Your message dated Sat, 08 Dec 2018 06:49:08 +0000
with message-id <[email protected]>
and subject line Bug#889147: fixed in abyss 2.1.5-1
has caused the Debian Bug report #889147,
regarding abyss: PairedDBG_LoadAlgorithm test fails on sparc64 due to strict
alignment violation
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
889147: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=889147
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: abyss
Severity: normal
Tags: patch upstream
Usertags: sparc64
Dear Maintainer,
This package currently FTBFS on sparc64 due to the
PairedDBG_LoadAlgorithm test failing with a SIGBUS. The Kmer.load and
Kmer.storeReverse methods in the Common/Kmer.cpp file cast a uint8_t*
to a size_t* without ensuring the pointer value has the proper
alignment.
To fix this I added an aligned stack allocated buffer and memcpy to
that. Stack allocated is appropriate because the buffer size is
small(32 bytes) and known at compile time.
-- System Information:
Debian Release: buster/sid
APT prefers unreleased
APT policy: (500, 'unreleased'), (500, 'unstable')
Architecture: sparc64
Kernel: Linux 4.14.0-3-sparc64-smp (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--- a/Common/Kmer.cpp
+++ b/Common/Kmer.cpp
@@ -188,9 +188,10 @@
Seq seq;
#if MAX_KMER > 96
# if WORDS_BIGENDIAN
- const size_t *s = reinterpret_cast<const size_t*>(src);
+ size_t buf[Kmer::NUM_BYTES];
+ memcpy(buf, src, Kmer::NUM_BYTES);
size_t *d = reinterpret_cast<size_t*>(&seq + 1);
- copy(s, s + Kmer::NUM_BYTES/sizeof(size_t),
reverse_iterator<size_t*>(d));
+ copy(buf, buf + Kmer::NUM_BYTES/sizeof(size_t),
reverse_iterator<size_t*>(d));
# else
uint8_t *d = reinterpret_cast<uint8_t*>(&seq);
memcpy(d, src, sizeof seq);
@@ -235,9 +236,10 @@
#if MAX_KMER > 96
# if WORDS_BIGENDIAN
const size_t *s = reinterpret_cast<const size_t*>(&seq);
- size_t *d = reinterpret_cast<size_t*>(dest);
+ size_t d[Kmer::NUM_BYTES];
copy(s, s + Kmer::NUM_BYTES/sizeof(size_t),
reverse_iterator<size_t*>(d +
Kmer::NUM_BYTES/sizeof(size_t)));
+ memcpy(dest, d, Kmer::NUM_BYTES);
reverse(dest, dest + Kmer::NUM_BYTES);
# else
memcpy(dest, &seq, Kmer::NUM_BYTES);
--- End Message ---
--- Begin Message ---
Source: abyss
Source-Version: 2.1.5-1
We believe that the bug you reported is fixed in the latest version of
abyss, 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 abyss 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: Sat, 08 Dec 2018 07:24:02 +0100
Source: abyss
Binary: abyss
Architecture: source
Version: 2.1.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Closes: 889147
Changes:
abyss (2.1.5-1) unstable; urgency=medium
.
* Fix strict alignment violation on sparc64 (Thanks to David Matthew Mattli
and James Clarke)
Closes: #889147
* New upstream version
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/copyright
Checksums-Sha1:
fd881a971ff61506b6c1b4a082c5d8c56f666980 2077 abyss_2.1.5-1.dsc
a513525e2249705f20bddfc3a0bdacb61a8ccd13 1063069 abyss_2.1.5.orig.tar.gz
01b1b25e5401c51871e6e39d0727efe37a66f325 757672 abyss_2.1.5-1.debian.tar.xz
Checksums-Sha256:
057c1c96918c458dae42b5eb2edbbca8f572024b39535b3aec1a514ba7a555e8 2077
abyss_2.1.5-1.dsc
cfd6091fa4b762e44e7427a9a710737614d73161b51309952ace202d6d904b50 1063069
abyss_2.1.5.orig.tar.gz
604a1c7338bb91c4a0fff918239ac7f5ba2edbfcd4596c9c56a81afc8f817654 757672
abyss_2.1.5-1.debian.tar.xz
Files:
de83a61a46fb754e13b6dd1ce12ab328 2077 science optional abyss_2.1.5-1.dsc
a716fc1ca89597283e2a5866ac78ff06 1063069 science optional
abyss_2.1.5.orig.tar.gz
ba9d7a546e7a306461a68a6537164ec1 757672 science optional
abyss_2.1.5-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=Yv61
-----END PGP SIGNATURE-----
--- End Message ---
