Debian Bug report logs - #811644
FTBFS with GCC 6: cannot convert x to y

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Martin Michlmayr <tbm@hpe.com>

To: submit@bugs.debian.org

Subject: FTBFS with GCC 6: cannot convert x to y

Date: Tue, 19 Jan 2016 16:34:06 -0800

Package: idba
Version: 1.1.2-1
Severity: important
User: debian-gcc@lists.debian.org
Usertags: ftbfs-gcc-6 gcc-6-cannot-convert

This package fails to build with GCC 6.  GCC 6 has not been released
yet, but it's expected that GCC 6 will become the default compiler for
stretch.

Note that only the first error is reported; there might be more.  You
can find a snapshot of GCC 6 in experimental.  To build with GCC 6,
you can set CC=gcc-6 CXX=g++-6 explicitly.

> sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
...
> g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
> ../src/sequence/sequence_reader.cpp: In member function 'virtual bool FastaReader::ReadRecord(Sequence&, std::__cxx11::string&, std::__cxx11::string&)':
> ../src/sequence/sequence_reader.cpp:50:40: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
>      return ReadFasta(*is_, seq, comment);
>                                         ^
> 
> ../src/sequence/sequence_reader.cpp: In member function 'virtual bool FastqReader::ReadRecord(Sequence&, std::__cxx11::string&, std::__cxx11::string&)':
> ../src/sequence/sequence_reader.cpp:55:49: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
>      return ReadFastq(*is_, seq, comment, quality);
>                                                  ^
> 
> Makefile:441: recipe for target 'sequence_reader.o' failed

-- 
Martin Michlmayr
Linux for HPE Helion, Hewlett Packard Enterprise

Message #10 received at submit@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@an3as.eu>

To: Yu Peng <ypeng@cs.hku.hk>, 811644@bugs.debian.org

Cc: submit@bugs.debian.org

Subject: Re: Bug#811644: FTBFS with GCC 6: cannot convert x to y

Date: Wed, 20 Jan 2016 09:43:23 +0100

Hi,

I just want to inform you that idba does not build with GCC 6 since
there are obviously some stricter type checkings done.  Please let
me know if you have some trouble to fix this.

Kind regards and thanks for providing idba as Free Software

      Andreas.

On Tue, Jan 19, 2016 at 04:34:06PM -0800, Martin Michlmayr wrote:
> Package: idba
> Version: 1.1.2-1
> Severity: important
> User: debian-gcc@lists.debian.org
> Usertags: ftbfs-gcc-6 gcc-6-cannot-convert
> 
> This package fails to build with GCC 6.  GCC 6 has not been released
> yet, but it's expected that GCC 6 will become the default compiler for
> stretch.
> 
> Note that only the first error is reported; there might be more.  You
> can find a snapshot of GCC 6 in experimental.  To build with GCC 6,
> you can set CC=gcc-6 CXX=g++-6 explicitly.
> 
> > sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux
> ...
> > g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
> > ../src/sequence/sequence_reader.cpp: In member function 'virtual bool FastaReader::ReadRecord(Sequence&, std::__cxx11::string&, std::__cxx11::string&)':
> > ../src/sequence/sequence_reader.cpp:50:40: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
> >      return ReadFasta(*is_, seq, comment);
> >                                         ^
> > 
> > ../src/sequence/sequence_reader.cpp: In member function 'virtual bool FastqReader::ReadRecord(Sequence&, std::__cxx11::string&, std::__cxx11::string&)':
> > ../src/sequence/sequence_reader.cpp:55:49: error: cannot convert 'std::istream {aka std::basic_istream<char>}' to 'bool' in return
> >      return ReadFastq(*is_, seq, comment, quality);
> >                                                  ^
> > 
> > Makefile:441: recipe for target 'sequence_reader.o' failed
> 
> -- 
> Martin Michlmayr
> Linux for HPE Helion, Hewlett Packard Enterprise
> 
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
> 

-- 
http://fam-tille.de

Message #26 received at 811644@bugs.debian.org (full text, mbox, reply):

From: Gert Wollny <gw.fossdev@gmail.com>

To: 811644@bugs.debian.org

Subject: re: FTBFS with GCC 6: cannot convert x to y

Date: Fri, 01 Jul 2016 14:59:57 +0200

Control: tags -1 pending 

Hi, 

I've uploaded a patch fixing this compiler problem, and I also added
another patch that makes sure the test suite is actually run during
package build. 

I don't ask for sponsoring though, because the package is somewhat
fishy:

In the source one gets by using 

  apt source idba 

no patches are applied or even listed. In the svn are two patches
however that are from 2014. They seem to be partially applied now, so
I've disabled one, and rebased the other. 

Also, when I run 

  svn-buildpackage 

the source tarball is not properly unpacked leaving me with an empty
tree and finally with an empty package. However, when I do 

   svn-buildpackage -S 

then the resulting source package is fine - i.e. I can unpack with
dpkg-source -x and compile it. 

Best, 
Gert 

Message #33 received at 811644-close@bugs.debian.org (full text, mbox, reply):

From: Gert Wollny <gw.fossdev@gmail.com>

To: 811644-close@bugs.debian.org

Subject: Bug#811644: fixed in idba 1.1.2-2

Date: Fri, 01 Jul 2016 22:22:03 +0000

Source: idba
Source-Version: 1.1.2-2

We believe that the bug you reported is fixed in the latest version of
idba, 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 811644@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Gert Wollny <gw.fossdev@gmail.com> (supplier of updated idba 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 ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Fri, 01 Jul 2016 17:10:01 +0200
Source: idba
Binary: idba
Architecture: source amd64
Version: 1.1.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Gert Wollny <gw.fossdev@gmail.com>
Description:
 idba       - iterative De Bruijn Graph De Novo short read assembler for transc
Closes: 811644
Changes:
 idba (1.1.2-2) unstable; urgency=medium
 .
   [Gert Wollny]
   * Team upload
   * d/p/gcc-6: Add patch to compile with g++-6, Closes: #811644
   * d/p/run_tests, d/rules, d/control: Run the test suite during
     package build
   * Update standards version to 3.9.8
   * d/p/clang: disable this patch, it seems to have been applied upstream
   * d/p/use-atomic-*: update patch
   * d/rules: enable parallel builds
 .
   [Andreas Tille]
   * Fix source code location
   * Move packaging from SVN to Git
   * DEP5 fix
   * Fix homepage
   * hardening=+all
   * Spelling fixes
Checksums-Sha1:
 e029a73439bd1f10936dee65d0d781ddcfcc1bc2 1884 idba_1.1.2-2.dsc
 45a36b2d770471a6eba688428713aa5ec10f4609 5532 idba_1.1.2-2.debian.tar.xz
 21a163eeacc6fc27637701cae22c6a8583714051 3128180 idba-dbgsym_1.1.2-2_amd64.deb
 682aa46d5f0bf41dc24069810104d2e15f29bfdd 277806 idba_1.1.2-2_amd64.deb
Checksums-Sha256:
 ea913b2025969782a0049f3183fb4316dd234f99b799ccc09c64ff1c9975020d 1884 idba_1.1.2-2.dsc
 85ff67a94ce1750ef82f757ea828740fa1cabf0ae9b967fc9d49c2b4919f43f7 5532 idba_1.1.2-2.debian.tar.xz
 f9a3b3017477350962f964d6fe1f9ceeb1b9ae6b3646685751496d15e7b73664 3128180 idba-dbgsym_1.1.2-2_amd64.deb
 014bfc62ef02a677f1edd760a1fe1ae9e68558d8bc698ddf9f984c3f5a473f7e 277806 idba_1.1.2-2_amd64.deb
Files:
 a36c182ac49e3d449c653381624879ea 1884 science optional idba_1.1.2-2.dsc
 8afe142a84b95b0a4bbfa04e4b369675 5532 science optional idba_1.1.2-2.debian.tar.xz
 c5e4991cc1687bd77c51a3c0cbb0364c 3128180 debug extra idba-dbgsym_1.1.2-2_amd64.deb
 dc8b6457bffeb76f63dcc353a34c4749 277806 science optional idba_1.1.2-2_amd64.deb

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