
> Currently there is an effort in Debian to build the distribution with
> the clang compiler that is a bit more strict about syntax.  A patch was
> provided to solve this problem which can be found here:
>
>
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/debian/patches/clang.patch?view=markup
>
> BTW, we also have applied another patch for some architectures.  Fell
> free to apply also this
>
>
> http://anonscm.debian.org/viewvc/debian-med/trunk/packages/idba/trunk/debian/patches/use-atomic-for-mips.patch?view=markup
>
> to your code (I forgot whether I just reported this to you - sorry if
> it is a duplicate).  Finally our sanity check has found a misspelling:
>
>    I: idba: spelling-error-in-binary usr/bin/idba_hybrid unkown unknown
>
> What I'm also wondering is:  You are providing a test directory which
> unfortunately only contains an empty Makefile.am (and the according
> Makefile.in).  We would be really interested to run some unit tests to
> prove the proper function of idba.
>
> Kind regards and thanks for providing idba as free software
>
>      Andreas.
>
>
> On Thu, Jun 19, 2014 at 05:12:39PM -0400, Alexander Ovchinnikov wrote:
> > Package: idba
> > Severity: minor
> > Tags: patch
> > User: pkg-llvm-team at lists.alioth.debian.org
> > Usertags: clang-ftbfs
> >
> > Hello,
> >
> > Using the rebuild infrastructure, your package fails to build with clang
> > (instead of gcc).
> >
> > We detected this kinf of error:
> > http://clang.debian.net/status.php?version=3.4.2&key=NON-POD
> >
> > Full build log is available here:
> > http://clang.debian.net/logs/2014-06-16/idba_1.1.1-2_unstable_clang.log
> >
> > Thanks,
> > Alexander
> >
> > -- System Information:
> > Debian Release: jessie/sid
> >   APT prefers unstable
> >   APT policy: (500, 'unstable')
> > Architecture: amd64 (x86_64)
> >
> > Kernel: Linux 3.13-1-amd64 (SMP w/1 CPU core)
> > Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> > Shell: /bin/sh linked to /bin/dash
>
> > --- idba-1.1.1/src/tools/parallel_rna_blat.cpp        2013-07-23
> 14:27:57.000000000 -0400
> > +++ idba-1.1.1-my/src/tools/parallel_rna_blat.cpp     2014-06-19
> 17:08:02.373666423 -0400
> > @@ -61,7 +61,7 @@
> >
> >  void SplitSequenceFile()
> >  {
> > -    FastaWriter writers[num_threads];
> > +    FastaWriter *writers = static_cast<FastaWriter
> *>(alloca(sizeof(FastaWriter) * num_threads));
> >      for (int i = 0; i < num_threads; ++i)
> >          writers[i].Open(split_files[i]);
> >
> > --- idba-1.1.1/src/release/parallel_blat.cpp  2013-07-23
> 14:27:57.000000000 -0400
> > +++ idba-1.1.1-my/src/release/parallel_blat.cpp       2014-06-19
> 17:09:06.758253507 -0400
> > @@ -61,7 +61,7 @@
> >
> >  void SplitSequenceFile()
> >  {
> > -    FastaWriter writers[num_threads];
> > +    FastaWriter *writers = static_cast<FastaWriter
> *>(alloca(sizeof(FastaWriter) * num_threads));
> >      for (int i = 0; i < num_threads; ++i)
> >          writers[i].Open(split_files[i]);
> >
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> >
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
>
> --
> http://fam-tille.de
>
>
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