Your message dated Sun, 22 Apr 2012 17:03:24 +0000
with message-id <[email protected]>
and subject line Bug#667293: fixed in mustang 3.2.1-3
has caused the Debian Bug report #667293,
regarding mustang: 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.
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--
667293: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=667293
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: mustang
Version: 3.2.1-1
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.
./src/superpose_on_core_2.cpp:578:9: error: 'sleep' 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/mustang_3.2.1-1_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.
[...]
g++ -traditional -Wall -O3 -c ./src/pdb_ripper_2.cpp -o ./obj/pdb_ripper.o
./src/pdb_ripper_2.cpp: In function 'int CHECK_NCHAINS_IN_PDB(char*)':
./src/pdb_ripper_2.cpp:53:6: warning: variable 'chain_id' set but not used
[-Wunused-but-set-variable]
g++ -traditional -Wall -O3 -c ./src/merge_global_local_libs.cpp -o
./obj/merge_global_local_libs.o
g++ -traditional -Wall -O3 -c ./src/ew_2.cpp -o ./obj/ew.o
./src/ew_2.cpp: In function 'void CALCULATE_EDGE_WEIGHTS(int, int, float***)':
./src/ew_2.cpp:217:29: warning: variable 'prev_ROTMAT' set but not used
[-Wunused-but-set-variable]
./src/ew_2.cpp:218:51: warning: variable 'prev_CM_S' set but not used
[-Wunused-but-set-variable]
./src/ew_2.cpp:218:67: warning: variable 'prev_CM_M' set but not used
[-Wunused-but-set-variable]
g++ -traditional -Wall -O3 -c ./src/refine_pairalgn_2.cpp -o
./obj/refine_pairalgn.o
g++ -traditional -Wall -O3 -c ./src/superpose_weightedRMS.cpp -o
./obj/superpose_weightedRMS.o
g++ -traditional -Wall -O3 -c ./src/superpose_2.cpp -o ./obj/superpose_2.o
g++ -traditional -Wall -O3 -c ./src/jacobi.cpp -o ./obj/jacobi.o
g++ -traditional -Wall -O3 -c ./src/3D_manip_functions.cpp -o
./obj/3D_manip_functions.o
./src/3D_manip_functions.cpp: In function 'void coordinate_transformer(float
(*)[500], float (*)[500], int, int, int, int)':
./src/3D_manip_functions.cpp:210:9: warning: variable 'AX' set but not used
[-Wunused-but-set-variable]
g++ -traditional -Wall -O3 -c ./src/extended_lib_gen_3.cpp -o
./obj/extended_lib_gen.o
./src/extended_lib_gen_3.cpp: In function 'void EXTENDED_LIBRARY_GENERATION()':
./src/extended_lib_gen_3.cpp:219:20: warning: variable 'AAA' set but not used
[-Wunused-but-set-variable]
g++ -traditional -Wall -O3 -c ./src/progress_align_3.cpp -o
./obj/progress_align.o
g++ -traditional -Wall -O3 -c ./src/neighbour_joining.cpp -o
./obj/neighbour_joining.o
g++ -traditional -Wall -O3 -c ./src/upgma.cpp -o ./obj/upgma.o
g++ -traditional -Wall -O3 -c ./src/superpose_on_core_2.cpp -o
./obj/superpose_on_core.o
./src/superpose_on_core_2.cpp: In function 'void SUPERPOSE_ON_CORE(char**)':
./src/superpose_on_core_2.cpp:578:9: error: 'sleep' was not declared in this
scope
make[1]: *** [obj/superpose_on_core.o] Error 1
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build: make -j1 returned exit code 2
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: mustang
Source-Version: 3.2.1-3
We believe that the bug you reported is fixed in the latest version of
mustang, which is due to be installed in the Debian FTP archive:
mustang-testdata_3.2.1-3_all.deb
to main/m/mustang/mustang-testdata_3.2.1-3_all.deb
mustang_3.2.1-3.debian.tar.gz
to main/m/mustang/mustang_3.2.1-3.debian.tar.gz
mustang_3.2.1-3.dsc
to main/m/mustang/mustang_3.2.1-3.dsc
mustang_3.2.1-3_amd64.deb
to main/m/mustang/mustang_3.2.1-3_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.
Andreas Tille <[email protected]> (supplier of updated mustang 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: Sun, 22 Apr 2012 18:18:34 +0200
Source: mustang
Binary: mustang mustang-testdata
Architecture: source amd64 all
Version: 3.2.1-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
mustang - multiple structural alignment of proteins
mustang-testdata - multiple structural alignment of proteins, test data
Closes: 667293
Changes:
mustang (3.2.1-3) unstable; urgency=low
.
* debian/upstream:
- Use BibTeX friendly formating of authors
* debian/patches/gcc-4.7.patch: Fix build issue with gcc-4.7
Closes: #667293
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Files:
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--- End Message ---
