Debian Bug report logs - #798932
bppphyview: FTBFS: TreeCommands.h:225: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'

version graph

Package: src:bppphyview; Maintainer for src:bppphyview is Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>;

Reported by: Chris Lamb <lamby@debian.org>

Date: Mon, 14 Sep 2015 08:57:10 UTC

Severity: serious

Tags: sid, stretch

Found in version bppphyview/0.3.0-1

Done: Andreas Beckmann <anbe@debian.org>

Bug is archived. No further changes may be made.

Toggle useless messages

View this report as an mbox folder, status mbox, maintainer mbox

Report forwarded to debian-bugs-dist@lists.debian.org, reproducible-builds@lists.alioth.debian.org, Loic Dachary <loic@dachary.org>:
Bug#798932; Package src:bppphyview. (Mon, 14 Sep 2015 08:57:15 GMT) (full text, mbox, link).

Acknowledgement sent to Chris Lamb <lamby@debian.org>:
New Bug report received and forwarded. Copy sent to reproducible-builds@lists.alioth.debian.org, Loic Dachary <loic@dachary.org>. (Mon, 14 Sep 2015 08:57:15 GMT) (full text, mbox, link).

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

From: Chris Lamb <lamby@debian.org>
To: submit@bugs.debian.org
Subject: bppphyview: FTBFS: TreeCommands.h:225: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Date: Mon, 14 Sep 2015 09:55:13 +0100
[Message part 1 (text/plain, inline)]
Source: bppphyview
Version: 0.3.0-1
Severity: serious
Justification: fails to build from source
User: reproducible-builds@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-builds@lists.alioth.debian.org

Dear Maintainer,

bppphyview fails to build from source in unstable/amd64, probably GCC-5
related:

  [..]

  CMakeFiles/phyview.dir/PhyView.cpp.o: In function
  `InsertSubtreeOnBranchCommand::InsertSubtreeOnBranchCommand(TreeDocument*,
  int, bpp::Node*)':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.h:225: undefined
  reference to `bpp::TextTools::toString[abi:cxx11](int)'
  CMakeFiles/phyview.dir/PhyView.cpp.o: In function `main':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/PhyView.cpp:1150: undefined
  reference to `bpp::IOTreeFactory::NEWICK_FORMAT[abi:cxx11]'
  CMakeFiles/phyview.dir/PhyView.cpp.o: In function `void
  std::__cxx11::basic_string<char, std::char_traits<char>,
  std::allocator<char> >::_M_construct_aux<char*>(char*, char*,
  std::__false_type)':
  /usr/include/c++/5/bits/basic_string.h:195: undefined reference to
  `bpp::IOTreeFactory::NEWICK_FORMAT[abi:cxx11]'
  CMakeFiles/phyview.dir/PhyView.cpp.o: In function
  `std::__cxx11::basic_string<char, std::char_traits<char>,
  std::allocator<char> >::assign(std::__cxx11::basic_string<char,
  std::char_traits<char>, std::allocator<char> > const&)':
  /usr/include/c++/5/bits/basic_string.h:1094: undefined reference to
  `bpp::IOTreeFactory::NHX_FORMAT[abi:cxx11]'
  /usr/include/c++/5/bits/basic_string.h:1094: undefined reference to
  `bpp::IOTreeFactory::NEWICK_FORMAT[abi:cxx11]'
  CMakeFiles/phyview.dir/TreeSubWindow.cpp.o: In function `QString
  bpp::QtTools::toQt<double>(bpp::Number<double> const&)':
  /usr/include/Bpp/Qt/QtTools.h:83: undefined reference to
  `bpp::TextTools::toString[abi:cxx11](double, int)'
  CMakeFiles/phyview.dir/TreeSubWindow.cpp.o: In function
  `TreeSubWindow::updateTable()':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeSubWindow.cpp:107:
  undefined reference to
  `bpp::TreeTemplateTools::getNodePropertyNames(bpp::Node const&,
  std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
  std::allocator<char> >,
  std::allocator<std::__cxx11::basic_string<char,
  std::char_traits<char>, std::allocator<char> > > >&)'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeSubWindow.cpp:109:
  undefined reference to
  `bpp::TreeTemplateTools::getBranchPropertyNames(bpp::Node const&,
  std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
  std::allocator<char> >,
  std::allocator<std::__cxx11::basic_string<char,
  std::char_traits<char>, std::allocator<char> > > >&)'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeSubWindow.cpp:122:
  undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeSubWindow.cpp:133:
  undefined reference to `bpp::TextTools::toString[abi:cxx11](double,
  int)'
  CMakeFiles/phyview.dir/TreeSubWindow.cpp.o: In function
  `ChangeNodeNameCommand::ChangeNodeNameCommand(TreeDocument*, int,
  std::__cxx11::basic_string<char, std::char_traits<char>,
  std::allocator<char> > const&)':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.h:266: undefined
  reference to `bpp::TextTools::toString[abi:cxx11](int)'
  CMakeFiles/phyview.dir/TreeSubWindow.cpp.o: In function
  `ChangeBranchLengthCommand::ChangeBranchLengthCommand(TreeDocument*,
  int, double)':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.h:254: undefined
  reference to `bpp::TextTools::toString[abi:cxx11](double, int)'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.h:254: undefined
  reference to `bpp::TextTools::toString[abi:cxx11](int)'
  CMakeFiles/phyview.dir/TreeCommands.cpp.o: In function
  `AttachDataCommand::addProperties_(bpp::Node*, bpp::DataTable const&,
  unsigned int, bool)':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:75: undefined
  reference to `bpp::TextTools::toString[abi:cxx11](int)'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:77: undefined
  reference to `bpp::DataTable::operator()[abi:cxx11](unsigned long,
  unsigned long) const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:80: undefined
  reference to `bpp::DataTable::operator()[abi:cxx11](unsigned long,
  unsigned long) const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:80: undefined
  reference to `bpp::DataTable::getColumnName[abi:cxx11](unsigned long)
  const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:90: undefined
  reference to `bpp::DataTable::operator()[abi:cxx11](unsigned long,
  unsigned long) const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:93: undefined
  reference to `bpp::DataTable::operator()[abi:cxx11](unsigned long,
  unsigned long) const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:93: undefined
  reference to `bpp::DataTable::getColumnName[abi:cxx11](unsigned long)
  const'
  CMakeFiles/phyview.dir/TreeCommands.cpp.o: In function
  `TranslateNodeNamesCommand::TranslateNodeNamesCommand(TreeDocument*,
  bpp::DataTable const&, unsigned int, unsigned int)':
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:45: undefined
  reference to `bpp::DataTable::getColumnName[abi:cxx11](unsigned long)
  const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:45: undefined
  reference to `bpp::DataTable::getColumnName[abi:cxx11](unsigned long)
  const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:51: undefined
  reference to `bpp::DataTable::operator()[abi:cxx11](unsigned long,
  unsigned long) const'
  /tmp/buildd/bppphyview-0.3.0/bppPhyView/TreeCommands.cpp:51: undefined
  reference to `bpp::DataTable::operator()[abi:cxx11](unsigned long,
  unsigned long) const'
  collect2: error: ld returned 1 exit status
  bppPhyView/CMakeFiles/phyview.dir/build.make:203: recipe for target
  'bppPhyView/phyview' failed
  make[3]: *** [bppPhyView/phyview] Error 1
  make[3]: Leaving directory '/tmp/buildd/bppphyview-0.3.0'
  CMakeFiles/Makefile2:299: recipe for target
  'bppPhyView/CMakeFiles/phyview.dir/all' failed
  make[2]: *** [bppPhyView/CMakeFiles/phyview.dir/all] Error 2
  make[2]: Leaving directory '/tmp/buildd/bppphyview-0.3.0'
  Makefile:136: recipe for target 'all' failed
  make[1]: *** [all] Error 2
  make[1]: Leaving directory '/tmp/buildd/bppphyview-0.3.0'
  debian/rules:103: recipe for target 'install-arch' failed
  make: *** [install-arch] Error 2
  dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
  status 2

  [..]

The full build log is attached or can be viewed here:

    https://reproducible.debian.net/logs/unstable/amd64/bppphyview_0.3.0-1.build1.log.gz


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby@debian.org / chris-lamb.co.uk
       `-

[bppphyview.0.3.0-1.unstable.amd64.log.txt (text/plain, attachment)]

Added tag(s) sid and stretch. Request was from Andreas Beckmann <anbe@debian.org> to control@bugs.debian.org. (Tue, 15 Sep 2015 02:57:07 GMT) (full text, mbox, link).

Reply sent to Andreas Beckmann <anbe@debian.org>:
You have taken responsibility. (Thu, 26 May 2016 21:45:04 GMT) (full text, mbox, link).

Notification sent to Chris Lamb <lamby@debian.org>:
Bug acknowledged by developer. (Thu, 26 May 2016 21:45:04 GMT) (full text, mbox, link).

Message #12 received at 798932-done@bugs.debian.org (full text, mbox, reply):

From: Andreas Beckmann <anbe@debian.org>
To: 798932-done@bugs.debian.org
Subject: Re: bppphyview: FTBFS: TreeCommands.h:225: undefined reference to `bpp::TextTools::toString[abi:cxx11](int)'
Date: Thu, 26 May 2016 23:40:37 +0200
On Mon, 14 Sep 2015 09:55:13 +0100 Chris Lamb <lamby@debian.org> wrote:
> bppphyview fails to build from source in unstable/amd64, probably GCC-5
> related:

and no longer reproducible after all the bpp libraries have undergone
the libstdc++v5 transition

Andreas

Bug archived. Request was from Debbugs Internal Request <owner@bugs.debian.org> to internal_control@bugs.debian.org. (Fri, 24 Jun 2016 07:28:11 GMT) (full text, mbox, link).

Send a report that this bug log contains spam.

Debian bug tracking system administrator <owner@bugs.debian.org>. Last modified: Sun Jul 2 10:05:19 2023; Machine Name: buxtehude

Debian Bug tracking system

Debbugs is free software and licensed under the terms of the GNU Public License version 2. The current version can be obtained from https://bugs.debian.org/debbugs-source/.

Copyright © 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson, 2005-2017 Don Armstrong, and many other contributors.