Bug#624979: marked as done (probalign: FTBFS: SafeVector.h:26:22: error: expected ')' before 'size')

Wed, 04 May 2011 07:30:23 -0700 

Your message dated Wed, 04 May 2011 14:28:51 +0000
with message-id <[email protected]>
and subject line Bug#624979: fixed in probalign 1.4-2
has caused the Debian Bug report #624979,
regarding probalign: FTBFS: SafeVector.h:26:22: error: expected ')' before 
'size'
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 [email protected]
immediately.)


-- 
624979: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=624979
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message --- 
Source: probalign
Version: 1.4-1
Severity: serious
Tags: wheezy sid
User: [email protected]
Usertags: qa-ftbfs-20110502 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part:
> g++ -O3 -W -Wall -funroll-loops -lm -o probalign Main.cc PostProbs.cc 
> ComputeAlignment.cc ReadMatrix.cc
> In file included from Main.cc:8:0:
> SafeVector.h:26:22: error: expected ')' before 'size'
> SafeVector.h:27:22: error: expected ')' before 'size'
> In file included from MultiSequence.h:18:0,
>                  from Main.cc:9:
> Sequence.h: In member function 'SafeVector<int>* Sequence::GetMapping() 
> const':
> Sequence.h:392:52: error: no matching function for call to 
> 'SafeVector<int>::SafeVector(int, int)'
> Sequence.h:392:52: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = int, SafeVector<TYPE> = SafeVector<int>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = int]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> In file included from Main.cc:9:0:
> MultiSequence.h: In member function 'char 
> MultiSequence::GetAnnotationChar(SafeVector<char>&)':
> MultiSequence.h:348:35: error: no matching function for call to 
> 'SafeVector<int>::SafeVector(int, int)'
> MultiSequence.h:348:35: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = int, SafeVector<TYPE> = SafeVector<int>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = int]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> MultiSequence.h: In member function 'void 
> MultiSequence::WriteALN(std::ostream&, int)':
> MultiSequence.h:495:67: error: no matching function for call to 
> 'SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >::SafeVector(int)'
> MultiSequence.h:495:67: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = __gnu_cxx::__normal_iterator<char*, 
> std::vector<char, std::allocator<char> > >, SafeVector<TYPE> = 
> SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 'int' to 
> 'const SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> __gnu_cxx::__normal_iterator<char*, std::vector<char, std::allocator<char> > 
> >]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> MultiSequence.h:496:47: error: no matching function for call to 
> 'SafeVector<int>::SafeVector(int)'
> MultiSequence.h:496:47: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = int, SafeVector<TYPE> = SafeVector<int>]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 'int' to 
> 'const SafeVector<int>&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = int]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> MultiSequence.h: In member function 'MultiSequence* 
> MultiSequence::Project(const std::set<int>&)':
> MultiSequence.h:652:67: error: no matching function for call to 
> 'SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >::SafeVector(std::set<int>::size_type)'
> MultiSequence.h:652:67: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = __gnu_cxx::__normal_iterator<char*, 
> std::vector<char, std::allocator<char> > >, SafeVector<TYPE> = 
> SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 
> 'std::set<int>::size_type' to 'const 
> SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> __gnu_cxx::__normal_iterator<char*, std::vector<char, std::allocator<char> > 
> >]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> MultiSequence.h:653:59: error: no matching function for call to 
> 'SafeVector<SafeVector<char>*>::SafeVector(std::set<int>::size_type)'
> MultiSequence.h:653:59: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = SafeVector<char>*, SafeVector<TYPE> = 
> SafeVector<SafeVector<char>*>]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 
> 'std::set<int>::size_type' to 'const SafeVector<SafeVector<char>*>&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> SafeVector<char>*]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> In file included from Main.cc:10:0:
> EvolutionaryTree.h: In static member function 'static TreeNode* 
> TreeNode::ComputeTree(const VVF&)':
> EvolutionaryTree.h:107:40: error: no matching function for call to 
> 'SafeVector<float>::SafeVector(int&)'
> EvolutionaryTree.h:107:40: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = float, SafeVector<TYPE> = SafeVector<float>]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 'int' to 
> 'const SafeVector<float>&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = float]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> EvolutionaryTree.h:108:48: error: no matching function for call to 
> 'SafeVector<TreeNode*>::SafeVector(int&, NULL)'
> EvolutionaryTree.h:108:48: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = TreeNode*, SafeVector<TYPE> = 
> SafeVector<TreeNode*>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> TreeNode*]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> EvolutionaryTree.h:109:38: error: no matching function for call to 
> 'SafeVector<int>::SafeVector(int&, int)'
> EvolutionaryTree.h:109:38: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = int, SafeVector<TYPE> = SafeVector<int>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = int]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> In file included from Main.cc:11:0:
> SparseMatrix.h: In member function 'VF* SparseMatrix::GetPosterior() const':
> SparseMatrix.h:236:62: error: no matching function for call to 
> 'SafeVector<float>::SafeVector(int)'
> SparseMatrix.h:236:62: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = float, SafeVector<TYPE> = SafeVector<float>]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 'int' to 
> 'const SafeVector<float>&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = float]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> Main.cc: In function 'MultiSequence* DoAlign(MultiSequence*)':
> Main.cc:255:41: error: no matching function for call to 
> 'SafeVector<float>::SafeVector(const int&, int)'
> Main.cc:255:41: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = float, SafeVector<TYPE> = SafeVector<float>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = float]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> Main.cc:260:15: error: no matching function for call to 
> 'SafeVector<SparseMatrix*>::SafeVector(const int&, NULL)'
> Main.cc:260:15: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = SparseMatrix*, SafeVector<TYPE> = 
> SafeVector<SparseMatrix*>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> SparseMatrix*]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> Main.cc: In function 'SafeVector<SafeVector<SparseMatrix*> > 
> DoRelaxation(MultiSequence*, SafeVector<SafeVector<SparseMatrix*> >&)':
> Main.cc:986:16: error: no matching function for call to 
> 'SafeVector<SparseMatrix*>::SafeVector(const int&, NULL)'
> Main.cc:986:16: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = SparseMatrix*, SafeVector<TYPE> = 
> SafeVector<SparseMatrix*>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> SparseMatrix*]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> Main.cc: In function 'void WriteAnnotation(MultiSequence*, const 
> SafeVector<SafeVector<SparseMatrix*> >&)':
> Main.cc:1329:42: error: no matching function for call to 
> 'SafeVector<int>::SafeVector(const int&, int)'
> Main.cc:1329:42: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = int, SafeVector<TYPE> = SafeVector<int>]
> SafeVector.h:28:3: note:   candidate expects 1 argument, 2 provided
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = int]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 2 provided
> Main.cc:1330:62: error: no matching function for call to 
> 'SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >::SafeVector(const int&)'
> Main.cc:1330:62: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = __gnu_cxx::__normal_iterator<char*, 
> std::vector<char, std::allocator<char> > >, SafeVector<TYPE> = 
> SafeVector<__gnu_cxx::__normal_iterator<char*, std::vector<char, 
> std::allocator<char> > > >]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 'const 
> int' to 'const SafeVector<__gnu_cxx::__normal_iterator<char*, 
> std::vector<char, std::allocator<char> > > >&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = 
> __gnu_cxx::__normal_iterator<char*, std::vector<char, std::allocator<char> > 
> >]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> In file included from PostProbs.cc:1:0:
> SafeVector.h:26:22: error: expected ')' before 'size'
> SafeVector.h:27:22: error: expected ')' before 'size'
> PostProbs.cc: In function 'VF* revers_partf(long double**, float, float, 
> float)':
> PostProbs.cc:140:54: error: no matching function for call to 
> 'SafeVector<float>::SafeVector(int)'
> PostProbs.cc:140:54: note: candidates are:
> SafeVector.h:28:3: note: SafeVector<TYPE>::SafeVector(const 
> SafeVector<TYPE>&) [with TYPE = float, SafeVector<TYPE> = SafeVector<float>]
> SafeVector.h:28:3: note:   no known conversion for argument 1 from 'int' to 
> 'const SafeVector<float>&'
> SafeVector.h:25:3: note: SafeVector<TYPE>::SafeVector() [with TYPE = float]
> SafeVector.h:25:3: note:   candidate expects 0 arguments, 1 provided
> In file included from ReadMatrix.cc:6:0:
> SafeVector.h:26:22: error: expected ')' before 'size'
> SafeVector.h:27:22: error: expected ')' before 'size'
> make[1]: *** [probalign] Error 1

The full build log is available from:
   
http://people.debian.org/~lucas/logs/2011/05/02/probalign_1.4-1_lsid64.buildlog

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 about 50 AMD64 nodes
of the Grid'5000 platform, using a clean chroot.  Internet was not
accessible from the build systems.

-- 
| Lucas Nussbaum
| [email protected]   http://www.lucas-nussbaum.net/ |
| jabber: [email protected]             GPG: 1024D/023B3F4F |

--- End Message ---
--- Begin Message --- 
Source: probalign
Source-Version: 1.4-2

We believe that the bug you reported is fixed in the latest version of
probalign, which is due to be installed in the Debian FTP archive:

probalign_1.4-2.debian.tar.gz
  to main/p/probalign/probalign_1.4-2.debian.tar.gz
probalign_1.4-2.dsc
  to main/p/probalign/probalign_1.4-2.dsc
probalign_1.4-2_amd64.deb
  to main/p/probalign/probalign_1.4-2_amd64.deb



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 probalign 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: SHA1

Format: 1.8
Date: Mon, 02 May 2011 17:02:21 +0200
Source: probalign
Binary: probalign
Architecture: source amd64
Version: 1.4-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description: 
 probalign  - multiple sequence alignment using partition function posterior pr
Closes: 624979
Changes: 
 probalign (1.4-2) unstable; urgency=low
 .
   * Standards-Version: 3.9.2 (no changes needed)
   * Debhelper 8 (control+compat)
   * debian/patches/fix-gcc-4.6.patch
     Closes: #624979
Checksums-Sha1: 
 c75cdb334b6c09154140b8c7e768cbe89817c6ed 1317 probalign_1.4-2.dsc
 98e9beaed5a6a6274cb565f46693595282baf625 2817 probalign_1.4-2.debian.tar.gz
 4ce5e1a27042dd078db4602fdbf9d781897d9522 76790 probalign_1.4-2_amd64.deb
Checksums-Sha256: 
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probalign_1.4-2.dsc
 729de8be2a0606cfaad4a6c4011de6cceb0b31f7e07176248fbea4412122f302 2817 
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 c1e07fdc6b06f595ca48abeb0308289167063755df79e673af1ce448e61c5318 76790 
probalign_1.4-2_amd64.deb
Files: 
 8fcd95516c3dafaf659b0d0127cd96cd 1317 science optional probalign_1.4-2.dsc
 af20cd6ec0b0f4be279c6a845a865aa6 2817 science optional 
probalign_1.4-2.debian.tar.gz
 cc0804f43ed3a2e6cbc2bbc6eb8a31e8 76790 science optional 
probalign_1.4-2_amd64.deb

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--- End Message ---

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