Your message dated Thu, 09 Oct 2014 13:00:09 +0000
with message-id <[email protected]>
and subject line Bug#749136: fixed in jellyfish 2.1.4-1
has caused the Debian Bug report #749136,
regarding jellyfish: FTBFS with clang instead of gcc
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
749136: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=749136
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: jellyfish
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).
See build logs here:
http://clang.debian.net/logs/2014-01-14/jellyfish_1.1.10-1_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
--- jellyfish-1.1.11/jellyfish/invertible_hash_array.hpp 2013-05-29 15:45:57.000000000 -0400
+++ jellyfish-1.1.11-my/jellyfish/invertible_hash_array.hpp 2014-05-24 09:09:09.986534767 -0400
@@ -636,7 +636,7 @@
bool _get_val(const size_t id, size_t &key_id, const word key, word &val,
bool full = false, bool carry_bit = false) const {
// Buffer for pre-cached information
- prefetch_info info_ary[prefetch_buffer::capacity()];
+ prefetch_info *info_ary = reinterpret_cast<prefetch_info *>(alloca(sizeof(prefetch_info) * prefetch_buffer::capacity()));
prefetch_buffer buffer(info_ary);
warm_up_cache(buffer, id, false);
--- End Message ---
--- Begin Message ---
Source: jellyfish
Source-Version: 2.1.4-1
We believe that the bug you reported is fixed in the latest version of
jellyfish, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated jellyfish package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 09 Oct 2014 13:15:34 +0200
Source: jellyfish
Binary: jellyfish libjellyfish-2.0-2 libjellyfish-2.0-dev jellyfish-examples
Architecture: source amd64
Version: 2.1.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
jellyfish - count k-mers in DNA sequences
jellyfish-examples - count k-mers in DNA sequences (examples for testing)
libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of
jellyfish)
libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of
jellyfish)
Closes: 749136
Changes:
jellyfish (2.1.4-1) unstable; urgency=medium
.
* New upstream version
* d/watch: point to new location on Github
* cme fix dpkg-control
* new upstream version needs autoreconf
* New Build-Depends: yaggo, pkg-config, bc, time, procps
* debian/rules: Make sure package builds twice in a row
* d/copyright:
- Adapted to file locations in new upstream version
- Additional copyright paragraph for included libjsoncpp
- Additional copyright paragraph for unit tests
* checking whether it is possible to use Debian packaged libjsoncpp
failed - add lintian override to use internal one
* Split libjellyfish and libjellyfish-dev packages up from single
package, add jellyfish-examples package containing test suite
* Add autopkgtest
* Fix FTBFS with clang (thanks for the patch to Martin Steghöfer)
Closes: #749136
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