Your message dated Tue, 22 Nov 2011 03:02:42 +0000
with message-id <e1rsgd8-0002d7...@franck.debian.org>
and subject line Bug#648803: fixed in bwa 0.6.0-2
has caused the Debian Bug report #648803,
regarding FTBFS: ksw.c:28:23: fatal error: emmintrin.h: No such file or
directory
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.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
648803: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=648803
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: bwa
Version: 0.6.0-1
Severity: serious
Justification: fails to build from source
Unfortunately, bwa version 0.6.0 seems to include a header that is
specific to amd64. For instance:
bwtmisc.c:172:7: warning: ignoring return value of 'fread', declared with
attribute warn_unused_result [-Wunused-result]
bwtmisc.c: In function 'bwt_pac2bwt':
bwtmisc.c:72:7: warning: ignoring return value of 'fread', declared with
attribute warn_unused_result [-Wunused-result]
bwtmisc.c: In function 'bwa_seq_len':
bwtmisc.c:51:7: warning: ignoring return value of 'fread', declared with
attribute warn_unused_result [-Wunused-result]
gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat
-Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro
-DHAVE_PTHREAD bwtindex.c -o bwtindex.o
gcc -c -Wall -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat
-Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro
-DHAVE_PTHREAD ksw.c -o ksw.o
ksw.c:28:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
make[2]: *** [ksw.o] Error 1
make[2]: Leaving directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
dh_auto_build: make -j1 CFLAGS=-Wall -g -O2 -fstack-protector
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security
-D_FORTIFY_SOURCE=2 -Wl,-z,relro returned exit code 2
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory `/build/buildd-bwa_0.6.0-1-armel-HDdcYb/bwa-0.6.0'
make: *** [build] Error 2
--
Charles
--- End Message ---
--- Begin Message ---
Source: bwa
Source-Version: 0.6.0-2
We believe that the bug you reported is fixed in the latest version of
bwa, which is due to be installed in the Debian FTP archive:
bwa_0.6.0-2.dsc
to main/b/bwa/bwa_0.6.0-2.dsc
bwa_0.6.0-2.tar.gz
to main/b/bwa/bwa_0.6.0-2.tar.gz
bwa_0.6.0-2_amd64.deb
to main/b/bwa/bwa_0.6.0-2_amd64.deb
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 648...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <ple...@debian.org> (supplier of updated bwa 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 ftpmas...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 22 Nov 2011 11:32:11 +0900
Source: bwa
Binary: bwa
Architecture: source amd64
Version: 0.6.0-2
Distribution: experimental
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Charles Plessy <ple...@debian.org>
Description:
bwa - Burrows-Wheeler Aligner
Closes: 648803
Changes:
bwa (0.6.0-2) experimental; urgency=low
.
[9410de3] Disable SSE2 everywhere except on amd64 (Closes: #648803).
[fb4c559] Reimplementation of Standard SW for when SSE2 is unavailable.
cherry picked from upstream commit 182cb2e.
This commit modifies upstream sources.
[9c93ccd] Use native format to bypass mandatory patch system.
Checksums-Sha1:
0defa5bfa75fd128b81ff2cce26f3560d3387790 1681 bwa_0.6.0-2.dsc
6c49a7a61d424bde502a03fb38858e8eebd588f1 169209 bwa_0.6.0-2.tar.gz
09224646b17bf5092150a41330b110201de9c346 152102 bwa_0.6.0-2_amd64.deb
Checksums-Sha256:
5f192c1147232c0b8fa581fa398167b518ac7e33adffc9245112f2291d9573fd 1681
bwa_0.6.0-2.dsc
8d917434fd8ccfff3685f9aab1214c512985f55d1ee8b8c7933fa358b184f5b5 169209
bwa_0.6.0-2.tar.gz
7984ef9c940d40b76781e487e45439a4de29823a588faa07de63aaf33f71dbf1 152102
bwa_0.6.0-2_amd64.deb
Files:
91ef0cb0d0d4ebeb33f28ae784c4e672 1681 science optional bwa_0.6.0-2.dsc
7d8655d45605071b3cf22c402208fbf9 169209 science optional bwa_0.6.0-2.tar.gz
b39ec9278cf86460cdb78f7745ac7d12 152102 science optional bwa_0.6.0-2_amd64.deb
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