Your message dated Sat, 18 Feb 2012 18:05:22 +0000
with message-id <e1ryoew-0004nz...@franck.debian.org>
and subject line Bug#660309: fixed in tophat 1.4.1-2
has caused the Debian Bug report #660309,
regarding tophat: broken code in configure script for determining CFLAGS
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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--
660309: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=660309
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: tophat
Version: 1.4.1-1
Severity: serious
tags: patch
The configure.ac file in your package contains code to determine c
compiler flags based on architecture. Unfortunately this code is
horriblly broken.
On i386 the configure script uses -march=i686. This is not acceptable in
debian as debian supports (at least in theory) processors down to the 486.
On all other debian architectures the configure script falls into a
broken* fallback test for -m64. This test always passes causing the
build to use -m64. This is tolerable (but pointless) on amd64 and
kfreebsd-amd64 and breaks the build on all other architectures.
Even more strangely the code seems to be setup to define
_FILE_OFFSET_BITS=64 on unknown architectures that don't support -m64
(though due to the broken -m64 test that codepath is never used) but not
on x86.
The attatched patch simply removes the broken checking code and leaves
EXT_CFLAGS empty on all architectures. I have tested that with this
patch the package builds on kfreebsd-i386.
* I have not determined exactly how it is broken but it seems to be
passing on all architectures. My suspsicion is the CFLAGS set before the
test aren't actually being used.
Description: Remove crazy cflag determination code
This code was broken (for example the test for -m64 plain doesn't work)
and does the wrong thing (uses -m686 on x86) for debian. Strip it out
completely
Author: Peter Michael Green <plugw...@p10link.net)
---
The information above should follow the Patch Tagging Guidelines, please
checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
are templates for supplementary fields that you might want to add:
Origin: <vendor|upstream|other>, <url of original patch>
Bug: <url in upstream bugtracker>
Bug-Debian: http://bugs.debian.org/<bugnumber>
Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
Forwarded: <no|not-needed|url proving that it has been forwarded>
Reviewed-By: <name and email of someone who approved the patch>
Last-Update: <YYYY-MM-DD>
--- tophat-1.4.1.orig/configure.ac
+++ tophat-1.4.1/configure.ac
@@ -75,26 +75,6 @@ generic_CFLAGS="-Wall -Wno-strict-aliasi
ext_CFLAGS=""
debug_CFLAGS="-g"
#echo "${host_cpu}-${host_os}"
-case "${host_cpu}-${host_os}" in
- i*86-*linux*)
- ext_CFLAGS="-march=i686";;
- i*86-darwin*)
- AC_ARG_ENABLE(universal, [ --enable-universal enable universal binary (Intel Apple only)],
- [is_uni=1], [is_uni=0])
- case $is_uni in
- 1) CFLAGS="-m64"
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM],
- [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"],
- [ext_CFLAGS="-arch i386 -arch ppc"]);;
- 0) CFLAGS="-m64"
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
- esac;;
- *)
- AC_MSG_CHECKING([if gcc accepts -m64])
- CFLAGS="-m64"
- AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])],
- [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);;
-esac
AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
[ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
--- End Message ---
--- Begin Message ---
Source: tophat
Source-Version: 1.4.1-2
We believe that the bug you reported is fixed in the latest version of
tophat, which is due to be installed in the Debian FTP archive:
tophat_1.4.1-2.debian.tar.gz
to main/t/tophat/tophat_1.4.1-2.debian.tar.gz
tophat_1.4.1-2.dsc
to main/t/tophat/tophat_1.4.1-2.dsc
tophat_1.4.1-2_amd64.deb
to main/t/tophat/tophat_1.4.1-2_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 660...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated tophat 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: SHA1
Format: 1.8
Date: Sat, 18 Feb 2012 08:22:50 +0100
Source: tophat
Binary: tophat
Architecture: source amd64
Version: 1.4.1-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
tophat - fast splice junction mapper for RNA-Seq reads
Closes: 660309
Changes:
tophat (1.4.1-2) unstable; urgency=low
.
[ Carlos Borroto ]
* added bowtie as a binary dependency
* suggests cufflinks
.
[ Andreas Tille ]
* debian/control: Added myself to uploaders
* debian/patches/remove_cflag_handling_in_configure.patch: Enable better
support for different architectures (Thanks to Peter Michael Green
<plugw...@p10link.net> for the patch)
Closes: #660309
* debian/upstream: Added references
Checksums-Sha1:
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a7a8844cb5f0452f5c8346404482d2c009d37c5d 6066 tophat_1.4.1-2.debian.tar.gz
306b6452a91a064be7b69dfbc9c1863a20cb8920 590580 tophat_1.4.1-2_amd64.deb
Checksums-Sha256:
6fe98a4dc953c685d442b4467c659539ad23d06d1ca3f0edb0d62f395be2d5a7 1467
tophat_1.4.1-2.dsc
d0c2b2363da39552e46382a87d923fa739ea3e7a1147b09e42adb84553db8c52 6066
tophat_1.4.1-2.debian.tar.gz
888dff1b1447c7027a5db07e7dfe71a2cf4d7dcaced8558269025293538a10bf 590580
tophat_1.4.1-2_amd64.deb
Files:
1875f784f42e233b9b0f719ec07ba1d1 1467 science optional tophat_1.4.1-2.dsc
88ce794402ca8912adc42f03b862fd13 6066 science optional
tophat_1.4.1-2.debian.tar.gz
da95d36c8cfab98119c4ef8d4c656dc6 590580 science optional
tophat_1.4.1-2_amd64.deb
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--- End Message ---
