[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]

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]);
>  

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