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

Fri Jun 20 21:35:30 UTC 2014

Hi,

On Fri, Jun 20, 2014 at 11:03:04AM -0700, Yu PENG wrote:
> I migrated idba code to github and applied the patches. (
> https://github.com/loneknightpy/idba/tree/idba-1.1.2)

Cool!  This might standardise our packaging procedure.

> 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
> ).

Debian is in general not interested in binary packages but only sources
(since we try to support more architectures and also try to use
different compilers (which has led to the latest patch).  If you are
on Github simply tagging a release might be sufficient to obtain the
source tarball.

Many thanks for your quick response

      Andreas.

> 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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