Source: last-align Version: 159-1 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++ -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 | [email protected] http://www.lucas-nussbaum.net/ | | jabber: [email protected] GPG: 1024D/023B3F4F | -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
