Package: seqan2
Version: 2.4.0+dfsg-8
Followup-For: Bug #892223
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu disco ubuntu-patch
Hello,
Unaligned access also affects armhf in certain circumstances (such as when
running on an arm64 kernel), which means this build failure was also
reproducible on armhf in Ubuntu:
https://launchpad.net/ubuntu/+source/seqan2/2.4.0+dfsg-8ubuntu1/+build/15588212
What I don't know is why the sparc64 test failures in Debian are a superset
of those on armhf in Ubuntu, or why the tests fail with a segfault on
sparc64 instead of the expected sigbus.
Regardless, I think the attached patch is worth applying in Debian (and
upstream); it may fix the sparc64 build failure, or if it doesn't, it should
be a partial fix.
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer https://www.debian.org/
slanga...@ubuntu.com vor...@debian.org
diff -Nru seqan2-2.4.0+dfsg/debian/control seqan2-2.4.0+dfsg/debian/control
--- seqan2-2.4.0+dfsg/debian/control 2018-05-15 11:19:57.000000000 -0700
+++ seqan2-2.4.0+dfsg/debian/control 2018-12-04 01:06:20.000000000 -0800
@@ -1,6 +1,5 @@
Source: seqan2
-Maintainer: Ubuntu Developers <ubuntu-devel-disc...@lists.ubuntu.com>
-XSBC-Original-Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
+Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Uploaders: Andreas Tille <ti...@debian.org>,
Michael R. Crusoe <michael.cru...@gmail.com>,
Kevin Murray <s...@kdmurray.id.au>
diff -Nru seqan2-2.4.0+dfsg/debian/patches/no-unaligned-access.patch
seqan2-2.4.0+dfsg/debian/patches/no-unaligned-access.patch
--- seqan2-2.4.0+dfsg/debian/patches/no-unaligned-access.patch 1969-12-31
16:00:00.000000000 -0800
+++ seqan2-2.4.0+dfsg/debian/patches/no-unaligned-access.patch 2018-12-04
01:06:20.000000000 -0800
@@ -0,0 +1,22 @@
+Description: use alignment-safe buffer handling.
+ Currently we are using assignment to copy the contents of a variable of
+ arbitrary type into a buffer, but this is not portable because the buffer
+ address may not be aligned. Use memcpy() instead, which should be
+ comparable performance ut alignment-safe.
+Author: Steve Langasek <steve.langa...@ubuntu.com>
+Bug-Debian: https://bugs.debian.org/892223
+
+Index: seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h
+===================================================================
+--- seqan2-2.4.0+dfsg.orig/include/seqan/basic/basic_stream.h
++++ seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h
+@@ -1200,7 +1200,8 @@
+ inline void
+ appendRawPodImpl(TTargetValue * &ptr, TValue const & val)
+ {
+- *reinterpret_cast<TValue* &>(ptr)++ = val;
++ std::memcpy(ptr, &val, sizeof(TValue));
++ ptr += sizeof(TValue);
+ }
+
+ template <typename TTarget, typename TValue>
diff -Nru seqan2-2.4.0+dfsg/debian/patches/series
seqan2-2.4.0+dfsg/debian/patches/series
--- seqan2-2.4.0+dfsg/debian/patches/series 2018-04-04 08:51:54.000000000
-0700
+++ seqan2-2.4.0+dfsg/debian/patches/series 2018-12-04 00:58:54.000000000
-0800
@@ -6,3 +6,4 @@
install_fiona_illumina
ctdVersion.patch
fix_manpage_formatting.patch
+no-unaligned-access.patch
