Your message dated Mon, 28 Aug 2017 21:21:53 +0000
with message-id <[email protected]>
and subject line Bug#853656: fixed in sga 0.10.15-3
has caused the Debian Bug report #853656,
regarding sga: ftbfs with GCC-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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immediately.)
--
853656: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853656
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:sga
Version: 0.10.15-2
Severity: normal
Tags: sid buster
User: [email protected]
Usertags: ftbfs-gcc-7
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/sga_0.10.15-2_unstable_gcc7.log
The last lines of the build log are at the end of this report.
To build with GCC 7, either set CC=gcc-7 CXX=g++-7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-7/porting_to.html
[...]
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall
-Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-MultiAlignment.o
`test -f 'MultiAlignment.cpp' || echo './'`MultiAlignment.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall
-Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-StdAlnTools.o
`test -f 'StdAlnTools.cpp' || echo './'`StdAlnTools.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall
-Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-VCFUtil.o `test -f
'VCFUtil.cpp' || echo './'`VCFUtil.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall
-Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-QualityTable.o
`test -f 'QualityTable.cpp' || echo './'`QualityTable.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall
-Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-BloomFilter.o
`test -f 'BloomFilter.cpp' || echo './'`BloomFilter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../Bigraph -I../Thirdparty -Wdate-time
-D_FORTIFY_SOURCE=2 -fopenmp -I/usr//include -I/usr//include/bamtools -Wall
-Wextra -Wno-unknown-pragmas -std=c++98 -O3 -c -o libutil_a-VariantIndex.o
`test -f 'VariantIndex.cpp' || echo './'`VariantIndex.cpp
VariantIndex.cpp: In member function 'VariantRecordVector
VariantIndex::getNearVariants(const string&, int, int) const':
VariantIndex.cpp:89:46: error: call of overloaded 'abs(long unsigned int)' is
ambiguous
if(abs(record.position - position) < distance)
^
In file included from /usr/include/c++/7/cstdlib:75:0,
from /usr/include/c++/7/bits/stl_algo.h:59,
from /usr/include/c++/7/algorithm:62,
from VariantIndex.cpp:11:
/usr/include/stdlib.h:735:12: note: candidate: int abs(int)
extern int abs (int __x) __THROW __attribute__ ((__const__)) __wur;
^~~
In file included from /usr/include/c++/7/cstdlib:77:0,
from /usr/include/c++/7/bits/stl_algo.h:59,
from /usr/include/c++/7/algorithm:62,
from VariantIndex.cpp:11:
/usr/include/c++/7/bits/std_abs.h:56:3: note: candidate: long int std::abs(long
int)
abs(long __i) { return __builtin_labs(__i); }
^~~
/usr/include/c++/7/bits/std_abs.h:61:3: note: candidate: long long int
std::abs(long long int)
abs(long long __x) { return __builtin_llabs (__x); }
^~~
/usr/include/c++/7/bits/std_abs.h:70:3: note: candidate: double std::abs(double)
abs(double __x)
^~~
/usr/include/c++/7/bits/std_abs.h:74:3: note: candidate: float std::abs(float)
abs(float __x)
^~~
/usr/include/c++/7/bits/std_abs.h:78:3: note: candidate: long double
std::abs(long double)
abs(long double __x)
^~~
Makefile:806: recipe for target 'libutil_a-VariantIndex.o' failed
make[3]: *** [libutil_a-VariantIndex.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/Util'
Makefile:359: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Makefile:300: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: make -j64 returned exit code 2
debian/rules:12: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
--- End Message ---
--- Begin Message ---
Source: sga
Source-Version: 0.10.15-3
We believe that the bug you reported is fixed in the latest version of
sga, 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 sga 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, 28 Aug 2017 21:36:06 +0200
Source: sga
Binary: sga
Architecture: source amd64
Version: 0.10.15-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
sga - de novo genome assembler that uses string graphs
Closes: 853656
Changes:
sga (0.10.15-3) unstable; urgency=medium
.
* Standards-Version: 4.1.0 (no changes needed)
* abs() requires int arguments
Closes: #853656
* Avoid privacy breaching links
* d/rules: do not parse d/changelog
* hardening=+all
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