[Debian-med-packaging] Bug#752122: Patch for idba to build with clang compiler (Was: Bug#752122: idba: FTBFS with clang instead of gcc)
Andreas Tille
andreas at an3as.eu
Fri Jun 20 22:25:03 UTC 2014
Hi again,
many thanks for the very quick response. I was able to download a
tarball from github but something seems wrong - it contains another
tarball which seems to be the proper one for a source distribution since
it contains the Makefile.in files and the configure script. I have
no personal experience with git but something in the tarball creation
seems to be wrong.
Kind regards
Andreas.
On Fri, Jun 20, 2014 at 02:55:34PM -0700, Yu PENG wrote:
> Ok, I created a release tag (
> https://github.com/loneknightpy/idba/releases/tag/1.1.2).
>
> Thanks,
> Yu Peng
>
>
>
> On Fri, Jun 20, 2014 at 2:35 PM, Andreas Tille <andreas at an3as.eu> wrote:
>
> > 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
> > > >
> > > >
> >
> > --
> > http://fam-tille.de
> >
> >
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