Your message dated Wed, 04 Apr 2012 12:02:32 +0000
with message-id <[email protected]>
and subject line Bug#667201: fixed in hhsuite 2.0.13-2
has caused the Debian Bug report #667201,
regarding hhsuite: ftbfs with GCC-4.7
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 this
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--
667201: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=667201
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: hhsuite
Version: 2.0.13-1
Severity: important
Tags: sid wheezy
User: [email protected]
Usertags: ftbfs-gcc-4.7
The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.
hhsearch.C:1374:65: error: 'R_OK' was not declared in this scope
The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/hhsuite_2.0.13-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.
Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html
To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
[...]
make[2]: Entering directory `/«PKGBUILDDIR»/data'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/«PKGBUILDDIR»/data'
make -C src all
make[2]: Entering directory `/«PKGBUILDDIR»/src'
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/aa.cc -o cs/aa.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/application.cc -o cs/application.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/as.cc -o cs/as.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/assert_helpers.cc -o cs/assert_helpers.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/blosum_matrix.cc -o cs/blosum_matrix.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/getopt_pp.cc -o cs/getopt_pp.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 -fopenmp -c cs/log.cc -o cs/log.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 hhblits.C -o hhblits cs/aa.o cs/application.o cs/as.o
cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o -lpthread
-fopenmp -lrt -lffindex
In file included from hhblits.C:263:0:
hhprefilter.C: In function 'void prefilter_db()':
hhprefilter.C:1048:38: warning: capture of variable 'cpu' with non-automatic
storage duration [enabled by default]
hhblits.C:173:5: note: 'int cpu' declared here
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics
-DHH_SSE3 -msse3 hhsearch.C -o hhsearch cs/aa.o cs/application.o cs/as.o
cs/assert_helpers.o cs/blosum_matrix.o cs/getopt_pp.o cs/log.o -lpthread -lrt
hhsearch.C: In function 'int main(int, char**)':
hhsearch.C:1374:65: error: 'R_OK' was not declared in this scope
hhsearch.C:1374:69: error: 'access' was not declared in this scope
hhsearch.C:1387:57: error: 'R_OK' was not declared in this scope
hhsearch.C:1387:61: error: 'access' was not declared in this scope
make[2]: *** [hhsearch] Error 1
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[1]: *** [all] Error 2
dh_auto_build: make -j1 returned exit code 2
make[1]: Leaving directory `/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: hhsuite
Source-Version: 2.0.13-2
We believe that the bug you reported is fixed in the latest version of
hhsuite, which is due to be installed in the Debian FTP archive:
hhsuite-data_2.0.13-2_all.deb
to main/h/hhsuite/hhsuite-data_2.0.13-2_all.deb
hhsuite-dbg_2.0.13-2_amd64.deb
to main/h/hhsuite/hhsuite-dbg_2.0.13-2_amd64.deb
hhsuite_2.0.13-2.debian.tar.gz
to main/h/hhsuite/hhsuite_2.0.13-2.debian.tar.gz
hhsuite_2.0.13-2.dsc
to main/h/hhsuite/hhsuite_2.0.13-2.dsc
hhsuite_2.0.13-2_amd64.deb
to main/h/hhsuite/hhsuite_2.0.13-2_amd64.deb
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.
Laszlo Kajan <[email protected]> (supplier of updated hhsuite 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: 1.8
Date: Wed, 04 Apr 2012 13:45:49 +0200
Source: hhsuite
Binary: hhsuite hhsuite-data hhsuite-dbg
Architecture: source amd64 all
Version: 2.0.13-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Laszlo Kajan <[email protected]>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment
(
hhsuite-dbg - sensitive protein sequence searching based on HMM-HMM alignment (
Closes: 667201
Changes:
hhsuite (2.0.13-2) unstable; urgency=low
.
* [Andreas Tille <[email protected]>]
debian/upstream:
- it is (now) possible to support more than one citation
- more verbose citation information
* [Laszlo Kajan <[email protected]]
Added #include <unistd.h> to src/hhsearch.C in order to fix compilation
issue with g++-4.7. (Closes: #667201)
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Files:
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hhsuite-data_2.0.13-2_all.deb
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hhsuite-dbg_2.0.13-2_amd64.deb
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