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 <andr...@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-t...@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-packag...@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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