Bug#831208: marked as done (dindel: FTBFS with GCC 6: DInDel.hpp:145:229: error: template argument 1 is invalid)

[Debian Bug Tracking System]

Your message dated Wed, 03 Aug 2016 18:21:07 +0000
with message-id <e1bv0mx-0001lz...@franck.debian.org>
and subject line Bug#831208: fixed in dindel 1.01+dfsg-2
has caused the Debian Bug report #831208,
regarding dindel: FTBFS with GCC 6: DInDel.hpp:145:229: error: template 
argument 1 is invalid
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
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
831208: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=831208
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: dindel
Version: 1.01+dfsg-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++ -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security 
> -I/usr/include/samtools -I/usr/include/seqan -I./  -Wno-deprecated  -O3  
> -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -D_IOLIB=2 -DMINREADS=2 -DDINDEL  -c 
> -o DInDel.o DInDel.cpp
> In file included from DInDel.cpp:29:0:
> DInDel.hpp:145:229: error: template argument 1 is invalid
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                                                                          ^
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:231: error: template argument 2 is invalid
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                                                                            ^
> DInDel.hpp:145:231: error: template argument 4 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                                                                          ^
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:231: error: template argument 2 is invalid
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                                                                            ^
> DInDel.hpp:145:231: error: template argument 4 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                                                                          ^
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:229: error: template argument 1 is invalid
> DInDel.hpp:145:229: error: template argument 2 is invalid
> DInDel.hpp:145:231: error: template argument 2 is invalid
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                                                                            ^
> DInDel.hpp:145:231: error: template argument 4 is invalid
> DInDel.hpp:145:175: error: 'map' is not a type
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                    ^~~
> DInDel.hpp:145:179: error: expected ',' or '...' before '<' token
>   void estimateHaplotypeFrequenciesPosterior(const vector<Haplotype> & haps, 
> const vector<Read> & reads, const vector<vector<MLAlignment> > & liks, 
> vector<double> & hapFreqs, map <int, vector<tuple<AlignedVariant, 
> double,double> > > & posteriors, uint32_t pos, uint32_t leftPos, ostream & 
> glfOutput);
>                                                                               
>                                                                               
>                        ^
> DInDel.cpp: In member function 'void 
> DetInDel::empiricalDistributionMethod(int, const std::vector<Read>&, 
> uint32_t, uint32_t, uint32_t, const AlignedCandidates&, OutputData&, 
> OutputData&)':
> DInDel.cpp:413:59: error: template argument 1 is invalid
>     map <int, vector<tuple<AlignedVariant, double, double> > > posteriors;
>                                                            ^
> DInDel.cpp:413:59: error: template argument 2 is invalid
> DInDel.cpp:413:61: error: template argument 2 is invalid
>     map <int, vector<tuple<AlignedVariant, double, double> > > posteriors;
>                                                              ^
> DInDel.cpp:413:61: error: template argument 4 is invalid
> DInDel.cpp:544:59: error: template argument 1 is invalid
>     map <int, vector<tuple<AlignedVariant, double, double> > > posteriors;
>                                                            ^
> DInDel.cpp:544:59: error: template argument 2 is invalid
> DInDel.cpp:544:61: error: template argument 2 is invalid
>     map <int, vector<tuple<AlignedVariant, double, double> > > posteriors;
>                                                              ^
> DInDel.cpp:544:61: error: template argument 4 is invalid
> DInDel.cpp:525:31: warning: ignoring return value of 'int system(const 
> char*)', declared with attribute warn_unused_result [-Wunused-result]
>       system(cmd.str().c_str());
>                                ^
> DInDel.cpp:629:31: warning: ignoring return value of 'int system(const 
> char*)', declared with attribute warn_unused_result [-Wunused-result]
>       system(cmd.str().c_str());
>                                ^
> make[1]: *** [DInDel.o] Error 1

The full build log is available from:
   
http://people.debian.org/~lucas/logs/2016/07/13/dindel_1.01+dfsg-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: dindel
Source-Version: 1.01+dfsg-2

We believe that the bug you reported is fixed in the latest version of
dindel, 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 dindel 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: Wed, 03 Aug 2016 17:35:20 +0000
Source: dindel
Binary: dindel
Architecture: source amd64
Version: 1.01+dfsg-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:
 dindel     - determines indel calls from short-read data
Closes: 831208
Changes:
 dindel (1.01+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Fix FTBFS with GCC 6.
     Closes: #831208
Checksums-Sha1:
 4980777abc3feae5d93b73c3e6d91940f878d8e9 2079 dindel_1.01+dfsg-2.dsc
 8760877fd4c0f414a2cadfa45bd0079a9221a93e 6568 dindel_1.01+dfsg-2.debian.tar.xz
 fd956796e4e7e49714afb1cd9839932b6d0e580f 3109770 
dindel-dbgsym_1.01+dfsg-2_amd64.deb
 d2b7e4cd94a53a282099c119f4487affd6734029 348160 dindel_1.01+dfsg-2_amd64.deb
Checksums-Sha256:
 2f44a2e9d7c2256d35b4c87f6e5e750f0bc9a3bfe802aa78f06d7db326bd0842 2079 
dindel_1.01+dfsg-2.dsc
 59dcf80635d6d1272af10db4be373fef211f0176982e1f083ee1c894ba611b04 6568 
dindel_1.01+dfsg-2.debian.tar.xz
 555f84490474b5261474fd0ee365c6d1f5848c9490d2869b537a2c2ca19c6a98 3109770 
dindel-dbgsym_1.01+dfsg-2_amd64.deb
 06d1dcf0999a3307b65e34e06c1c63ebf5eaeedec40c44d4b399c672177f7d23 348160 
dindel_1.01+dfsg-2_amd64.deb
Files:
 deef70a9892504aef84471055f5c0f22 2079 science optional dindel_1.01+dfsg-2.dsc
 8df9b75e27fb57fdc8b591d82b97c7d0 6568 science optional 
dindel_1.01+dfsg-2.debian.tar.xz
 938cdde65c83a37788b97b1b77c25943 3109770 debug extra 
dindel-dbgsym_1.01+dfsg-2_amd64.deb
 97af9af9ee5a7b2a0b70c1aa40929317 348160 science optional 
dindel_1.01+dfsg-2_amd64.deb

-----BEGIN PGP SIGNATURE-----
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=Sg70
-----END PGP SIGNATURE-----

--- End Message ---