* Package: sci-biology/last-162-r1 * Repository: gentoo * Maintainer: weaver@gentoo.org sci-biology@gentoo.org * USE: elibc_glibc kernel_linux test userland_GNU x86 * FEATURES: sandbox test userpriv usersandbox >>> Unpacking source... >>> Unpacking last-162.zip to /var/tmp/portage/sci-biology/last-162-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/last-162-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/last-162-r1/work/last-162 ... * Applying 162-ldflags.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/last-162-r1/work/last-162 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/last-162-r1/work/last-162 ... make -j14 -e -C src CXX=i686-pc-linux-gnu-g++ 'STRICT=-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu' make: Entering directory `/var/tmp/portage/sci-biology/last-162-r1/work/last-162/src' i686-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -O2 -pipe -o lastdb Alphabet.cc MultiSequence.cc CyclicSubsetSeed.cc SubsetSuffixArray.cc LastdbArguments.cc io.cc fileMap.cc SubsetSuffixArraySort.cc lastdb.cc gcc -O2 -pipe -c CA_code/lambda_calculator.c i686-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Igumbel_params -O2 -pipe -o lastex Alphabet.cc LastexArguments.cc io.cc ScoreMatrix.cc lastex.cc gumbel_params/*.cpp i686-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -O2 -pipe -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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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&, 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&, 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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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: In member function ‘T cbrc::XdropAligner::diag(const std::vector >&, 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 >&, 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 >&, 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 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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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::.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:324:6: error: prototype for ‘void cbrc::Xdrop3FrameAligner::traceThreeFrame(std::vector&, 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&, 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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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 >&, 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/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-linux-gnu/bits/c++config.h:155:26: note: ‘std::size_t’ /usr/lib/gcc/i686-pc-linux-gnu/4.6.0/include/g++-v4/i686-pc-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 >&, 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 >&, 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 >&, 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 >&, 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: *** [lastal] Error 1 make: *** Waiting for unfinished jobs.... make: Leaving directory `/var/tmp/portage/sci-biology/last-162-r1/work/last-162/src' emake failed * ERROR: sci-biology/last-162-r1 failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2314: Called die * The specific snippet of code: * emake -e -C src CXX="$(tc-getCXX)" STRICT="${LDFLAGS}" || die * * If you need support, post the output of 'emerge --info =sci-biology/last-162-r1', * the complete build log and the output of 'emerge -pqv =sci-biology/last-162-r1'. * The complete build log is located at '/var/log/portage/build/sci-biology/last-162-r1:20110414-033425.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/last-162-r1/temp/environment'. * S: '/var/tmp/portage/sci-biology/last-162-r1/work/last-162'