Your message dated Sun, 11 Dec 2016 15:48:21 +0000
with message-id <[email protected]>
and subject line Bug#847574: fixed in abyss 2.0.2-2
has caused the Debian Bug report #847574,
regarding abyss: FTBFS on mips and other big-endian architectures
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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847574: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847574
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: abyss
Version: 2.0.2-1
Severity: important
Tags: sid + patch
Justification: FTBFS
User: [email protected]
Usertags: mips-patch
Forwarded: https://github.com/bcgsc/abyss/pull/139
Hi,
Package abyss FTBFS on mips and other big-endian architectures with followind
error:
> Kmer.cpp: In function 'Seq load(const uint8_t*)':
> Kmer.cpp:193:14: error: 'SEQ_WORDS' was not declared in this scope
> copy(s, s + SEQ_WORDS, reverse_iterator<uint64_t*>(d));
> ^~~~~~~~~
> Kmer.cpp: In function 'void storeReverse(uint8_t*, Seq)':
> Kmer.cpp:239:14: error: 'SEQ_WORDS' was not declared in this scope
> copy(s, s + SEQ_WORDS,
^~~~~~~~~
build log:
https://buildd.debian.org/status/fetch.php?pkg=abyss&arch=mips&ver=2.0.2-1&stamp=1478005755
After adding the missing SEQ_WORDS define for big-endian the build passed,
but the following tests failed:
> FAIL: common_kmer
> FAIL: BloomFilter
> FAIL: Konnector_DBGBloomAlgorithms
> FAIL: Konnector_konnector
> FAIL: PairedDBG_LoadAlgorithm
> FAIL: PairedDBG_KmerPair
Comparison of values returned by load and storeReverse methods between mipsel
and mips showed that the data contained in variable seq (type of std::bitset) is
in wrong byte order.
Conversion of arrays bigger than architecture's word size into bitset is working
by going sequentially through memory and converting the values into binary word
by word. It does not care about endianness.
So, on 32bit big-endian architectures the conversion must be done in 32bit
chunks and every chunk must be copied in reverse byte order.
The existing code in load and storeReverse methods was suitable for 64bit
big-endian architectures, it copies 64bit chunks of the array in reverse order.
The attached patch fixes the conversion of array to bitset (and vice versa) by
changing the uint64_t type to size_t in load and storeReverse methods.
This enables to use the same code on 32 and 64 bit architectures.
With this patch I was able to build abyss successfully on mips. This patch was
successfully tested on 64bit big-endian mips too.
Thanks,
Daniel
--- abyss-2.0.2.orig/Common/Kmer.cpp
+++ abyss-2.0.2/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);
--- End Message ---
--- Begin Message ---
Source: abyss
Source-Version: 2.0.2-2
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: Sun, 11 Dec 2016 14:24:34 +0100
Source: abyss
Binary: abyss
Architecture: source
Version: 2.0.2-2
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: 847574
Changes:
abyss (2.0.2-2) unstable; urgency=medium
.
* FTBFS on mips and other big-endian architectures (Thanks for the patch
to Daniel Knezevic <[email protected]>)
Closes: #847574
* debhelper 10
* d/watch: version=4
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