Your message dated Fri, 05 Aug 2016 22:37:16 +0000
with message-id <e1bvnjw-0001hx...@franck.debian.org>
and subject line Bug#831151: fixed in nanopolish 0.4.0-2
has caused the Debian Bug report #831151,
regarding nanopolish: FTBFS with GCC 6:
src/common/nanopolish_variant.cpp:27:79: error: no matching function for call
to 'max(int, __gnu_cxx::__enable_if<true, double>::__type)'
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.)
--
831151: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=831151
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: nanopolish
Version: 0.4.0-1
Severity: serious
Tags: stretch sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20160713 qa-ftbfs
Justification: FTBFS with GCC 6 on amd64
Hi,
During a rebuild of all packages in sid using the gcc-defaults package
available in experimental to make GCC default to version 6, your package failed
to build on amd64. For more information about GCC 6 and Stretch, see:
- https://wiki.debian.org/GCC6
- https://lists.debian.org/debian-devel-announce/2016/06/msg00007.html
Relevant part (hopefully):
> g++ -o src/common/nanopolish_variant.o -c -g -O2 -fstack-protector-strong
> -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time
> -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src
> -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC
> src/common/nanopolish_variant.cpp
> src/common/nanopolish_variant.cpp: In function 'std::vector<Variant>
> extract_variants(const string&, const string&)':
> src/common/nanopolish_variant.cpp:27:79: error: no matching function for call
> to 'max(int, __gnu_cxx::__enable_if<true, double>::__type)'
> par.band_width = std::max(20, abs(reference.size() - haplotype.size()) *
> 2);
>
> ^
> In file included from /usr/include/c++/6/algorithm:61:0,
> from src/common/nanopolish_variant.cpp:8:
> /usr/include/c++/6/bits/stl_algobase.h:219:5: note: candidate: template<class
> _Tp> const _Tp& std::max(const _Tp&, const _Tp&)
> max(const _Tp& __a, const _Tp& __b)
> ^~~
> /usr/include/c++/6/bits/stl_algobase.h:219:5: note: template argument
> deduction/substitution failed:
> src/common/nanopolish_variant.cpp:27:79: note: deduced conflicting types
> for parameter 'const _Tp' ('int' and '__gnu_cxx::__enable_if<true,
> double>::__type {aka double}')
> par.band_width = std::max(20, abs(reference.size() - haplotype.size()) *
> 2);
>
> ^
> In file included from /usr/include/c++/6/algorithm:61:0,
> from src/common/nanopolish_variant.cpp:8:
> /usr/include/c++/6/bits/stl_algobase.h:265:5: note: candidate: template<class
> _Tp, class _Compare> const _Tp& std::max(const _Tp&, const _Tp&, _Compare)
> max(const _Tp& __a, const _Tp& __b, _Compare __comp)
> ^~~
> /usr/include/c++/6/bits/stl_algobase.h:265:5: note: template argument
> deduction/substitution failed:
> src/common/nanopolish_variant.cpp:27:79: note: deduced conflicting types
> for parameter 'const _Tp' ('int' and '__gnu_cxx::__enable_if<true,
> double>::__type {aka double}')
> par.band_width = std::max(20, abs(reference.size() - haplotype.size()) *
> 2);
>
> ^
> In file included from /usr/include/c++/6/algorithm:62:0,
> from src/common/nanopolish_variant.cpp:8:
> /usr/include/c++/6/bits/stl_algo.h:3459:5: note: candidate: template<class
> _Tp> _Tp std::max(std::initializer_list<_Tp>)
> max(initializer_list<_Tp> __l)
> ^~~
> /usr/include/c++/6/bits/stl_algo.h:3459:5: note: template argument
> deduction/substitution failed:
> src/common/nanopolish_variant.cpp:27:79: note: mismatched types
> 'std::initializer_list<_Tp>' and 'int'
> par.band_width = std::max(20, abs(reference.size() - haplotype.size()) *
> 2);
>
> ^
> In file included from /usr/include/c++/6/algorithm:62:0,
> from src/common/nanopolish_variant.cpp:8:
> /usr/include/c++/6/bits/stl_algo.h:3465:5: note: candidate: template<class
> _Tp, class _Compare> _Tp std::max(std::initializer_list<_Tp>, _Compare)
> max(initializer_list<_Tp> __l, _Compare __comp)
> ^~~
> /usr/include/c++/6/bits/stl_algo.h:3465:5: note: template argument
> deduction/substitution failed:
> src/common/nanopolish_variant.cpp:27:79: note: mismatched types
> 'std::initializer_list<_Tp>' and 'int'
> par.band_width = std::max(20, abs(reference.size() - haplotype.size()) *
> 2);
>
> ^
> make[1]: *** [src/common/nanopolish_variant.o] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2016/07/13/nanopolish_0.4.0-1_unstable_gcc6.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
Source: nanopolish
Source-Version: 0.4.0-2
We believe that the bug you reported is fixed in the latest version of
nanopolish, 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 831...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sascha Steinbiss <sa...@debian.org> (supplier of updated nanopolish 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 05 Aug 2016 20:51:28 +0000
Source: nanopolish
Binary: nanopolish
Architecture: source amd64
Version: 0.4.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Sascha Steinbiss <sa...@debian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Closes: 831151
Changes:
nanopolish (0.4.0-2) unstable; urgency=medium
.
* Team upload.
* Fix FTBFS with GCC 6 (Closes: #831151)
* Enable full hardening.
* Fix Vcs-Browser link.
* Use secure Vcs-*.
* Bump Standards-Version.
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Files:
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