[med-svn] [abyss] 01/04: FTBFS on mips and other big-endian architectures

[Andreas Tille]

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tille pushed a commit to branch master
in repository abyss.

commit 465c10a403e09b30586f33f45398c0b9593f8eb4
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 11 14:22:22 2016 +0100

    FTBFS on mips and other big-endian architectures
---
 debian/changelog                |  8 ++++++++
 debian/patches/big_endian.patch | 35 +++++++++++++++++++++++++++++++++++
 debian/patches/series           |  1 +
 3 files changed, 44 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 3f73077..9fd85b9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+abyss (2.0.2-2) UNRELEASED; urgency=medium
+
+  * FTBFS on mips and other big-endian architectures (Thanks for the patch
+    to Daniel Knezevic <Daniel.Knezevic at imgtec.com>)
+    Closes: #847574
+
+ -- Andreas Tille <tille at debian.org>  Sun, 11 Dec 2016 14:21:23 +0100
+
 abyss (2.0.2-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/patches/big_endian.patch b/debian/patches/big_endian.patch
new file mode 100644
index 0000000..ef65295
--- /dev/null
+++ b/debian/patches/big_endian.patch
@@ -0,0 +1,35 @@
+Author: Daniel Knezevic <Daniel.Knezevic at imgtec.com>
+Last-Update: Fri, 9 Dec 2016 15:27:02 UTC
+Bug-Debian: https://bugs.debian.org/847574
+Description: Fix FTBFS on mips and other big-endian architectures
+
+--- a/Common/Kmer.cpp
++++ b/Common/Kmer.cpp
+@@ -188,9 +188,9 @@ static Seq load(const uint8_t *src)
+ 	Seq seq;
+ #if MAX_KMER > 96
+ # if WORDS_BIGENDIAN
+-	const uint64_t *s = reinterpret_cast<const uint64_t*>(src);
+-	uint64_t *d = reinterpret_cast<uint64_t*>(&seq + 1);
+-	copy(s, s + SEQ_WORDS, reverse_iterator<uint64_t*>(d));
++	const size_t *s = reinterpret_cast<const size_t*>(src);
++	size_t *d = reinterpret_cast<size_t*>(&seq + 1);
++	copy(s, s + 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);
+@@ -234,10 +234,10 @@ static void storeReverse(uint8_t *dest,
+ {
+ #if MAX_KMER > 96
+ # if WORDS_BIGENDIAN
+-	const uint64_t *s = reinterpret_cast<const uint64_t*>(&seq);
+-	uint64_t *d = reinterpret_cast<uint64_t*>(dest);
+-	copy(s, s + SEQ_WORDS,
+-			reverse_iterator<uint64_t*>(d + SEQ_WORDS));
++	const size_t *s = reinterpret_cast<const size_t*>(&seq);
++	size_t *d = reinterpret_cast<size_t*>(dest);
++	copy(s, s + Kmer::NUM_BYTES/sizeof(size_t),
++			reverse_iterator<size_t*>(d +  Kmer::NUM_BYTES/sizeof(size_t)));
+ 	reverse(dest, dest + Kmer::NUM_BYTES);
+ # else
+ 	memcpy(dest, &seq, Kmer::NUM_BYTES);
diff --git a/debian/patches/series b/debian/patches/series
index 55be171..6fcb267 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ abyss-pe.patch
 # gtest.patch
 abyss-32-bit.patch
 fix_bash_script.patch
+big_endian.patch

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