[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]

I migrated idba code to github and applied the patches. (
https://github.com/loneknightpy/idba/tree/idba-1.1.2) You can find the
binary package here (
https://github.com/loneknightpy/idba/blob/idba-1.1.2/idba-1.1.2.tar.gz?raw=true
).

Thanks,


On Fri, Jun 20, 2014 at 9:19 AM, Andreas Tille <andreas at an3as.eu> wrote:

> Hi,
>
> thanks for the quick and helpful reply.  Feel free to ping me once your
> next release is ready.
>
> Kind regards
>
>       Andreas.
>
> On Fri, Jun 20, 2014 at 08:54:25AM -0700, Yu PENG wrote:
> > 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
> > >
> > >
>
> --
> http://fam-tille.de
>
>
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