[Debian-med-packaging] Build problem for last-align with gcc-4.6 (patch)
Martin Frith
martin at cbrc.jp
Tue May 10 11:42:10 UTC 2011
Hi Andreas,
many thanks: it's fixed in the latest version. Sorry for my delayed
reply - it was the "golden week" holiday here in Japan.
Have a nice day,
Martin Frith
http://www.cbrc.jp/~martin/
On Mon, May 02, 2011 at 04:23:32PM +0200, Andreas Tille wrote:
> Hi,
>
> I would like to let you know that there occured a build problem with
> gcc-4.6 in Debian. The fix is quite simple:
>
>
> --- last-162.orig/src/XdropAligner.hh
> +++ last-162/src/XdropAligner.hh
> @@ -12,6 +12,7 @@
> #include <vector>
> #include <cassert>
> #include <climits> // INT_MAX
> +#include <cstddef>
>
> namespace cbrc{
>
>
> I prepared this for the Debian package. (For the Debian maintainers as
> a warning: currently help2man seems not to be installable in unstable
> and thus the build fails - I hope this will be solved soon.)
>
> Kind regards
>
> Andreas.
>
> ----- Forwarded message from Lucas Nussbaum <lucas at lucas-nussbaum.net> -----
>
> X-Debian-PR-Message: report 625084
> X-Debian-PR-Package: src:last-align
> X-Debian-PR-Keywords: sid wheezy
> X-Debian-PR-Source: last-align
> Date: Mon, 2 May 2011 14:33:28 +0200
> From: Lucas Nussbaum <lucas at lucas-nussbaum.net>
> To: submit at bugs.debian.org
> X-Spam_score: -5.2
> Subject: Bug#625084: last-align: FTBFS:
> XdropAligner.hh:33:6: error: 'size_t' has not been declared
>
> Source: last-align
> Version: 159-1
> Severity: serious
> Tags: wheezy sid
> User: debian-qa at lists.debian.org
> 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++ -Wall -W -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -g -O2 -g -O2 -Wall -o lastal Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastalArguments.cc io.cc fileMap.cc ScoreMatrix.cc DiagonalTable.cc SegmentPair.cc Alignment.cc XdropAligner.cc SegmentPairPot.cc AlignmentPot.cc GeneralizedAffineGapCosts.cc Centroid.cc LambdaCalculator.cc QualityScoreCalculator.cc GeneticCode.cc Xdrop3FrameAligner.cc AlignmentWrite.cc MultiSequenceQual.cc SegmentPairPssm.cc XdropAlignerPssm.cc lastal.cc lambda_calculator.o
> > In file included from Xdrop3FrameAligner.hh:12:0,
> > from Alignment.hh:7,
> > from Alignment.cc:3:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Alignment.hh:7:0,
> > from Alignment.cc:3:
> > Xdrop3FrameAligner.hh: At global scope:
> > Xdrop3FrameAligner.hh:22:9: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:22:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:25:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:4: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:19: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:34:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:23: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:39:32: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:43:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:44:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:46:51: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:44: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::hori3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:54:47: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:55:40: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::vert3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:66:46: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:67:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::diag3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:78:39: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:79:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Alignment.cc:4:0:
> > Centroid.hh: In member function 'void cbrc::Centroid::reset()':
> > Centroid.hh:35:37: error: request for member 'size' in '((cbrc::Centroid*)this)->cbrc::Centroid::xa->cbrc::XdropAligner::offsets', which is of non-class type 'const int'
> > In file included from XdropAligner.cc:3:0:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.cc: At global scope:
> > XdropAligner.cc:21:5: error: prototype for 'int cbrc::XdropAligner::match(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], const int (*)[64], size_t, size_t)' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:78:14: error: candidate is: static int cbrc::XdropAligner::match(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], const int (*)[64], int, int)
> > XdropAligner.cc:37:53: error: no 'size_t cbrc::XdropAligner::fillBeg(size_t) const' member function declared in class 'cbrc::XdropAligner'
> > XdropAligner.cc:42:53: error: no 'size_t cbrc::XdropAligner::fillEnd(size_t) const' member function declared in class 'cbrc::XdropAligner'
> > XdropAligner.cc: In member function 'void cbrc::XdropAligner::reset(const cbrc::GeneralizedAffineGapCosts&)':
> > XdropAligner.cc:48:11: error: request for member 'resize' in '((cbrc::XdropAligner*)this)->cbrc::XdropAligner::offsets', which is of non-class type 'int'
> > XdropAligner.cc:54:3: error: 'bestAntiDiagonal' was not declared in this scope
> > XdropAligner.cc:55:3: error: 'bestPos1' was not declared in this scope
> > XdropAligner.cc: At global scope:
> > XdropAligner.cc:59:6: error: prototype for 'void cbrc::XdropAligner::initScores(size_t, size_t)' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:86:8: error: candidate is: void cbrc::XdropAligner::initScores(int, int)
> > XdropAligner.cc:73:6: error: prototype for 'void cbrc::XdropAligner::updateBest(int, size_t, const int*)' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:87:8: error: candidate is: void cbrc::XdropAligner::updateBest(int, int, const int*)
> > XdropAligner.cc:83:33: error: no 'size_t cbrc::XdropAligner::newFillBeg(size_t, size_t, size_t, size_t) const' member function declared in class 'cbrc::XdropAligner'
> > XdropAligner.cc:99:33: error: no 'size_t cbrc::XdropAligner::newFillEnd(size_t, size_t, size_t, size_t) const' member function declared in class 'cbrc::XdropAligner'
> > XdropAligner.cc:115:5: error: prototype for 'int cbrc::XdropAligner::fill(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&)' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:50:7: error: candidates are: int cbrc::XdropAligner::fill(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&)
> > XdropAligner.hh:32:7: error: int cbrc::XdropAligner::fill(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&, const int (*)[64])
> > XdropAligner.cc:235:6: error: prototype for 'void cbrc::XdropAligner::traceback(std::vector<cbrc::SegmentPair>&, const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], const int (*)[64], const cbrc::GeneralizedAffineGapCosts&) const' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:40:8: error: candidate is: void cbrc::XdropAligner::traceback(std::vector<cbrc::SegmentPair>&, const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], const int (*)[64], const cbrc::GeneralizedAffineGapCosts&) const
> > In file included from Xdrop3FrameAligner.hh:12:0,
> > from Alignment.hh:7,
> > from AlignmentPot.hh:8,
> > from AlignmentPot.cc:3:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Alignment.hh:7:0,
> > from AlignmentPot.hh:8,
> > from AlignmentPot.cc:3:
> > Xdrop3FrameAligner.hh: At global scope:
> > Xdrop3FrameAligner.hh:22:9: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:22:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:25:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:4: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:19: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:34:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:23: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:39:32: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:43:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:44:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:46:51: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:44: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::hori3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:54:47: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:55:40: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::vert3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:66:46: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:67:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::diag3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:78:39: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:79:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Centroid.hh:5:0,
> > from Centroid.cc:3:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Centroid.cc:3:0:
> > Centroid.hh: In member function 'void cbrc::Centroid::reset()':
> > Centroid.hh:35:37: error: request for member 'size' in '((cbrc::Centroid*)this)->cbrc::Centroid::xa->cbrc::XdropAligner::offsets', which is of non-class type 'const int'
> > Centroid.cc: In member function 'double cbrc::Centroid::diag(const dmatrix_t&, size_t, size_t) const':
> > Centroid.cc:75:15: error: 'const class cbrc::XdropAligner' has no member named 'fillBeg'
> > Centroid.cc:76:16: error: 'const class cbrc::XdropAligner' has no member named 'fillEnd'
> > Centroid.cc: In constructor 'cbrc::Centroid::Centroid(const cbrc::XdropAligner&, const int (*)[64], double)':
> > Centroid.cc:84:58: error: request for member 'size' in 'xa_->cbrc::XdropAligner::offsets', which is of non-class type 'const int'
> > Centroid.cc: In member function 'double cbrc::Centroid::forward(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const cbrc::GeneralizedAffineGapCosts&)':
> > Centroid.cc:170:42: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:172:41: error: invalid types 'const int[size_t]' for array subscript
> > Centroid.cc:226:54: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc: In member function 'double cbrc::Centroid::backward(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const cbrc::GeneralizedAffineGapCosts&)':
> > Centroid.cc:310:53: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:312:42: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:314:41: error: invalid types 'const int[size_t]' for array subscript
> > Centroid.cc:345:31: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:351:49: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:377:54: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc: In member function 'double cbrc::Centroid::dp(double)':
> > Centroid.cc:473:42: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:475:41: error: invalid types 'const int[size_t]' for array subscript
> > Centroid.cc:501:54: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc: In member function 'void cbrc::Centroid::computeExpectedCounts(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const cbrc::GeneralizedAffineGapCosts&, cbrc::ExpectedCount&) const':
> > Centroid.cc:597:42: error: invalid types 'const int[const size_t]' for array subscript
> > Centroid.cc:599:41: error: invalid types 'const int[size_t]' for array subscript
> > Centroid.cc:659:54: error: invalid types 'const int[const size_t]' for array subscript
> > In file included from Centroid.hh:5:0,
> > from Centroid.cc:3:
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > Centroid.cc:77:57: instantiated from here
> > XdropAligner.hh:106:5: error: 'fillBeg' was not declared in this scope
> > XdropAligner.hh:107:5: error: 'fillEnd' was not declared in this scope
> > XdropAligner.hh: At global scope:
> > XdropAligner.hh:104:5: warning: unused parameter 'matrix' [-Wunused-parameter]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > Centroid.cc:488:40: instantiated from here
> > XdropAligner.hh:137:5: error: 'fillEnd' was not declared in this scope
> > XdropAligner.hh:137:5: error: 'fillBeg' was not declared in this scope
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > Centroid.cc:543:23: instantiated from here
> > XdropAligner.hh:116:5: error: 'fillBeg' was not declared in this scope
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > Centroid.cc:544:23: instantiated from here
> > XdropAligner.hh:127:5: error: 'fillEnd' was not declared in this scope
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > XdropAligner.hh:109:3: warning: control reaches end of non-void function [-Wreturn-type]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > XdropAligner.hh:131:3: warning: control reaches end of non-void function [-Wreturn-type]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > XdropAligner.hh:120:3: warning: control reaches end of non-void function [-Wreturn-type]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const [with T = double]':
> > XdropAligner.hh:143:3: warning: control reaches end of non-void function [-Wreturn-type]
> > Centroid.cc: In member function 'double cbrc::Centroid::diag(const dmatrix_t&, size_t, size_t) const':
> > Centroid.cc:81:3: warning: control reaches end of non-void function [-Wreturn-type]
> > In file included from Xdrop3FrameAligner.hh:12:0,
> > from Xdrop3FrameAligner.cc:3:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Xdrop3FrameAligner.cc:3:0:
> > Xdrop3FrameAligner.hh: At global scope:
> > Xdrop3FrameAligner.hh:22:9: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:22:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:25:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:4: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:19: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:34:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:23: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:39:32: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:43:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:44:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:46:51: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:44: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::hori3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:54:47: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:55:40: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::vert3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:66:46: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:67:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::diag3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:78:39: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:79:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.cc: At global scope:
> > Xdrop3FrameAligner.cc:14:1: error: prototype for 'const uchar* cbrc::Xdrop3FrameAligner::seqPtr2(const uchar*, size_t, cbrc::XdropAligner::direction, size_t, size_t)' does not match any in class 'cbrc::Xdrop3FrameAligner'
> > Xdrop3FrameAligner.hh:46:23: error: candidate is: static const uchar* cbrc::Xdrop3FrameAligner::seqPtr2(const uchar*, int, cbrc::XdropAligner::direction, int, int)
> > Xdrop3FrameAligner.cc:33:5: error: prototype for 'int cbrc::Xdrop3FrameAligner::match2(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], size_t, size_t, size_t)' does not match any in class 'cbrc::Xdrop3FrameAligner'
> > Xdrop3FrameAligner.hh:37:7: error: candidate is: int cbrc::Xdrop3FrameAligner::match2(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, int, int)
> > Xdrop3FrameAligner.cc: In member function 'void cbrc::Xdrop3FrameAligner::reset3(const cbrc::GeneralizedAffineGapCosts&)':
> > Xdrop3FrameAligner.cc:49:11: error: request for member 'resize' in '((cbrc::Xdrop3FrameAligner*)this)->cbrc::Xdrop3FrameAligner::<anonymous>.cbrc::XdropAligner::offsets', which is of non-class type 'int'
> > Xdrop3FrameAligner.cc:67:3: error: 'bestAntiDiagonal' was not declared in this scope
> > Xdrop3FrameAligner.cc:68:3: error: 'bestPos1' was not declared in this scope
> > Xdrop3FrameAligner.cc: At global scope:
> > Xdrop3FrameAligner.cc:72:49: error: no 'size_t cbrc::Xdrop3FrameAligner::finiteBeg(size_t)' member function declared in class 'cbrc::Xdrop3FrameAligner'
> > Xdrop3FrameAligner.cc:85:49: error: no 'size_t cbrc::Xdrop3FrameAligner::finiteEnd(size_t)' member function declared in class 'cbrc::Xdrop3FrameAligner'
> > Xdrop3FrameAligner.cc:98:5: error: prototype for 'int cbrc::Xdrop3FrameAligner::fillThreeFrame(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], int, const cbrc::GeneralizedAffineGapCosts&, int, size_t)' does not match any in class 'cbrc::Xdrop3FrameAligner'
> > Xdrop3FrameAligner.hh:21:7: error: candidate is: int cbrc::Xdrop3FrameAligner::fillThreeFrame(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, const cbrc::GeneralizedAffineGapCosts&, int, int)
> > Xdrop3FrameAligner.cc:320:6: error: prototype for 'void cbrc::Xdrop3FrameAligner::traceThreeFrame(std::vector<cbrc::SegmentPair>&, const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], const cbrc::GeneralizedAffineGapCosts&, int, size_t)' does not match any in class 'cbrc::Xdrop3FrameAligner'
> > Xdrop3FrameAligner.hh:29:8: error: candidate is: void cbrc::Xdrop3FrameAligner::traceThreeFrame(std::vector<cbrc::SegmentPair>&, const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], const cbrc::GeneralizedAffineGapCosts&, int, int)
> > In file included from Xdrop3FrameAligner.hh:12:0,
> > from Alignment.hh:7,
> > from AlignmentWrite.cc:3:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from Alignment.hh:7:0,
> > from AlignmentWrite.cc:3:
> > Xdrop3FrameAligner.hh: At global scope:
> > Xdrop3FrameAligner.hh:22:9: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:22:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:25:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:4: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:31:19: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:34:24: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:38:23: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:39:32: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:8: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:40:29: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:43:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:44:3: error: 'size_t' does not name a type
> > Xdrop3FrameAligner.hh:46:51: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:47:44: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:52:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:64:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:5: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh:76:26: error: 'size_t' has not been declared
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::hori3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:54:47: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:55:40: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::vert3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:66:46: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:67:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh: In member function 'T cbrc::Xdrop3FrameAligner::diag3(const std::vector<std::vector<T> >&, int, int) const':
> > Xdrop3FrameAligner.hh:78:39: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > Xdrop3FrameAligner.hh:79:39: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > In file included from XdropAlignerPssm.cc:3:0:
> > XdropAligner.hh:33:6: error: 'size_t' has not been declared
> > XdropAligner.hh:33:21: error: 'size_t' has not been declared
> > XdropAligner.hh:42:5: error: 'size_t' has not been declared
> > XdropAligner.hh:42:20: error: 'size_t' has not been declared
> > XdropAligner.hh:51:6: error: 'size_t' has not been declared
> > XdropAligner.hh:51:21: error: 'size_t' has not been declared
> > XdropAligner.hh:56:3: error: 'size_t' has not been declared
> > XdropAligner.hh:56:18: error: 'size_t' has not been declared
> > XdropAligner.hh:67:3: error: 'size_t' does not name a type
> > XdropAligner.hh:68:3: error: 'size_t' does not name a type
> > XdropAligner.hh:74:16: error: 'size_t' was not declared in this scope
> > XdropAligner.hh:74:16: note: suggested alternatives:
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > /usr/include/c++/4.6/x86_64-linux-gnu/bits/c++config.h:155:26: note: 'std::size_t'
> > XdropAligner.hh:74:23: error: template argument 1 is invalid
> > XdropAligner.hh:74:23: error: template argument 2 is invalid
> > XdropAligner.hh:79:7: error: 'size_t' has not been declared
> > XdropAligner.hh:79:22: error: 'size_t' has not been declared
> > XdropAligner.hh:81:7: error: 'size_t' has not been declared
> > XdropAligner.hh:81:28: error: 'size_t' has not been declared
> > XdropAligner.hh:83:3: error: 'size_t' does not name a type
> > XdropAligner.hh:84:3: error: 'size_t' does not name a type
> > XdropAligner.hh:86:20: error: 'size_t' has not been declared
> > XdropAligner.hh:86:41: error: 'size_t' has not been declared
> > XdropAligner.hh:87:31: error: 'size_t' has not been declared
> > XdropAligner.hh:88:3: error: 'size_t' does not name a type
> > XdropAligner.hh:89:3: error: 'size_t' does not name a type
> > XdropAligner.hh:93:41: error: 'size_t' has not been declared
> > XdropAligner.hh:94:21: error: 'size_t' has not been declared
> > XdropAligner.hh:105:4: error: 'size_t' has not been declared
> > XdropAligner.hh:105:25: error: 'size_t' has not been declared
> > XdropAligner.hh:114:4: error: 'size_t' has not been declared
> > XdropAligner.hh:114:25: error: 'size_t' has not been declared
> > XdropAligner.hh:125:4: error: 'size_t' has not been declared
> > XdropAligner.hh:125:25: error: 'size_t' has not been declared
> > XdropAligner.hh:136:4: error: 'size_t' has not been declared
> > XdropAligner.hh:136:25: error: 'size_t' has not been declared
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::cell(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:106:5: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:106:5: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> > XdropAligner.hh:107:5: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh:108:68: error: invalid types 'const int[int]' for array subscript
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::hori(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:116:43: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::vert(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:127:43: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAligner.hh: In member function 'T cbrc::XdropAligner::diag(const std::vector<std::vector<T> >&, int, int) const':
> > XdropAligner.hh:138:36: error: there are no arguments to 'fillBeg' that depend on a template parameter, so a declaration of 'fillBeg' must be available [-fpermissive]
> > XdropAligner.hh:139:37: error: there are no arguments to 'fillEnd' that depend on a template parameter, so a declaration of 'fillEnd' must be available [-fpermissive]
> > XdropAlignerPssm.cc: At global scope:
> > XdropAlignerPssm.cc:11:5: error: prototype for 'int cbrc::XdropAligner::fill(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&, const int (*)[64])' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:50:7: error: candidates are: int cbrc::XdropAligner::fill(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&)
> > XdropAligner.hh:32:7: error: int cbrc::XdropAligner::fill(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&, const int (*)[64])
> > XdropAlignerPssm.cc:23:5: error: prototype for 'int cbrc::XdropAligner::fillPssm(const uchar*, const uchar*, size_t, size_t, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&, const int (*)[64])' does not match any in class 'cbrc::XdropAligner'
> > XdropAligner.hh:55:7: error: candidate is: int cbrc::XdropAligner::fillPssm(const uchar*, const uchar*, int, int, cbrc::XdropAligner::direction, const int (*)[64], int, int, const cbrc::GeneralizedAffineGapCosts&, const int (*)[64])
> > make[1]: *** [lastal] Error 1
>
> The full build log is available from:
> http://people.debian.org/~lucas/logs/2011/05/02/last-align_159-1_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
> | lucas at lucas-nussbaum.net http://www.lucas-nussbaum.net/ |
> | jabber: lucas at nussbaum.fr GPG: 1024D/023B3F4F |
>
>
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging at lists.alioth.debian.org
> http://lists.alioth.debian.org/mailman/listinfo/debian-med-packaging
>
>
> ----- End forwarded message -----
>
> --
> http://fam-tille.de
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