Your message dated Fri, 14 Oct 2016 19:33:38 +0000
with message-id <e1bv8ec-00055q...@franck.debian.org>
and subject line Bug#840775: fixed in bowtie 1.1.2-6
has caused the Debian Bug report #840775,
regarding bowtie: enable some more 64-bit arches
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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--
840775: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=840775
Debian Bug Tracking System
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--- Begin Message ---
Source: bowtie
Version: 1.1.2-5
Severity: wishlist
Tags: patch
Hi,
I've attached a patch adding support for all the other 64-bit arches
which have Debian ports.
Instead of listing them all in the Makefile, I invoked gcc to ask if it
was using 64-bit pointers (using __LP64__). This is important on some
arches (like mips) since the 32-bit mips buildds run 64-bit kernels and
running "uname -m" gives "mips64".
Tested on mips64el.
Thanks,
James
diff -Nru bowtie-1.1.2/debian/control bowtie-1.1.2/debian/control
--- bowtie-1.1.2/debian/control 2016-05-25 23:44:22.000000000 +0100
+++ bowtie-1.1.2/debian/control 2016-10-14 14:47:00.000000000 +0100
@@ -15,7 +15,7 @@
Homepage: http://bowtie-bio.sourceforge.net/
Package: bowtie
-Architecture: amd64 kfreebsd-amd64 arm64 ppc64el
+Architecture: alpha any-amd64 arm64 mips64el ppc64 ppc64el s390x sparc64
Depends: ${shlibs:Depends},
${misc:Depends},
python
diff -Nru bowtie-1.1.2/debian/patches/gcc-64bit.patch bowtie-1.1.2/debian/patches/gcc-64bit.patch
--- bowtie-1.1.2/debian/patches/gcc-64bit.patch 1970-01-01 01:00:00.000000000 +0100
+++ bowtie-1.1.2/debian/patches/gcc-64bit.patch 2016-10-14 14:47:00.000000000 +0100
@@ -0,0 +1,23 @@
+Description: Use gcc to determine if an arch is 64-bit
+ uname -m is misleading when determining if an arch is 64-bit or not
+ - It indicates the _build_ machine's processor which may not be the same as the
+ processor the code is being built for (cross compiling).
+ - It fails if a 32-bit compiler is used on a 64-bit cpu (eg build i386 packages
+ on x86_64). This is common on the mips buildds.
+ Therefore ask GCC if this architecture is 64-bit. Using __LP64__ is the easiest
+ method, but is not portable and probably only works with GCC and Clang
+ unfortunatly.
+Author: James Cowgill <jcowg...@debian.org>
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/Makefile
++++ b/Makefile
+@@ -125,7 +125,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
+ VERSION = $(shell cat VERSION)
+
+ BITS=32
+-ifneq (,$(filter $(shell uname -m), aarch64 ppc64le x86_64))
++ifeq (1,$(shell echo __LP64__ | $(CC) -P -E -))
+ BITS=64
+ endif
+ # msys will always be 32 bit so look at the cpu arch instead.
diff -Nru bowtie-1.1.2/debian/patches/series bowtie-1.1.2/debian/patches/series
--- bowtie-1.1.2/debian/patches/series 2016-05-25 23:03:35.000000000 +0100
+++ bowtie-1.1.2/debian/patches/series 2016-10-14 14:47:00.000000000 +0100
@@ -12,3 +12,4 @@
enable_arm64.patch
spelling.patch
reproducible.patch
+gcc-64bit.patch
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: bowtie
Source-Version: 1.1.2-6
We believe that the bug you reported is fixed in the latest version of
bowtie, 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 840...@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 bowtie 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...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 14 Oct 2016 20:53:17 +0200
Source: bowtie
Binary: bowtie bowtie-examples
Architecture: source
Version: 1.1.2-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
bowtie - Ultrafast memory-efficient short read aligner
bowtie-examples - Examples for bowtie, the ultrafast memory-efficient short
read al
Closes: 840775
Changes:
bowtie (1.1.2-6) unstable; urgency=medium
.
* Enable build on all 64bit architectures (thanks for the patch to James
Cowgill <jcowg...@debian.org>)
Closes: #840775
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