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 <[email protected]> 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 <[email protected]> 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: [email protected] > > > > > 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 > > > > > [email protected] > > > > > > > > > > > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging > > > > > > > > > > > > -- > > > > http://fam-tille.de > > > > > > > > > > > > -- > > http://fam-tille.de > > > > -- http://fam-tille.de -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
