[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
ypeng at cs.hku.hk
Fri Jun 20 22:33:23 UTC 2014
Here is the problem I have: I use auto tool (autoconf, automake, configure
and make dist-gzip) to generate the distribution tarball. All Makefile and
Makefile.in are generated from Makefile.am. I don't want to check in
generated files, because they will be changed dramatically even you only
introduce one more file. I cannot find a way to let github generate my
tarball automatically. Currently, i check the tarball in the git repository
directly.
Please let me if you know what is the standard way to generate this
tarball.
Thanks,
Yu Peng
On Fri, Jun 20, 2014 at 3:25 PM, Andreas Tille <andreas at an3as.eu> wrote:
> 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
> > >
> > >
>
> --
> http://fam-tille.de
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20140620/ff233670/attachment-0001.html>
More information about the Debian-med-packaging
mailing list