Your message dated Sun, 15 Apr 2007 08:32:04 +0000
with message-id <[EMAIL PROTECTED]>
and subject line Bug#417482: fixed in probcons 1.12-1
has caused the attached Bug report 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 I am
talking about this indicates a serious mail system misconfiguration
somewhere. Please contact me immediately.)
Debian bug tracking system administrator
(administrator, Debian Bugs database)
--- Begin Message ---
Package: probcons
Version: 1.11-1
Usertags: ftbfs-gcc-4.3
Tags: patch
Your package fails to build with GCC 4.3. Version 4.3 has not been
released yet but I'm building with a snapshot in order to find errors
and give people an advance warning. In GCC 4.3, the C++ header
dependencies have been cleaned up. The advantage of this is that
programs will compile faster. The downside is that you actually
need to directly #include everything you use (but you really should
do this anyway, otherwise your program won't work with any compiler
other than GCC). Some background of this can be found at
http://gcc.gnu.org/PR28080
You can reproduce this problem with gcc-snapshot (20070326-1 or higher)
from unstable.
> Automatic build of probcons_1.11-1 on em64t by sbuild/amd64 0.53
...
> g++ -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=2 -DVERSION="1.11"
> -funroll-loops -lm -o probcons Main.cc
> In file included from Main.cc:11:
> ProbabilisticModel.h: In member function 'void
> ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&,
> const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const':
> ProbabilisticModel.h:492: warning: suggest parentheses around && within ||
> Main.cc: In function 'bool GetInteger(char*, int*)':
> Main.cc:547: error: 'LONG_MAX' was not declared in this scope
> Main.cc:547: error: 'LONG_MIN' was not declared in this scope
> Main.cc:548: error: 'INT_MIN' was not declared in this scope
> Main.cc:548: error: 'INT_MAX' was not declared in this scope
> make[1]: *** [probcons] Error 1
--- Main.cc~ 2007-04-02 21:12:48.000000000 +0000
+++ Main.cc 2007-04-02 21:12:58.000000000 +0000
@@ -18,6 +18,7 @@
#include <list>
#include <set>
#include <algorithm>
+#include <climits>
#include <cstdio>
#include <cstdlib>
#include <cerrno>
--- Main-RNA.cc~ 2007-04-02 21:13:49.000000000 +0000
+++ Main-RNA.cc 2007-04-02 21:13:56.000000000 +0000
@@ -18,6 +18,7 @@
#include <list>
#include <set>
#include <algorithm>
+#include <climits>
#include <cstdio>
#include <cstdlib>
#include <cerrno>
--- MakeGnuPlot.cc~ 2007-04-02 21:15:34.000000000 +0000
+++ MakeGnuPlot.cc 2007-04-02 21:15:39.000000000 +0000
@@ -2,6 +2,7 @@
// MakeGnuPlot.cc
/////////////////////////////////////////////////////////////////
+#include <cstdlib>
#include <iostream>
#include <fstream>
--
Martin Michlmayr
http://www.cyrius.com/
--- End Message ---
--- Begin Message ---
Source: probcons
Source-Version: 1.12-1
We believe that the bug you reported is fixed in the latest version of
probcons, which is due to be installed in the Debian FTP archive:
probcons-extra_1.12-1_i386.deb
to pool/main/p/probcons/probcons-extra_1.12-1_i386.deb
probcons_1.12-1.diff.gz
to pool/main/p/probcons/probcons_1.12-1.diff.gz
probcons_1.12-1.dsc
to pool/main/p/probcons/probcons_1.12-1.dsc
probcons_1.12-1_i386.deb
to pool/main/p/probcons/probcons_1.12-1_i386.deb
probcons_1.12.orig.tar.gz
to pool/main/p/probcons/probcons_1.12.orig.tar.gz
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.
Charles Plessy <[EMAIL PROTECTED]> (supplier of updated probcons 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: SHA1
Format: 1.7
Date: Wed, 4 Apr 2007 09:56:46 +0900
Source: probcons
Binary: probcons-extra probcons
Architecture: source i386
Version: 1.12-1
Distribution: unstable
Urgency: low
Maintainer: Debian-Med Packaging Team <[EMAIL PROTECTED]>
Changed-By: Charles Plessy <[EMAIL PROTECTED]>
Description:
probcons - PROBabilistic CONSistency-based multiple sequence alignment
probcons-extra - Extra programs from the probcons package
Closes: 417482
Changes:
probcons (1.12-1) unstable; urgency=low
.
* New upstream release, buildable with gcc 4.3 (Closes: #417482)
* Add Subversion repository URL to debian/control.
* Including /usr/share/dpatch/dpatch.make in debian/rules.
* Updated manpages using the template of docbook-xsl 1.71.0.dfsg.1-1.1.
Files:
19d0827972c5ad0e6d0f700c2568e87a 869 science optional probcons_1.12-1.dsc
a658e24b07aaa9e8194317345133ac9d 43200 science optional
probcons_1.12.orig.tar.gz
6c4f64bbbe3256b6e3f10c374586124a 18546 science optional probcons_1.12-1.diff.gz
16829eb01515aa135a17a42acc6cd0d2 157946 science optional
probcons_1.12-1_i386.deb
718ce3906911ff5f7db512eeb30d83b2 48566 science extra
probcons-extra_1.12-1_i386.deb
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.6 (GNU/Linux)
iD8DBQFGIdlvipBneRiAKDwRAnTIAJ9onqRfHd3B5PYrin09hrcI5EnqlQCgqLOd
obUzSBf/W3y9LoffxP05Sq4=
=XD60
-----END PGP SIGNATURE-----
--- End Message ---
