Your message dated Mon, 18 May 2015 13:03:47 +0000
with message-id <[email protected]>
and subject line Bug#780409: fixed in abyss 1.5.2-2
has caused the Debian Bug report #780409,
regarding abyss: FTBFS on 32-bit 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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--
780409: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=780409
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: abyss
Version: 1.5.2-1
Severity: normal
Tags: patch
Hi maintainer
Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and
powerpc) in Ubuntu [1].
Previous versions built fine on all architectures.
I found there were a couple of places in the code that was introduced in
version 1.5.2 where size_t data type was used instead of a fixed size
data type.
I was able to get abyss 1.5.2-1 to build on amd64, i386 and armhf with
the attached patch in place and all unit tests passed.
I have no idea where to begin actually testing abyss itself.
Is it worth me uploading abyss with this patch into Ubuntu?
This will at least allow version 1.5.2-1 to migrate from proposed to
release.
Alternatively, is this software useful on a 32-bit system? The other
solution is for me to disable building for these architectures.
Regards
Graham
[1] https://launchpad.net/ubuntu/+source/abyss/1.5.2-1
--- a/Common/StringUtil.h
+++ b/Common/StringUtil.h
@@ -106,7 +106,7 @@
return false;
}
-static inline size_t SIToBytes(std::istringstream& iss)
+static inline unsigned long long SIToBytes(std::istringstream& iss)
{
double size;
std::string units;
@@ -122,7 +122,7 @@
// no units given; clear fail flag
// and assume bytes
iss.clear(std::ios::eofbit);
- return (size_t)ceil(size);
+ return (unsigned long long)ceil(size);
}
if (units.size() > 1) {
@@ -133,22 +133,22 @@
switch(tolower(units[0])) {
case 'k':
- size *= (size_t)1<<10; break;
+ size *= (unsigned long long)1<<10; break;
case 'm':
- size *= (size_t)1<<20; break;
+ size *= (unsigned long long)1<<20; break;
case 'g':
- size *= (size_t)1<<30; break;
+ size *= (unsigned long long)1<<30; break;
case 't':
- size *= (size_t)1<<40; break;
+ size *= (unsigned long long)1<<40; break;
default:
iss.setstate(std::ios::failbit);
return 0;
}
- return (size_t)ceil(size);
+ return (unsigned long long)ceil(size);
}
-static inline size_t SIToBytes(const std::string& str)
+static inline unsigned long long SIToBytes(const std::string& str)
{
std::istringstream iss(str);
return SIToBytes(iss);
--- a/Bloom/Bloom.h
+++ b/Bloom/Bloom.h
@@ -165,10 +165,10 @@
// bloom filter bits
size_t bits = endBitPos - startBitPos + 1;
- size_t bytes = (bits + 7) / 8;
+ unsigned long bytes = (bits + 7) / 8;
char buf[IO_BUFFER_SIZE];
for (size_t i = 0, j = 0; i < bytes;) {
- size_t writeSize = std::min(IO_BUFFER_SIZE, bytes - i);
+ unsigned long writeSize = std::min(IO_BUFFER_SIZE, bytes - i);
for (size_t k = 0; k < writeSize; k++) {
buf[k] = 0;
for (unsigned l = 0; l < 8; l++, j++) {
@@ -270,11 +270,11 @@
size_t offset = header.startBitPos;
size_t bits = header.endBitPos - header.startBitPos + 1;
- size_t bytes = (bits + 7) / 8;
+ unsigned long bytes = (bits + 7) / 8;
char buf[IO_BUFFER_SIZE];
for (size_t i = 0, j = offset; i < bytes; ) {
- size_t readSize = std::min(IO_BUFFER_SIZE, bytes - i);
+ unsigned long readSize = std::min(IO_BUFFER_SIZE, bytes - i);
in.read(buf, readSize);
assert(in);
for (size_t k = 0; k < readSize; k++) {
--- End Message ---
--- Begin Message ---
Source: abyss
Source-Version: 1.5.2-2
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: Mon, 18 May 2015 14:24:21 +0200
Source: abyss
Binary: abyss
Architecture: source amd64
Version: 1.5.2-2
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: 780409
Changes:
abyss (1.5.2-2) unstable; urgency=medium
.
* abyss-fixmate and DistanceEst are expected to be in /usr/bin by sga
* configure was missing ghc -> mention this fact in README.source for
further inspection
* Fix FTBFS on 32-bit architectures (thanks for the patch to Graham
Inggs <[email protected]>)
Closes: #780409
* cme fix dpkg-control
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