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);
