configure.ac:8: installing `config/config.guess' configure.ac:8: installing `config/config.sub' configure.ac:61: installing `config/install-sh' configure.ac:61: installing `config/missing' libGenome/Makefile.am: installing `config/depcomp' Makefile.am: installing `./INSTALL' Makefile.am: installing `./COPYING' configure: WARNING: latex not found - will not generate doxygen PostScript documentation configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation configure.ac:64: installing `config/config.guess' configure.ac:64: installing `config/config.sub' configure.ac:52: installing `config/install-sh' configure.ac:52: installing `config/missing' libMUSCLE/Makefile.am: installing `config/depcomp' Makefile.am: installing `./INSTALL' configure: WARNING: latex not found - will not generate doxygen PostScript documentation configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation aligngivenpath.cpp: In function ‘void muscle::AppendTplInserts(const muscle::MSA&, unsigned int&, unsigned int, const muscle::MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, muscle::MSA&, unsigned int&)’: aligngivenpath.cpp:188: warning: unused variable ‘uLengthA’ aligngivenpath.cpp:189: warning: unused variable ‘uLengthB’ aligngivenpath.cpp: In function ‘void muscle::AlignTwoMSAsGivenPath(const muscle::PWPath&, const muscle::MSA&, const muscle::MSA&, muscle::MSA&)’: aligngivenpath.cpp:337: warning: unused variable ‘uColA’ aligngivenpath.cpp:338: warning: unused variable ‘uColB’ aligngivenpath.cpp:348: warning: unused variable ‘uColA’ aligngivenpath.cpp:356: warning: unused variable ‘uColB’ aligngivenpathsw.cpp: In function ‘void muscle::AppendUnalignedTerminals(const muscle::MSA&, unsigned int&, unsigned int, const muscle::MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, muscle::MSA&, unsigned int&)’: aligngivenpathsw.cpp:60: warning: unused variable ‘uLengthA’ aligngivenpathsw.cpp:61: warning: unused variable ‘uLengthB’ aligngivenpathsw.cpp: In function ‘void muscle::AlignTwoMSAsGivenPathSW(const muscle::PWPath&, const muscle::MSA&, const muscle::MSA&, muscle::MSA&)’: aligngivenpathsw.cpp:206: warning: unused variable ‘uColA’ aligngivenpathsw.cpp:207: warning: unused variable ‘uColB’ aligngivenpathsw.cpp:217: warning: unused variable ‘uColA’ aligngivenpathsw.cpp:225: warning: unused variable ‘uColB’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used alpha.cpp: In function ‘unsigned int muscle::GetAlphaSize(muscle::ALPHA)’: alpha.cpp:86: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used anchoredpp.cpp: In function ‘muscle::SCORE muscle::ScoreSeqPairLetters(const muscle::MSA&, unsigned int, const muscle::MSA&, unsigned int, muscle::SCORE*)’: anchoredpp.cpp:40: warning: unused variable ‘scoreGaps’ anchoredpp.cpp:41: warning: unused variable ‘bGapping1’ anchoredpp.cpp:42: warning: unused variable ‘bGapping2’ anchoredpp.cpp: In function ‘void muscle::AnchoredProfileProfile(muscle::MSA&, muscle::MSA&, muscle::MSA&)’: anchoredpp.cpp:486: warning: unused variable ‘uId’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used anchors.cpp: In function ‘void muscle::MergeBestCols(const muscle::SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)’: anchors.cpp:164: warning: unused variable ‘uWindowCenter’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used anchors.cpp:108: warning: ‘void muscle::ListBestCols(const muscle::MSA&, const muscle::SCORE*, const muscle::SCORE*, unsigned int*, unsigned int)’ defined but not used bittraceback.cpp: In function ‘const char* muscle::BitsToStr(char)’: bittraceback.cpp:20: warning: deprecated conversion from string constant to ‘char*’ bittraceback.cpp: In function ‘void muscle::BitTraceBack(char**, unsigned int, unsigned int, char, muscle::PWPath&)’: bittraceback.cpp:149: warning: unused variable ‘Bits’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used bittraceback.cpp:18: warning: ‘const char* muscle::BitsToStr(char)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used clust.cpp: In member function ‘void muscle::Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)’: clust.cpp:169: warning: enumeration value ‘JOIN_Undefined’ not handled in switch clust.cpp: In member function ‘void muscle::Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’: clust.cpp:186: warning: unused variable ‘uClusterCount’ clust.cpp: In member function ‘void muscle::Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’: clust.cpp:206: warning: unused variable ‘uClusterCount’ clust.cpp: In member function ‘float muscle::Clust::ComputeDist(unsigned int, unsigned int)’: clust.cpp:297: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch clust.cpp: In member function ‘float muscle::Clust::ComputeDistMAFFT(unsigned int, unsigned int)’: clust.cpp:362: warning: unused variable ‘dDistLR’ clust.cpp: In member function ‘float muscle::Clust::ComputeMetric(unsigned int, unsigned int) const’: clust.cpp:613: warning: enumeration value ‘JOIN_Undefined’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used cluster.cpp: In member function ‘void muscle::ClusterTree::Create(const muscle::DistFunc&)’: cluster.cpp:269: warning: unused variable ‘dMaxDist’ cluster.cpp:285: warning: ‘uIndexClosest2’ may be used uninitialized in this function cluster.cpp:284: warning: ‘uIndexClosest1’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ color.cpp:36: warning: missing braces around initializer for ‘const int [23]’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used color.cpp:74: warning: ‘int muscle::BlosumScore(char, char)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used diffobjscore.cpp: In function ‘muscle::SCORE muscle::ScoreLetters(const muscle::MSA&, const unsigned int*, unsigned int)’: diffobjscore.cpp:78: warning: unused variable ‘uSeqCount’ diffobjscore.cpp:79: warning: unused variable ‘uColCount’ diaglist.cpp: In member function ‘void muscle::DiagList::FromPath(const muscle::PWPath&)’: diaglist.cpp:54: warning: ‘uStartPosB’ may be used uninitialized in this function diaglist.cpp:53: warning: ‘uStartPosA’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used difftrees.cpp: In function ‘void muscle::DiffTrees(const muscle::Tree&, const muscle::Tree&, muscle::Tree&, unsigned int*)’: difftrees.cpp:163: warning: unused variable ‘uLeafCount2’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used dpreglist.cpp: In function ‘void muscle::DiagListToDPRegionList(const muscle::DiagList&, muscle::DPRegionList&, unsigned int, unsigned int)’: dpreglist.cpp:84: warning: unused variable ‘uDiagLengthMinusCaps’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used In file included from enumopts.cpp:10: ../libMUSCLE/enums.h:15: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:15: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:15: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:15: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:22: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:22: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:22: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:22: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:22: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:28: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:28: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:28: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:28: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:36: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:36: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:36: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:36: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:36: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:36: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:41: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:41: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:41: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:49: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:49: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:49: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:49: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:49: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:49: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:63: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:70: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:70: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:70: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:70: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:70: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:79: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:88: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:94: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:94: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:94: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/enums.h:94: warning: missing braces around initializer for ‘muscle::EnumOpt’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used estring.cpp: In function ‘void muscle::EstringsToPath(const short int*, const short int*, muscle::PWPath&)’: estring.cpp:379: warning: ‘cType’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used estring.cpp:466: warning: ‘bool muscle::CanMultiplyEstrings(const short int*, const short int*)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used fasta.cpp: In member function ‘void muscle::MSA::FromFASTAFile(muscle::TextFile&)’: fasta.cpp:17: warning: unused variable ‘uSeqCount’ fasta.cpp:18: warning: unused variable ‘uColCount’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used fastdistkmer.cpp: In function ‘void muscle::FastDistKmer(const muscle::SeqVect&, muscle::DistFunc&)’: fastdistkmer.cpp:238: warning: unused variable ‘KD’ fastdistmafft.cpp: In function ‘void muscle::DistKmer6_6(const muscle::SeqVect&, muscle::DistFunc&)’: fastdistmafft.cpp:241: warning: unused variable ‘pName1’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used fastdistmafft.cpp:107: warning: ‘void muscle::ListCount(const unsigned char*)’ defined but not used fastdistnuc.cpp: In function ‘void muscle::DistKmer4_6(const muscle::SeqVect&, muscle::DistFunc&)’: fastdistnuc.cpp:226: warning: unused variable ‘pName1’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used fastdistnuc.cpp:88: warning: ‘void muscle::ListCount(const unsigned char*)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used finddiags.cpp:14: warning: ‘char* muscle::TupleToStr(int)’ defined but not used finddiagsn.cpp: In function ‘char* muscle::TupleToStr(int)’: finddiagsn.cpp:19: warning: comparison between signed and unsigned integer expressions ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used finddiagsn.cpp:15: warning: ‘char* muscle::TupleToStr(int)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalignle.cpp: In function ‘muscle::SCORE muscle::GlobalAlignLE(const muscle::ProfPos*, unsigned int, const muscle::ProfPos*, unsigned int, muscle::PWPath&)’: glbalignle.cpp:403: warning: ‘uInsertPos’ may be used uninitialized in this function ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalignsimple.cpp:32: warning: ‘void muscle::ListTB(const char*, const muscle::ProfPos*, const muscle::ProfPos*, unsigned int, unsigned int)’ defined but not used glbalignsimple.cpp:56: warning: ‘void muscle::ListDP(const muscle::SCORE*, const muscle::ProfPos*, const muscle::ProfPos*, unsigned int, unsigned int)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalignsp.cpp: In function ‘muscle::SCORE muscle::GlobalAlignSP(const muscle::ProfPos*, unsigned int, const muscle::ProfPos*, unsigned int, muscle::PWPath&)’: glbalignsp.cpp:275: warning: ‘uInsertPos’ may be used uninitialized in this function glbalignsp.cpp:342: warning: ‘uInsertPos’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalignspn.cpp: In function ‘muscle::SCORE muscle::GlobalAlignSPN(const muscle::ProfPos*, unsigned int, const muscle::ProfPos*, unsigned int, muscle::PWPath&)’: glbalignspn.cpp:310: warning: ‘uInsertPos’ may be used uninitialized in this function glbalignspn.cpp:377: warning: ‘uInsertPos’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalignss.cpp: In function ‘muscle::SCORE muscle::GlobalAlignSS(const muscle::Seq&, const muscle::Seq&, muscle::PWPath&)’: glbalignss.cpp:180: warning: unused variable ‘ptrRowA’ glbalignss.cpp:122: warning: unused variable ‘uPrefixCountA’ glbalignss.cpp:123: warning: unused variable ‘uPrefixCountB’ glbalignss.cpp:224: warning: ‘uInsertPos’ may be used uninitialized in this function glbalignss.cpp:286: warning: ‘uInsertPos’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalignss.cpp:14: warning: ‘muscle::SCORE muscle::Subst(const muscle::Seq&, const muscle::Seq&, unsigned int, unsigned int)’ defined but not used glbalndimer.cpp: In function ‘muscle::SCORE muscle::ScoreProfPosDimer(const muscle::ProfPos&, const muscle::ProfPos&)’: glbalndimer.cpp:126: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch glbalndimer.cpp:126: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used glbalndimer.cpp:17: warning: ‘const char* muscle::LocalScoreToStr(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used In file included from globalswin32.cpp:1: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used makerootmsa.cpp: In function ‘void muscle::PathSeq(const muscle::Seq&, const muscle::PWPath&, bool, muscle::Seq&)’: makerootmsa.cpp:20: warning: unused variable ‘uSeqLength’ makerootmsa.cpp: In function ‘short int* muscle::MakeRootSeqE(const muscle::Seq&, const muscle::Tree&, unsigned int, const muscle::ProgNode*, muscle::Seq&, short int*, short int*)’: makerootmsa.cpp:95: warning: unused variable ‘Path’ makerootmsa.cpp: In function ‘void muscle::MakeRootMSA(const muscle::SeqVect&, const muscle::Tree&, muscle::ProgNode*, muscle::MSA&)’: makerootmsa.cpp:169: warning: unused variable ‘uTreeNodeCount’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used makerootmsa.cpp:14: warning: ‘void muscle::PathSeq(const muscle::Seq&, const muscle::PWPath&, bool, muscle::Seq&)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used msa2.cpp: In function ‘void muscle::SetMSAWeightsMuscle(muscle::MSA&)’: msa2.cpp:360: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch msa2.cpp: In function ‘void muscle::MSAAppend(muscle::MSA&, const muscle::MSA&)’: msa2.cpp:479: warning: unused variable ‘uColCountCat’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used msa.cpp:388: warning: ‘void muscle::FmtChar(char, unsigned int)’ defined but not used msa.cpp:395: warning: ‘void muscle::FmtInt(unsigned int, unsigned int)’ defined but not used msa.cpp:410: warning: ‘void muscle::FmtInt0(unsigned int, unsigned int)’ defined but not used msa.cpp:422: warning: ‘void muscle::FmtPad(unsigned int)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used msf.cpp:27: warning: ‘const char* muscle::strfind(const char*, const char*)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used objscore2.cpp: In function ‘muscle::SCORE muscle::TermGapScore(bool)’: objscore2.cpp:24: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch objscore2.cpp: In function ‘muscle::SCORE muscle::ScoreSeqPairLetters(const muscle::MSA&, unsigned int, const muscle::MSA&, unsigned int)’: objscore2.cpp:64: warning: unused variable ‘scoreGaps’ objscore2.cpp:65: warning: unused variable ‘bGapping1’ objscore2.cpp:66: warning: unused variable ‘bGapping2’ objscore2.cpp: In function ‘muscle::SCORE muscle::ObjScoreDP(const muscle::MSA&, const muscle::MSA&, muscle::SCORE*)’: objscore2.cpp:316: warning: unused variable ‘uColCount2’ objscore2.cpp: In function ‘muscle::SCORE muscle::ObjScoreXP(const muscle::MSA&, const muscle::MSA&)’: objscore2.cpp:495: warning: unused variable ‘w’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used objscore.cpp: In function ‘muscle::SCORE muscle::ObjScore(const muscle::MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)’: objscore.cpp:33: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch objscore.cpp:33: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:91: warning: missing braces around initializer for ‘muscle::VALUE_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ options.cpp:133: warning: missing braces around initializer for ‘muscle::FLAG_OPT’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ pam200mafft.cpp:34: warning: missing braces around initializer for ‘const float [23]’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used params.cpp: In function ‘void muscle::SetPPScore(bool)’: params.cpp:449: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used phy3.cpp: In function ‘void muscle::CalcInfo(const muscle::Tree&, unsigned int, unsigned int, muscle::EdgeInfo**)’: phy3.cpp:127: warning: unused variable ‘dThisDist’ phy3.cpp: In function ‘void muscle::FindRoot(const muscle::Tree&, unsigned int*, unsigned int*, double*, double*, muscle::ROOT)’: phy3.cpp:169: warning: unused variable ‘uLeafCount’ phy3.cpp:192: warning: unused variable ‘dAllMaxDist’ phy3.cpp:193: warning: unused variable ‘uMaxFrom’ phy3.cpp:194: warning: unused variable ‘uMaxTo’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used phy3.cpp:47: warning: ‘void muscle::ListEIs(muscle::EdgeInfo**, unsigned int)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used phy.cpp: In member function ‘void muscle::Tree::RootUnrootedTree(muscle::ROOT)’: phy.cpp:667: warning: unused variable ‘dEdgeLength’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used physeq.cpp: In member function ‘void muscle::MSA::ToPhySequentialFile(muscle::TextFile&) const’: physeq.cpp:62: warning: comparison between signed and unsigned integer expressions physeq.cpp:73: warning: comparison between signed and unsigned integer expressions physeq.cpp: In member function ‘void muscle::MSA::ToPhyInterleavedFile(muscle::TextFile&) const’: physeq.cpp:114: warning: comparison between signed and unsigned integer expressions physeq.cpp:126: warning: comparison between signed and unsigned integer expressions ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used In file included from ../libMUSCLE/clustsetmsa.h:5, from profdb.cpp:9: ../libMUSCLE/msadist.h: In member function ‘double muscle::MSADist::ComputeDist(const muscle::MSA&, unsigned int, unsigned int)’: ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used profilefrommsa.cpp: In function ‘void muscle::ListProfile(const muscle::ProfPos*, unsigned int, const muscle::MSA*)’: profilefrommsa.cpp:134: warning: comparison between signed and unsigned integer expressions profilefrommsa.cpp: In function ‘unsigned int muscle::ResidueGroupFromFCounts(const muscle::FCOUNT*)’: profilefrommsa.cpp:233: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch profilefrommsa.cpp: In function ‘muscle::ProfPos* muscle::ProfileFromMSA(const muscle::MSA&)’: profilefrommsa.cpp:248: warning: unused variable ‘uSeqCount’ profilefrommsa.cpp:257: warning: unused variable ‘uHydrophobicRunLength’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used profilefrommsa.cpp:18: warning: ‘const char* muscle::LocalScoreToStr(muscle::SCORE)’ defined but not used progalign.cpp: In function ‘muscle::ProgNode* muscle::ProgressiveAlignE(const muscle::SeqVect&, const muscle::Tree&, muscle::MSA&)’: progalign.cpp:43: warning: unused variable ‘uIterCount’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used pwpath.cpp: In member function ‘void muscle::PWPath::Validate() const’: pwpath.cpp:81: warning: unused variable ‘LastEdge’ pwpath.cpp: In member function ‘void muscle::PWPath::FromFile(muscle::TextFile&)’: pwpath.cpp:214: warning: unused variable ‘uEdgeIndex’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used readmx.cpp: In function ‘float (* muscle::ReadMx(muscle::TextFile&))[32][32]’: readmx.cpp:86: warning: comparison between signed and unsigned integer expressions readmx.cpp:87: warning: comparison between signed and unsigned integer expressions ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used readmx.cpp:32: warning: ‘unsigned int muscle::MxCharToLetter(char)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used realigndiffse.cpp: In function ‘void muscle::RealignDiffsE(const muscle::MSA&, const muscle::SeqVect&, const muscle::Tree&, const muscle::Tree&, const unsigned int*, muscle::MSA&, muscle::ProgNode*)’: realigndiffse.cpp:74: warning: unused variable ‘uNewRight’ realigndiffse.cpp:77: warning: unused variable ‘uOldRight’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used In file included from ../libMUSCLE/clustsetmsa.h:5, from refine.cpp:9: ../libMUSCLE/msadist.h: In member function ‘double muscle::MSADist::ComputeDist(const muscle::MSA&, unsigned int, unsigned int)’: ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used refinehoriz.cpp: In function ‘bool muscle::RefineHoriz(muscle::MSA&, const muscle::Tree&, unsigned int, bool, bool)’: refinehoriz.cpp:273: warning: ‘bRight’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used refinesubfams.cpp: In function ‘bool muscle::RefineSubfams(muscle::MSA&, const muscle::Tree&, unsigned int)’: refinesubfams.cpp:65: warning: unused variable ‘uNodeCount’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used refinew.cpp: In function ‘void muscle::AppendMSA(muscle::MSA&, const muscle::MSA&)’: refinew.cpp:25: warning: unused variable ‘uColCountCat’ refinew.cpp: In function ‘void muscle::RefineW(const muscle::MSA&, muscle::MSA&)’: refinew.cpp:151: warning: unused variable ‘uSeqCount’ refinew.cpp:155: warning: unused variable ‘uColCountCat’ refinew.cpp:192: warning: unused variable ‘uOutCols’ ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used scoregaps.cpp:40: warning: ‘void muscle::FreeGapInfo(muscle::GAPINFO*)’ defined but not used scoregaps.cpp:83: warning: ‘muscle::SCORE muscle::Penalty(unsigned int, bool)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used setnewhandler.cpp:13: warning: ignoring #pragma omp critical setnewhandler.cpp:29: warning: ignoring #pragma omp critical ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used spfast.cpp: In function ‘char* muscle::GapTypeToStr(int)’: spfast.cpp:20: warning: deprecated conversion from string constant to ‘char*’ spfast.cpp:21: warning: deprecated conversion from string constant to ‘char*’ spfast.cpp:22: warning: deprecated conversion from string constant to ‘char*’ spfast.cpp:23: warning: deprecated conversion from string constant to ‘char*’ spfast.cpp:26: warning: deprecated conversion from string constant to ‘char*’ spfast.cpp: In function ‘muscle::SCORE muscle::ObjScoreSPDimer(const muscle::MSA&)’: spfast.cpp:254: warning: unused variable ‘uSeqCount’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used spfast.cpp:16: warning: ‘char* muscle::GapTypeToStr(int)’ defined but not used spfast.cpp:61: warning: ‘muscle::SCORE muscle::SPColBrute(const muscle::MSA&, unsigned int)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used subfams.cpp:12: warning: ‘void muscle::GetMostDistantPair(muscle::DistFunc&, unsigned int*, unsigned int*)’ defined but not used subfams.cpp:42: warning: ‘void muscle::InitializeSingleSource(muscle::DistFunc&, unsigned int)’ defined but not used subfams.cpp:54: warning: ‘void muscle::Relax(muscle::DistFunc&, unsigned int, unsigned int)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used sw.cpp:23: warning: ‘void muscle::ListDP(const muscle::SCORE*, const muscle::ProfPos*, const muscle::ProfPos*, unsigned int, unsigned int)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used textfile.cpp: In member function ‘void muscle::TextFile::PutChar(char)’: textfile.cpp:109: warning: unused variable ‘i’ textfile.cpp: In member function ‘void muscle::TextFile::PutString(const char*)’: textfile.cpp:122: warning: unused variable ‘iError’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used traceback.cpp: In function ‘muscle::SCORE muscle::TraceBack(const muscle::ProfPos*, unsigned int, const muscle::ProfPos*, unsigned int, const muscle::SCORE*, const muscle::SCORE*, const muscle::SCORE*, muscle::PWPath&)’: traceback.cpp:23: warning: unused variable ‘uPrefixCountB’ traceback.cpp:70: warning: ‘cPrevEdgeType’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used tracebacksw.cpp: In function ‘void muscle::TraceBackSW(const muscle::ProfPos*, unsigned int, const muscle::ProfPos*, unsigned int, const muscle::SCORE*, const muscle::SCORE*, const muscle::SCORE*, unsigned int, unsigned int, muscle::PWPath&)’: tracebacksw.cpp:24: warning: unused variable ‘uPrefixCountB’ tracebacksw.cpp:31: warning: unused variable ‘scoreMax’ tracebacksw.cpp:45: warning: ‘cPrevEdgeType’ may be used uninitialized in this function ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used In file included from ../libMUSCLE/clustsetmsa.h:5, from treefrommsa.cpp:5: ../libMUSCLE/msadist.h: In member function ‘double muscle::MSADist::ComputeDist(const muscle::MSA&, unsigned int, unsigned int)’: ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch ../libMUSCLE/msadist.h:26: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used typetostr.cpp: In function ‘const char* muscle::SecsToStr(long unsigned int)’: typetostr.cpp:15: warning: format ‘%02d’ expects type ‘int’, but argument 3 has type ‘long int’ typetostr.cpp:15: warning: format ‘%02d’ expects type ‘int’, but argument 4 has type ‘long int’ typetostr.cpp:15: warning: format ‘%02d’ expects type ‘int’, but argument 5 has type ‘long int’ ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used upgma2.cpp: In member function ‘virtual void muscle::DistCalcTest::CalcDistRange(unsigned int, muscle::dist_t*) const’: upgma2.cpp:373: warning: missing braces around initializer for ‘muscle::dist_t [5]’ upgma2.cpp:373: warning: missing braces around initializer for ‘muscle::dist_t [5]’ upgma2.cpp:373: warning: missing braces around initializer for ‘muscle::dist_t [5]’ upgma2.cpp:373: warning: missing braces around initializer for ‘muscle::dist_t [5]’ upgma2.cpp:373: warning: missing braces around initializer for ‘muscle::dist_t [5]’ upgma2.cpp:375: warning: array subscript is above array bounds upgma2.cpp: In function ‘void muscle::UPGMA2(const muscle::DistCalc&, muscle::Tree&, muscle::LINKAGE)’: upgma2.cpp:254: warning: ‘dtNewDist’ may be used uninitialized in this function usage.cpp:8: warning: ignoring #pragma omp critical ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h: At global scope: ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used upgma2.cpp:70: warning: ‘void muscle::ListState()’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used make[1]: *** No rule to make target `../libMUSCLE/libMUSCLE-3.7.la', needed by `muscle'. Stop. make[1]: *** Waiting for unfinished jobs.... ../libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used make: *** [all-recursive] Error 1 configure.ac:66: installing `config/config.guess' configure.ac:66: installing `config/config.sub' configure.ac:54: installing `config/install-sh' configure.ac:54: installing `config/missing' libMems/Makefile.am: installing `config/depcomp' configure: WARNING: latex not found - will not generate doxygen PostScript documentation configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation In file included from ../libMems/DNAFileSML.h:16, from DNAFileSML.cpp:15: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from DNAFileSML.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/FileSML.h:21, from ../libMems/DNAFileSML.h:16, from DNAFileSML.cpp:15: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/RepeatHash.h:16, from RepeatHash.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: RepeatHash.cpp:64: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MatchFinder.h:16, from MatchFinder.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions MatchFinder.cpp: In member function ‘virtual boolean mems::MatchFinder::SearchRange(std::vector >&, std::vector >&)’: MatchFinder.cpp:270: warning: comparison between signed and unsigned integer expressions MatchFinder.cpp:273: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: MatchFinder.cpp:444: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from DNAMemorySML.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MemorySML.h:17, from ../libMems/DNAMemorySML.h:17, from DNAMemorySML.cpp:14: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MemorySML.h:17, from MemorySML.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from SortedMerList.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from SortedMerList.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ SortedMerList.cpp: In member function ‘virtual void mems::SortedMerList::FindAll(const std::string&, std::vector >)’: SortedMerList.cpp:227: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function ‘virtual void mems::SortedMerList::translate(uint8*, const gnSeqC*, gnSeqI) const’: SortedMerList.cpp:404: warning: array subscript has type ‘char’ SortedMerList.cpp: In member function ‘virtual void mems::SortedMerList::translate32(uint32*, const gnSeqC*, gnSeqI) const’: SortedMerList.cpp:433: warning: array subscript has type ‘char’ SortedMerList.cpp: In member function ‘virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector >&)’: SortedMerList.cpp:543: warning: array subscript has type ‘char’ SortedMerList.cpp:555: warning: array subscript has type ‘char’ SortedMerList.cpp: In member function ‘virtual uint64 mems::SortedMerList::GetSeedMer(gnSeqI) const’: SortedMerList.cpp:738: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function ‘virtual void mems::SortedMerList::Create(const genome::gnSequence&, uint64)’: SortedMerList.cpp:789: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function ‘virtual gnSeqI mems::SortedMerList::UniqueMerCount()’: SortedMerList.cpp:467: warning: ‘prev_mer.mems::bmer::mer’ may be used uninitialized in this function In file included from FileSML.cpp:10: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/FileSML.h:20, from FileSML.cpp:10: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/FileSML.h:21, from FileSML.cpp:10: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from ../libMems/Aligner.h:18, from FileSML.cpp:12: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from FileSML.cpp:12: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/GreedyBreakpointElimination.h:15, from ../libMems/Aligner.h:26, from FileSML.cpp:12: ../libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from FileSML.cpp:12: ../libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions FileSML.cpp: In function ‘void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector >&, int)’: FileSML.cpp:253: warning: comparison between signed and unsigned integer expressions FileSML.cpp: In member function ‘void mems::FileSML::dmCreate(const genome::gnSequence&, uint64)’: FileSML.cpp:297: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions MemHash.cpp: In member function ‘virtual void mems::MemHash::SetDirection(mems::MatchHashEntry&)’: MemHash.cpp:194: warning: comparison between signed and unsigned integer expressions MemHash.cpp:200: warning: comparison between signed and unsigned integer expressions MemHash.cpp: In member function ‘virtual mems::MatchHashEntry* mems::MemHash::AddHashEntry(mems::MatchHashEntry&)’: MemHash.cpp:245: warning: unused variable ‘submem’ ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: FileSML.cpp:679: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h: In member function ‘void mems::MatchFinder::ExtendMatch(UngappedMatchType&, std::vector >&, gnSeqI, gnSeqI) [with UngappedMatchType = mems::MatchHashEntry]’: MemHash.cpp:226: instantiated from here ../libMems/MatchFinder.h:227: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h:250: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h:332: warning: comparison between signed and unsigned integer expressions ../libMems/MatchFinder.h:338: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: MemHash.cpp:330: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used ../libMems/dmSML/sml.h:21: warning: ‘uint8* mems::CreateBasicDNATable()’ defined but not used ../libMems/dmSML/sml.h:41: warning: ‘mems::DNA_TABLE’ defined but not used ../libMems/dmSML/sml.h:45: warning: ‘mems::seed_mask’ defined but not used ../libMems/dmSML/sml.h:46: warning: ‘mems::mask_length’ defined but not used ../libMems/dmSML/sml.h:47: warning: ‘mems::mask_weight’ defined but not used ../libMems/dmSML/dmsort.h:108: warning: ‘mems::buffer_t* mems::AllocateFree()’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:110: warning: ‘int mems::ComputeBinNumber(const unsigned char*)’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:113: warning: ‘int mems::ComputeNNNNNBinNumber(const unsigned char*)’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:115: warning: ‘int mems::ComputeAsciiBinNumber(const unsigned char*)’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:117: warning: ‘void mems::DoBinning()’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:123: warning: ‘void mems::DoReading()’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:125: warning: ‘void mems::HandleBinWriteCompletions()’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:127: warning: ‘void mems::HandleSeqbufWriteCompletions()’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:131: warning: ‘void mems::Translate32(uint32*, const char*, unsigned int)’ declared ‘static’ but never defined ../libMems/dmSML/dmsort.h:135: warning: ‘void mems::HandleReadingCompletions()’ declared ‘static’ but never defined MatchHashEntry.cpp: In static member function ‘static boolean mems::MatchHashEntry::start_lessthan_ptr(const mems::MatchHashEntry*, const mems::MatchHashEntry*)’: MatchHashEntry.cpp:37: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:37: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp: In static member function ‘static int64 mems::MatchHashEntry::start_compare(const mems::MatchHashEntry&, const mems::MatchHashEntry&)’: MatchHashEntry.cpp:81: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:81: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp: In member function ‘virtual void mems::MatchHashEntry::CalculateOffset()’: MatchHashEntry.cpp:153: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp: In member function ‘boolean mems::MatchHashEntry::Contains(const mems::MatchHashEntry&) const’: MatchHashEntry.cpp:176: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:191: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:191: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: MatchHashEntry.cpp:203: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:203: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:203: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: MatchHashEntry.cpp:203: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/gnAlignedSequences.h:32, from ../libMems/Interval.h:19, from Interval.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from IntervalList.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/IntervalList.h:20, from IntervalList.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/IntervalList.h:20, from IntervalList.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from IntervalList.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: IntervalList.cpp:25: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/gnAlignedSequences.h:32, from gnAlignedSequences.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ gnAlignedSequences.cpp: In member function ‘void mems::gnAlignedSequences::constructFromClustalW(std::string)’: gnAlignedSequences.cpp:47: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘void mems::gnAlignedSequences::constructFromPhylip(std::string)’: gnAlignedSequences.cpp:60: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘void mems::gnAlignedSequences::constructFromMSF(std::string)’: gnAlignedSequences.cpp:73: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘void mems::gnAlignedSequences::constructFromNexus(std::string)’: gnAlignedSequences.cpp:95: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘void mems::gnAlignedSequences::constructFromMega(std::string)’: gnAlignedSequences.cpp:108: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In static member function ‘static boolean mems::gnAlignedSequences::isSupportedFormat(const std::string&)’: gnAlignedSequences.cpp:129: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputPhylip(std::ostream&) const’: gnAlignedSequences.cpp:179: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputClustalW(std::ostream&) const’: gnAlignedSequences.cpp:221: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:227: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:245: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputMSF(std::ostream&) const’: gnAlignedSequences.cpp:275: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:280: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:313: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:320: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:333: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputNexus(std::ostream&) const’: gnAlignedSequences.cpp:366: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:367: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:372: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:384: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:400: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:409: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:414: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputMega(std::ostream&) const’: gnAlignedSequences.cpp:521: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:530: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:541: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputCodon(std::ostream&) const’: gnAlignedSequences.cpp:566: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:582: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:596: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::outputWithConsensus(std::ostream&)’: gnAlignedSequences.cpp:618: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:634: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:648: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:657: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:671: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘mems::gnAlignedSequences mems::gnAlignedSequences::getCodons(int, int, int)’: gnAlignedSequences.cpp:696: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::removeAlignedSeq(unsigned int)’: gnAlignedSequences.cpp:737: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::constructClustalWAlignedSequenceList(std::ifstream&)’: gnAlignedSequences.cpp:1101: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::constructPhylipAlignedSequenceList(std::ifstream&)’: gnAlignedSequences.cpp:1147: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1170: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::constructMSFAlignedSequenceList(std::ifstream&)’: gnAlignedSequences.cpp:1211: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::constructNexusAlignedSequenceList(std::ifstream&)’: gnAlignedSequences.cpp:1259: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1257: warning: unused variable ‘newFilter’ gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::constructMegaAlignedSequenceList(std::ifstream&)’: gnAlignedSequences.cpp:1315: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::buildConsensus()’: gnAlignedSequences.cpp:1384: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1390: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1409: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘void mems::gnAlignedSequences::addSequence(genome::gnSequence, std::string, int, std::string)’: gnAlignedSequences.cpp:1477: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1492: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp: In member function ‘bool mems::gnAlignedSequences::coordinates(std::string)’: gnAlignedSequences.cpp:1558: warning: comparison between signed and unsigned integer expressions ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from MatchList.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/MatchList.h:18, from MatchList.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MatchList.h:18, from MatchList.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/Aligner.h:16, from Aligner.cpp:9: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MemorySML.h:17, from ../libMems/DNAMemorySML.h:17, from ../libMems/Aligner.h:17, from Aligner.cpp:9: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/MatchList.h:25, from MatchList.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Aligner.h:18, from Aligner.cpp:9: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: MatchList.cpp:26: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from ../libMems/GreedyBreakpointElimination.h:15, from ../libMems/Aligner.h:26, from Aligner.cpp:9: ../libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from Aligner.cpp:9: ../libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:26, from Aligner.cpp:10: ../libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: ../libMems/Scoring.h:133: warning: array subscript has type ‘char’ ../libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from Aligner.cpp:10: ../libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: ../libMems/Islands.h:135: warning: array subscript has type ‘char’ ../libMems/Islands.h:136: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from Aligner.cpp:14: ../libMems/DistanceMatrix.h: In function ‘void mems::SingleCopyDistanceMatrix(MatchVector&, std::vector >&, NumericMatrix&)’: ../libMems/DistanceMatrix.h:241: warning: suggest explicit braces to avoid ambiguous ‘else’ ../libMems/DistanceMatrix.h:246: warning: suggest explicit braces to avoid ambiguous ‘else’ ../libMems/DistanceMatrix.h: In function ‘void mems::TransformDistanceIdentity(NumericMatrix&)’: ../libMems/DistanceMatrix.h:277: warning: comparison between signed and unsigned integer expressions ../libMems/DistanceMatrix.h:278: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘boolean mems::validateLCB(mems::MatchList&)’: Aligner.cpp:47: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::EliminateOverlaps(mems::MatchList&)’: Aligner.cpp:76: warning: comparison between signed and unsigned integer expressions Aligner.cpp:77: warning: comparison between signed and unsigned integer expressions Aligner.cpp:80: warning: comparison between signed and unsigned integer expressions Aligner.cpp:84: warning: comparison between signed and unsigned integer expressions Aligner.cpp:127: warning: comparison between signed and unsigned integer expressions Aligner.cpp:164: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In constructor ‘mems::Aligner::Aligner(uint)’: ../libMems/Aligner.h:201: warning: ‘mems::Aligner::debug’ will be initialized after ../libMems/Aligner.h:200: warning: ‘uint32 mems::Aligner::seq_count’ Aligner.cpp:180: warning: when initialized here ../libMems/Aligner.h:223: warning: ‘mems::Aligner::permutation_weight’ will be initialized after ../libMems/Aligner.h:208: warning: ‘int64 mems::Aligner::cur_min_coverage’ Aligner.cpp:180: warning: when initialized here ../libMems/Aligner.h:208: warning: ‘mems::Aligner::cur_min_coverage’ will be initialized after ../libMems/Aligner.h:206: warning: ‘uint mems::Aligner::max_extension_iters’ Aligner.cpp:180: warning: when initialized here ../libMems/Aligner.h: In copy constructor ‘mems::Aligner::Aligner(const mems::Aligner&)’: ../libMems/Aligner.h:223: warning: ‘mems::Aligner::permutation_weight’ will be initialized after ../libMems/Aligner.h:222: warning: ‘std::string mems::Aligner::permutation_filename’ Aligner.cpp:191: warning: when initialized here ../libMems/Aligner.h:222: warning: ‘mems::Aligner::permutation_filename’ will be initialized after ../libMems/Aligner.h:206: warning: ‘uint mems::Aligner::max_extension_iters’ Aligner.cpp:191: warning: when initialized here Aligner.cpp: In function ‘boolean mems::checkCollinearity(mems::Match*, mems::Match*)’: Aligner.cpp:269: warning: comparison between signed and unsigned integer expressions Aligner.cpp:270: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::scanFit(std::list >&, std::_List_iterator&, mems::Match*, uint)’: Aligner.cpp:292: warning: comparison between signed and unsigned integer expressions Aligner.cpp:318: warning: comparison between signed and unsigned integer expressions Aligner.cpp:320: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::AaronsLCB(mems::MatchList&, std::set, std::allocator >&)’: Aligner.cpp:385: warning: comparison between signed and unsigned integer expressions Aligner.cpp:415: warning: comparison between signed and unsigned integer expressions Aligner.cpp:430: warning: comparison between signed and unsigned integer expressions Aligner.cpp:434: warning: comparison between signed and unsigned integer expressions Aligner.cpp:510: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::GetLCBCoverage(mems::MatchList&, uint64&)’: Aligner.cpp:602: warning: unused variable ‘debug’ Aligner.cpp: In function ‘void mems::computeLCBAdjacencies_v2(mems::IntervalList&, std::vector >&, std::vector >&)’: Aligner.cpp:664: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::CreateGapSearchList(std::vector >&, const std::vector >&, std::vector >, std::allocator > > >&, boolean)’: Aligner.cpp:738: warning: comparison between signed and unsigned integer expressions Aligner.cpp:739: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::SearchLCBGaps(mems::MatchList&, const std::vector >, std::allocator > > >&, mems::MaskedMemHash&)’: Aligner.cpp:929: warning: comparison between signed and unsigned integer expressions Aligner.cpp:798: warning: unused variable ‘lcbI’ Aligner.cpp: In function ‘void mems::transposeMatches(mems::MatchList&, uint, const std::vector >&)’: Aligner.cpp:991: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1012: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function ‘void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)’: Aligner.cpp:1099: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1100: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1118: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1126: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1242: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::AlignLCBInParallel(bool, mems::GappedAligner*, mems::MatchList&, mems::Interval&, mems::AlnProgressTracker&)’: Aligner.cpp:1305: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1318: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1300: warning: unused variable ‘galI’ Aligner.cpp: In member function ‘void mems::Aligner::AlignLCB(mems::MatchList&, mems::Interval&)’: Aligner.cpp:1405: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1405: warning: suggest parentheses around && within || Aligner.cpp:1403: warning: unused variable ‘matchI’ Aligner.cpp: In member function ‘void mems::Aligner::SearchWithinLCB(mems::MatchList&, std::vector, std::allocator > >&, bool, bool)’: Aligner.cpp:1495: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1495: warning: suggest parentheses around && within || Aligner.cpp:1478: warning: unused variable ‘config_value’ Aligner.cpp: In function ‘int64 mems::greedyBreakpointElimination(gnSeqI, std::vector >&, std::vector >&, std::ostream*)’: Aligner.cpp:1642: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1646: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1690: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1690: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1694: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1699: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1702: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1704: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1715: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1715: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1722: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1723: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1730: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1730: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1747: warning: suggest parentheses around comparison in operand of != Aligner.cpp:1773: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1780: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In function ‘void mems::filterMatches(std::vector >&, std::vector, std::allocator > >&, std::vector >&)’: Aligner.cpp:1822: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1838: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1841: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1841: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1851: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1851: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function ‘void mems::Aligner::WritePermutation(std::vector >&, std::string)’: Aligner.cpp:1894: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1898: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1901: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1907: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function ‘void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector, std::allocator > >&, boolean, std::ostream*)’: Aligner.cpp:1994: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2029: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2042: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2046: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2040: warning: unused variable ‘prev_size’ Aligner.cpp:2124: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2139: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: Aligner.cpp:1804: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h: In function ‘int64 mems::greedyBreakpointElimination_v4(std::vector >&, std::vector >&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::SimpleBreakpointScorer]’: Aligner.cpp:2099: instantiated from here ../libMems/GreedyBreakpointElimination.h:664: warning: unused variable ‘seq_count’ ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::Match*, _Compare = mems::MatchStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::MatchStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]’ Aligner.cpp:1873: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: Aligner.cpp:2288: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/Islands.h:16, from Islands.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/IntervalList.h:20, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from ../libMems/Islands.h:18, from Islands.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Aligner.h:18, from ../libMems/Islands.h:23, from Islands.cpp:13: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/GreedyBreakpointElimination.h:15, from ../libMems/Aligner.h:26, from ../libMems/Islands.h:23, from Islands.cpp:13: ../libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:23, from Islands.cpp:13: ../libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:26, from Islands.cpp:13: ../libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: ../libMems/Scoring.h:133: warning: array subscript has type ‘char’ ../libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from Islands.cpp:13: ../libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: ../libMems/Islands.h:135: warning: array subscript has type ‘char’ ../libMems/Islands.h:136: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ Islands.cpp: In function ‘void mems::addUnalignedIntervals(mems::IntervalList&, std::set, std::allocator >, std::vector >)’: Islands.cpp:279: warning: comparison between signed and unsigned integer expressions Islands.cpp: In function ‘void mems::findIslandsBetweenLCBs(mems::IntervalList&, uint, std::ostream&)’: Islands.cpp:307: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: Islands.cpp:320: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/MaskedMemHash.h:16, from MaskedMemHash.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions MaskedMemHash.cpp: In member function ‘virtual boolean mems::MaskedMemHash::HashMatch(std::list >&)’: MaskedMemHash.cpp:56: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: MaskedMemHash.cpp:65: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/GappedAlignment.h:17, from GappedAlignment.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions In file included from MuscleInterface.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/muscle.h:54:1: warning: "assert" redefined In file included from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/pending/integer_log2.hpp:18, from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/pending/lowest_bit.hpp:18, from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/dynamic_bitset/dynamic_bitset.hpp:41, from /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/dynamic_bitset.hpp:15, from ../libMems/AbstractMatch.h:21, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: /usr/include/assert.h:88:1: warning: this is the location of the previous definition ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/MuscleInterface.h:18, from MuscleInterface.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/MuscleInterface.h:20, from MuscleInterface.cpp:13: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp: In function ‘char** mems::parseCommand(const std::string&)’: MuscleInterface.cpp:78: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:61: warning: unused variable ‘token_count’ MuscleInterface.cpp: In function ‘bool mems::pipeExec(char**, const std::string&, const std::string&, std::string&, std::string&)’: MuscleInterface.cpp:95: warning: unused variable ‘stderr_pipe’ MuscleInterface.cpp: In member function ‘virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector >&)’: MuscleInterface.cpp:449: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:450: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:461: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:429: warning: unused variable ‘gap_size’ MuscleInterface.cpp:434: warning: unused variable ‘align_seqs’ MuscleInterface.cpp: In member function ‘boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::AbstractMatch*, mems::AbstractMatch*, std::vector >&)’: MuscleInterface.cpp:550: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:551: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:575: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:630: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:633: warning: unused variable ‘gap_end’ MuscleInterface.cpp:634: warning: unused variable ‘gap_start’ MuscleInterface.cpp:524: warning: unused variable ‘gap_size’ MuscleInterface.cpp:534: warning: unused variable ‘align_seqs’ MuscleInterface.cpp: In member function ‘bool mems::MuscleInterface::ProfileAlign(const mems::GappedAlignment&, const mems::GappedAlignment&, mems::GappedAlignment&, bool)’: MuscleInterface.cpp:1022: warning: unused variable ‘seqI’ ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/RepeatMatchList.h:21, from RepeatMatchList.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/RepeatMatchList.h:18, from RepeatMatchList.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/RepeatMatchList.h:18, from RepeatMatchList.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/intmath.h:61: warning: ‘double muscle::ScoreToDouble(muscle::SCORE)’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from ../libMems/MatchList.h:25, from ../libMems/RepeatMatchList.h:21, from RepeatMatchList.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: RepeatMatchList.cpp:300: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: RepeatMatch.cpp:51: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions RepeatMatch.cpp:51: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions RepeatMatch.cpp:51: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: RepeatMatch.cpp:51: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17, from Backbone.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/gnAlignedSequences.h:32, from ../libMems/Interval.h:19, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from Backbone.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MemorySML.h:17, from ../libMems/DNAMemorySML.h:17, from ../libMems/Aligner.h:17, from ../libMems/ProgressiveAligner.h:17, from Backbone.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/Aligner.h:18, from ../libMems/ProgressiveAligner.h:17, from Backbone.cpp:13: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17, from Backbone.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/GreedyBreakpointElimination.h:15, from ../libMems/Aligner.h:26, from ../libMems/ProgressiveAligner.h:17, from Backbone.cpp:13: ../libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/ProgressiveAligner.h:17, from Backbone.cpp:13: ../libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:26, from ../libMems/ProgressiveAligner.h:21, from Backbone.cpp:13: ../libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: ../libMems/Scoring.h:133: warning: array subscript has type ‘char’ ../libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from ../libMems/ProgressiveAligner.h:21, from Backbone.cpp:13: ../libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: ../libMems/Islands.h:135: warning: array subscript has type ‘char’ ../libMems/Islands.h:136: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ Backbone.cpp: In function ‘void mems::collapseCollinear(mems::IntervalList&)’: Backbone.cpp:141: warning: unused variable ‘unknown_count’ Backbone.cpp: In function ‘double mems::computeGC(std::vector >&)’: Backbone.cpp:310: warning: array subscript has type ‘char’ Backbone.cpp: In function ‘void mems::mergePairwiseHomologyPredictions(std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >&, mems::pairwise_genome_hss_t&, std::vector >, std::allocator > > >&)’: Backbone.cpp:536: warning: comparison between signed and unsigned integer expressions Backbone.cpp:587: warning: comparison between signed and unsigned integer expressions Backbone.cpp: In function ‘void mems::unalignIslands(mems::IntervalList&, std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >&, std::vector >, std::allocator > > >&)’: Backbone.cpp:743: warning: comparison between signed and unsigned integer expressions Backbone.cpp: In function ‘void mems::createBackboneList(const mems::IntervalList&, mems::backbone_list_t&)’: Backbone.cpp:853: warning: comparison between signed and unsigned integer expressions Backbone.cpp:853: warning: comparison between signed and unsigned integer expressions Backbone.cpp:855: warning: comparison between signed and unsigned integer expressions Backbone.cpp:855: warning: comparison between signed and unsigned integer expressions Backbone.cpp:857: warning: comparison between signed and unsigned integer expressions Backbone.cpp:857: warning: comparison between signed and unsigned integer expressions Backbone.cpp: In function ‘void mems::addUniqueSegments(std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, size_t)’: Backbone.cpp:999: warning: comparison between signed and unsigned integer expressions Backbone.cpp: In function ‘void mems::mergeAdjacentSegments(std::vector, std::allocator > >, std::allocator, std::allocator > > > >&)’: Backbone.cpp:1031: warning: suggest parentheses around comparison in operand of ^ Backbone.cpp: In function ‘void mems::writeBackboneSeqCoordinates(mems::backbone_list_t&, mems::IntervalList&, std::ostream&)’: Backbone.cpp:1175: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ ../libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: ../libMems/Backbone.h:120: instantiated from here ../libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ ../libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: ../libMems/Backbone.h:122: instantiated from here ../libMems/Islands.h:231: warning: unused variable ‘iv’ ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::GenericInterval, std::allocator > > >]’: Backbone.cpp:69: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::GenericInterval, std::allocator > > >, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: Backbone.cpp:344: instantiated from here ../libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::AbstractMatch, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: Backbone.cpp:895: instantiated from here ../libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/PairwiseMatchFinder.h:16, from PairwiseMatchFinder.cpp:13: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning ../libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::CompactGappedAlignment, std::allocator > > >, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ../libMems/Islands.h:291: instantiated from ‘void mems::HssArrayToCga(const MatchVector&, std::vector >&, mems::hss_array_t&, std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’ Backbone.cpp:351: instantiated from here ../libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SortedMerList.h:19, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/PairwiseMatchFinder.h:16, from PairwiseMatchFinder.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MatchFinder.h:16, from ../libMems/MemHash.h:20, from ../libMems/PairwiseMatchFinder.h:16, from PairwiseMatchFinder.cpp:13: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ ../libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::CropRight(gnSeqI, uint) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ../libMems/ProgressiveAligner.h:536: instantiated from ‘void mems::GenericMatchSeqManipulator::CropRight(MatchType*&, gnSeqI) const [with MatchType = mems::CompactGappedAlignment, std::allocator > > >]’ ../libMems/ProgressiveAligner.h:596: instantiated from ‘void mems::applyBreakpoints(std::vector >&, std::vector >&, Maniplator&) [with T = mems::CompactGappedAlignment, std::allocator > > >*, Maniplator = mems::GenericMatchSeqManipulator, std::allocator > > > >]’ Backbone.cpp:363: instantiated from here ../libMems/CompactGappedAlignment.h:620: warning: unused variable ‘pre_lend’ ../libMems/CompactGappedAlignment.h:621: warning: unused variable ‘pre_lend0’ ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::CompactGappedAlignment, std::allocator > > >]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::CompactGappedAlignment, std::allocator > > >*, _Compare = mems::SingleStartComparator, std::allocator > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator > > >**, std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> > >, _Size = long int, _Compare = mems::SingleStartComparator, std::allocator > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator, std::allocator > > >**, std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> > >, _Compare = mems::SingleStartComparator, std::allocator > > > >]’ Backbone.cpp:362: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::Match*, _Compare = mems::SingleStartComparator, std::allocator > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SingleStartComparator, std::allocator > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SingleStartComparator, std::allocator > > >]’ Backbone.cpp:487: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SingleStartComparator]’ Backbone.cpp:738: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/PairwiseMatchFinder.h:16, from PairwiseMatchFinder.cpp:13: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: ../libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ ../libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ ../libMems/ProgressiveAligner.h:521: instantiated from here ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: PairwiseMatchFinder.cpp:73: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: Backbone.cpp:1191: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/gnAlignedSequences.h:32, from ../libMems/Interval.h:19, from ../libMems/SuperInterval.h:8, from ../libMems/ProgressiveAligner.h:16, from ProgressiveAligner.cpp:14: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/MemorySML.h:17, from ../libMems/DNAMemorySML.h:17, from ../libMems/Aligner.h:17, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from ../libMems/Aligner.h:18, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/GreedyBreakpointElimination.h:15, from ../libMems/Aligner.h:26, from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/ProgressiveAligner.h:17, from ProgressiveAligner.cpp:14: ../libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:26, from ../libMems/ProgressiveAligner.h:21, from ProgressiveAligner.cpp:14: ../libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: ../libMems/Scoring.h:133: warning: array subscript has type ‘char’ ../libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from ../libMems/ProgressiveAligner.h:21, from ProgressiveAligner.cpp:14: ../libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: ../libMems/Islands.h:135: warning: array subscript has type ‘char’ ../libMems/Islands.h:136: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from ProgressiveAligner.cpp:25: ../libMems/PairwiseMatchAdapter.h: In member function ‘virtual uint mems::PairwiseMatchAdapter::UsedSeq(uint) const’: ../libMems/PairwiseMatchAdapter.h:101: warning: comparison between signed and unsigned integer expressions ../libMems/PairwiseMatchAdapter.h:103: warning: comparison between signed and unsigned integer expressions In file included from ProgressiveAligner.cpp:26: ../libMems/DistanceMatrix.h: In function ‘void mems::SingleCopyDistanceMatrix(MatchVector&, std::vector >&, NumericMatrix&)’: ../libMems/DistanceMatrix.h:241: warning: suggest explicit braces to avoid ambiguous ‘else’ ../libMems/DistanceMatrix.h:246: warning: suggest explicit braces to avoid ambiguous ‘else’ ../libMems/DistanceMatrix.h: In function ‘void mems::TransformDistanceIdentity(NumericMatrix&)’: ../libMems/DistanceMatrix.h:277: warning: comparison between signed and unsigned integer expressions ../libMems/DistanceMatrix.h:278: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In function ‘boolean mems::my_validateLCB(mems::MatchList&)’: ProgressiveAligner.cpp:83: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In function ‘double mems::getDefaultBreakpointPenalty(std::vector >&)’: ProgressiveAligner.cpp:111: warning: unused variable ‘default_mer_size’ ../libMems/ProgressiveAligner.h: In constructor ‘mems::ProgressiveAligner::ProgressiveAligner(uint)’: ../libMems/ProgressiveAligner.h:216: warning: ‘mems::ProgressiveAligner::conservation_dist_scale’ will be initialized after ../libMems/ProgressiveAligner.h:215: warning: ‘double mems::ProgressiveAligner::bp_dist_scale’ ProgressiveAligner.cpp:136: warning: when initialized here ../libMems/ProgressiveAligner.h:220: warning: ‘mems::ProgressiveAligner::max_gapped_alignment_length’ will be initialized after ../libMems/ProgressiveAligner.h:218: warning: ‘double mems::ProgressiveAligner::bp_dist_estimate_score’ ProgressiveAligner.cpp:136: warning: when initialized here ../libMems/ProgressiveAligner.h:218: warning: ‘mems::ProgressiveAligner::bp_dist_estimate_score’ will be initialized after ../libMems/ProgressiveAligner.h:213: warning: ‘bool mems::ProgressiveAligner::use_seed_families’ ProgressiveAligner.cpp:136: warning: when initialized here ../libMems/ProgressiveAligner.h:213: warning: ‘mems::ProgressiveAligner::use_seed_families’ will be initialized after ../libMems/ProgressiveAligner.h:205: warning: ‘bool mems::ProgressiveAligner::using_cache_db’ ProgressiveAligner.cpp:136: warning: when initialized here ProgressiveAligner.cpp: In function ‘boolean mems::getInterveningCoordinates(const mems::AbstractMatch*, uint, mems::Match*, mems::Match*, uint, int64&, int64&)’: ProgressiveAligner.cpp:568: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:569: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::pairwiseAnchorSearch(mems::MatchList&, mems::Match*, mems::Match*, const mems::AbstractMatch*, uint, uint)’: ProgressiveAligner.cpp:608: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In function ‘int mems::IsDenseEnough(mems::GappedAlignment*)’: ProgressiveAligner.cpp:1018: warning: unused variable ‘seqs’ ProgressiveAligner.cpp: In function ‘void mems::splitGappedAlignment(const mems::GappedAlignment&, mems::GappedAlignment&, mems::GappedAlignment&, std::vector >&, std::vector >&)’: ProgressiveAligner.cpp:1042: warning: unused variable ‘aln’ ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::refineAlignment(mems::GappedAlignment&, node_id_t, bool, mems::AlnProgressTracker&)’: ProgressiveAligner.cpp:1182: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:1186: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In function ‘void mems::markAsRefined(PhyloTree&, node_id_t)’: ProgressiveAligner.cpp:1779: warning: unused variable ‘refined_count’ ProgressiveAligner.cpp: In member function ‘bool mems::ProgressiveAligner::validateSuperIntervals(node_id_t, node_id_t, node_id_t)’: ProgressiveAligner.cpp:2817: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:2822: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In function ‘void mems::findMidpoint(PhyloTree&, node_id_t&, node_id_t&)’: ProgressiveAligner.cpp:2984: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:3049: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In function ‘void mems::chooseNextAlignmentPair(PhyloTree&, node_id_t&, node_id_t&, node_id_t&)’: ProgressiveAligner.cpp:3144: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:3157: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:3161: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::extractAlignment(node_id_t, size_t, mems::CompactGappedAlignment, std::allocator > > >&)’: ProgressiveAligner.cpp:3335: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::CreatePairwiseBPDistance(boost::multi_array >&)’: ProgressiveAligner.cpp:3394: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::alignPP(mems::IntervalList&, mems::IntervalList&, mems::IntervalList&)’: ProgressiveAligner.cpp:3657: warning: unused variable ‘bp_range’ ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::align(std::vector >&, mems::IntervalList&)’: ProgressiveAligner.cpp:3901: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ ProgressiveAligner.cpp: In function ‘void mems::applyAncestralBreakpoints(const std::vector >&, std::vector >&, uint, Manipulator&) [with T = mems::AbstractMatch*, Manipulator = mems::AbstractMatchSeqManipulator]’: ProgressiveAligner.cpp:363: instantiated from here ProgressiveAligner.cpp:259: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::Interval, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ProgressiveAligner.cpp:461: instantiated from here ../libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::AbstractMatch, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ProgressiveAligner.cpp:473: instantiated from here ../libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::translate(mems::CompactGappedAlignment&, uint, uint, bool) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ProgressiveAligner.cpp:476: instantiated from here ../libMems/CompactGappedAlignment.h:350: warning: unused variable ‘my_orient’ ../libMems/CompactGappedAlignment.h:362: warning: unused variable ‘my_lend’ ../libMems/CompactGappedAlignment.h:363: warning: unused variable ‘my_len’ ../libMems/CompactGappedAlignment.h:364: warning: unused variable ‘my_count’ ../libMems/CompactGappedAlignment.h:365: warning: unused variable ‘seqI’ ../libMems/CompactGappedAlignment.h:370: warning: unused variable ‘cur_bit’ ProgressiveAligner.cpp: In function ‘void mems::applyAncestralBreakpoints(const std::vector >&, std::vector >&, uint, Manipulator&) [with T = mems::SuperInterval, Manipulator = mems::SuperIntervalManipulator]’: ProgressiveAligner.cpp:544: instantiated from here ProgressiveAligner.cpp:259: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::CompactGappedAlignment, std::allocator > > >, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ProgressiveAligner.cpp:1700: instantiated from here ../libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h: In function ‘double mems::GetPairwiseAnchorScore(MatchVector&, std::vector >&, const mems::PairwiseScoringScheme&, mems::SeedOccurrenceList&, mems::SeedOccurrenceList&, bool) [with MatchVector = std::vector >]’: ProgressiveAligner.cpp:1826: instantiated from here ../libMems/GreedyBreakpointElimination.h:429: warning: unused variable ‘uni_count’ ../libMems/GreedyBreakpointElimination.h:430: warning: unused variable ‘uni_score’ ../libMems/GreedyBreakpointElimination.h: In function ‘double mems::greedySearch(SearchScorer&) [with SearchScorer = mems::EvenFasterSumOfPairsBreakpointScorer]’: ProgressiveAligner.cpp:2245: instantiated from here ../libMems/GreedyBreakpointElimination.h:765: warning: unused variable ‘report_frequency’ ../libMems/ProgressiveAligner.h: In function ‘uint64 mems::SimpleGetLCBCoverage(MatchVector&) [with MatchVector = std::vector >]’: ProgressiveAligner.cpp:2293: instantiated from here ../libMems/ProgressiveAligner.h:413: warning: unused variable ‘debug’ ../libMems/GreedyBreakpointElimination.h: In function ‘int64 mems::greedyBreakpointElimination_v4(std::vector >&, std::vector >&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::SimpleBreakpointScorer]’: ProgressiveAligner.cpp:2301: instantiated from here ../libMems/GreedyBreakpointElimination.h:664: warning: unused variable ‘seq_count’ ../libMems/GreedyBreakpointElimination.h: In function ‘void mems::filterMatches_v2(std::vector >&, std::vector >&, std::vector >&, MatchVector&) [with MatchVector = std::vector >]’: ProgressiveAligner.cpp:2303: instantiated from here ../libMems/GreedyBreakpointElimination.h:337: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:2303: instantiated from here ../libMems/GreedyBreakpointElimination.h:356: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:359: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:359: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:2303: instantiated from here ../libMems/GreedyBreakpointElimination.h:369: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:369: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h: In function ‘void mems::addUnalignedIntervals_v2(MatchVectorType&, std::set, std::allocator >, std::vector >) [with MatchVectorType = std::vector >]’: ProgressiveAligner.cpp:2329: instantiated from here ../libMems/ProgressiveAligner.h:476: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp: In member function ‘void mems::ProgressiveAligner::recurseOnPairs(const std::vector >&, const std::vector >&, const GappedAlignmentType&, Matrix >&, Matrix, std::allocator > > >&, Matrix, std::allocator > > >&, boost::multi_array >, std::allocator > > >, 2ul, std::allocator >, std::allocator > > > > >&) [with GappedAlignmentType = mems::CompactGappedAlignment, std::allocator > > >]’: ProgressiveAligner.cpp:2458: instantiated from here ProgressiveAligner.cpp:697: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h: In function ‘double mems::GetPairwiseAnchorScore(MatchVector&, std::vector >&, const mems::PairwiseScoringScheme&, mems::SeedOccurrenceList&, mems::SeedOccurrenceList&, bool) [with MatchVector = mems::GenericMatchList]’: ProgressiveAligner.cpp:3420: instantiated from here ../libMems/GreedyBreakpointElimination.h:429: warning: unused variable ‘uni_count’ ../libMems/GreedyBreakpointElimination.h:430: warning: unused variable ‘uni_score’ ../libMems/GreedyBreakpointElimination.h: In function ‘int64 mems::greedyBreakpointElimination_v4(std::vector >&, std::vector >&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = mems::GreedyRemovalScorer]’: ProgressiveAligner.cpp:3434: instantiated from here ../libMems/GreedyBreakpointElimination.h:664: warning: unused variable ‘seq_count’ ../libMems/GreedyBreakpointElimination.h: In function ‘void mems::filterMatches_v2(std::vector >&, std::vector >&, std::vector >&, MatchVector&) [with MatchVector = mems::GenericMatchList]’: ProgressiveAligner.cpp:3437: instantiated from here ../libMems/GreedyBreakpointElimination.h:337: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:356: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:359: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:359: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:369: warning: comparison between signed and unsigned integer expressions ../libMems/GreedyBreakpointElimination.h:369: warning: comparison between signed and unsigned integer expressions ../libMems/PhyloTree.h: In member function ‘void PhyloTree::readTree(std::istream&) [with T = mems::AlignmentTreeNode]’: ProgressiveAligner.cpp:3624: instantiated from here ../libMems/PhyloTree.h:160: warning: unused variable ‘already_read_name’ ../libMems/DistanceMatrix.h: In function ‘void mems::SingleCopyDistanceMatrix(MatchVector&, std::vector >&, NumericMatrix&) [with MatchVector = mems::MatchList]’: ProgressiveAligner.cpp:3817: instantiated from here ../libMems/DistanceMatrix.h:213: warning: comparison between signed and unsigned integer expressions ProgressiveAligner.cpp:3817: instantiated from here ../libMems/DistanceMatrix.h:200: warning: unused variable ‘seqI’ ../libMems/DistanceMatrix.h:201: warning: unused variable ‘seqJ’ ../libMems/ProgressiveAligner.h: In function ‘void mems::EliminateOverlaps_v2(MatchVector&, const std::vector >&, bool) [with MatchVector = mems::GenericMatchList]’: ../libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = mems::MatchList]’ ProgressiveAligner.cpp:656: instantiated from here ../libMems/ProgressiveAligner.h:316: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:317: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:320: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:324: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = mems::MatchList]’ ProgressiveAligner.cpp:656: instantiated from here ../libMems/ProgressiveAligner.h:369: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = mems::MatchList]’ ProgressiveAligner.cpp:656: instantiated from here ../libMems/ProgressiveAligner.h:305: warning: unused variable ‘seq_count’ ../libMems/ProgressiveAligner.h: In function ‘void mems::EliminateOverlaps_v2(MatchVector&, const std::vector >&, bool) [with MatchVector = std::vector >]’: ../libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = std::vector >]’ ProgressiveAligner.cpp:962: instantiated from here ../libMems/ProgressiveAligner.h:316: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:317: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:320: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:324: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = std::vector >]’ ProgressiveAligner.cpp:962: instantiated from here ../libMems/ProgressiveAligner.h:369: warning: comparison between signed and unsigned integer expressions ../libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = std::vector >]’ ProgressiveAligner.cpp:962: instantiated from here ../libMems/ProgressiveAligner.h:305: warning: unused variable ‘seq_count’ ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SingleStartComparator]’ ProgressiveAligner.cpp:3305: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: ../libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ ProgressiveAligner.cpp:346: instantiated from here ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::CompactGappedAlignment, std::allocator > > >]’: ProgressiveAligner.cpp:1532: instantiated from ‘bool mems::CgaBsComp::operator()(const mems::_sort_tracker_type&, const mems::_sort_tracker_type&) [with CompType = mems::SingleStartComparator, std::allocator > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = boost::tuples::tuple, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, _Compare = mems::CgaBsComp, std::allocator > > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>*, std::vector, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > > >, _Size = long int, _Compare = mems::CgaBsComp, std::allocator > > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>*, std::vector, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator, std::allocator > > >*, std::vector >, std::allocator > > >*, mems::AbstractMatch*, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > > >, _Compare = mems::CgaBsComp, std::allocator > > > > >]’ ProgressiveAligner.cpp:1629: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::MatchStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::MatchStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]’ ../libMems/GreedyBreakpointElimination.h:388: instantiated from ‘void mems::filterMatches_v2(std::vector >&, std::vector >&, std::vector >&, MatchVector&) [with MatchVector = std::vector >]’ ProgressiveAligner.cpp:2303: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ ../libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::GenericInterval, std::allocator > > >]’: ../libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::GenericInterval, std::allocator > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::Interval*, _Compare = mems::SSC, std::allocator > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC, std::allocator > > > >]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC, std::allocator > > > >]’ ProgressiveAligner.cpp:2643: instantiated from here ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions ../libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::CropRight(gnSeqI, uint) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: ProgressiveAligner.cpp:3946: instantiated from here ../libMems/CompactGappedAlignment.h:620: warning: unused variable ‘pre_lend’ ../libMems/CompactGappedAlignment.h:621: warning: unused variable ‘pre_lend0’ ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: ProgressiveAligner.cpp:3946: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/graph/dijkstra_shortest_paths.hpp: In function ‘void boost::dijkstra_shortest_paths_no_init(const VertexListGraph&, typename boost::graph_traits::vertex_descriptor, PredecessorMap, DistanceMap, WeightMap, IndexMap, Compare, Combine, DistZero, DijkstraVisitor, ColorMap) [with VertexListGraph = boost::adjacency_list, boost::property >, boost::no_property, boost::listS>, DijkstraVisitor = boost::dijkstra_visitor, PredecessorMap = boost::dummy_property_map, DistanceMap = boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, int, int&, boost::vertex_distance_t>, WeightMap = boost::adj_list_edge_property_map >, boost::edge_weight2_t>, IndexMap = boost::vec_adj_list_vertex_id_map, long unsigned int>, Compare = std::less, Combine = boost::closed_plus, DistZero = int, ColorMap = boost::iterator_property_map, long unsigned int>, boost::default_color_type, boost::default_color_type&>]’: /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/graph/dijkstra_shortest_paths.hpp:81: warning: ‘bfs_vis.boost::detail::dijkstra_bfs_visitor, boost::relaxed_heap, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, int, int&, boost::vertex_distance_t>, std::less >, boost::vec_adj_list_vertex_id_map, long unsigned int> >, boost::adj_list_edge_property_map >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, int, int&, boost::vertex_distance_t>, boost::closed_plus, std::less >::m_decreased’ may be used uninitialized in this function /tmp/mauve_snapshot/build_scripts/build/include/boost-1_38/boost/graph/dijkstra_shortest_paths.hpp:205: note: ‘bfs_vis.boost::detail::dijkstra_bfs_visitor, boost::relaxed_heap, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, int, int&, boost::vertex_distance_t>, std::less >, boost::vec_adj_list_vertex_id_map, long unsigned int> >, boost::adj_list_edge_property_map >, boost::edge_weight2_t>, boost::dummy_property_map, boost::vec_adj_list_vertex_property_map, boost::property >, boost::no_property, boost::listS>, boost::adjacency_list, boost::property >, boost::no_property, boost::listS>*, int, int&, boost::vertex_distance_t>, boost::closed_plus, std::less >::m_decreased’ was declared here In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/gnAlignedSequences.h:32, from ../libMems/Interval.h:19, from ../libMems/SuperInterval.h:8, from SuperInterval.cpp:6: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ ../libMems/SuperInterval.h: In constructor ‘mems::SuperInterval::SuperInterval()’: ../libMems/SuperInterval.h:67: warning: ‘mems::SuperInterval::length’ will be initialized after ../libMems/SuperInterval.h:66: warning: ‘int64 mems::SuperInterval::left_end’ SuperInterval.cpp:16: warning: when initialized here ../libMems/SuperInterval.h:66: warning: ‘mems::SuperInterval::left_end’ will be initialized after ../libMems/SuperInterval.h:42: warning: ‘size_t mems::SuperInterval::c1_siv’ SuperInterval.cpp:16: warning: when initialized here ../libMems/SuperInterval.h: In constructor ‘mems::SuperInterval::SuperInterval(const mems::Interval&)’: ../libMems/SuperInterval.h:67: warning: ‘mems::SuperInterval::length’ will be initialized after ../libMems/SuperInterval.h:66: warning: ‘int64 mems::SuperInterval::left_end’ SuperInterval.cpp:24: warning: when initialized here ../libMems/SuperInterval.h:66: warning: ‘mems::SuperInterval::left_end’ will be initialized after ../libMems/SuperInterval.h:42: warning: ‘size_t mems::SuperInterval::c1_siv’ SuperInterval.cpp:24: warning: when initialized here ../libMems/SuperInterval.h: In copy constructor ‘mems::SuperInterval::SuperInterval(const mems::SuperInterval&)’: ../libMems/SuperInterval.h:67: warning: ‘mems::SuperInterval::length’ will be initialized after ../libMems/SuperInterval.h:39: warning: ‘mems::Interval mems::SuperInterval::reference_iv’ SuperInterval.cpp:34: warning: when initialized here ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used In file included from ../libMems/DNAFileSML.h:16, from ../libMems/MatchList.h:19, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, from ../libMems/GreedyBreakpointElimination.h:14, from GreedyBreakpointElimination.cpp:6: ../libMems/FileSML.h:16: warning: ignoring #pragma warning ../libMems/FileSML.h:17: warning: ignoring #pragma warning ../libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from ../libMems/SubstitutionMatrix.h:16, from ../libMems/GreedyBreakpointElimination.h:12, from GreedyBreakpointElimination.cpp:6: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from ../libMems/SortedMerList.h:24, from ../libMems/SeedOccurrenceList.h:5, from ../libMems/GreedyBreakpointElimination.h:13, from GreedyBreakpointElimination.cpp:6: ../libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used ../libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used In file included from ../libMems/SeedOccurrenceList.h:9, from ../libMems/GreedyBreakpointElimination.h:13, from GreedyBreakpointElimination.cpp:6: ../libMems/Files.h: In function ‘void deleteRegisteredFiles()’: ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/GreedyBreakpointElimination.h:15, from GreedyBreakpointElimination.cpp:6: ../libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions ../libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Aligner.h:18, from ../libMems/ProgressiveAligner.h:17, from GreedyBreakpointElimination.cpp:7: ../libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: ../libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions ../libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/ProgressiveAligner.h:17, from GreedyBreakpointElimination.cpp:7: ../libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions ../libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from ../libMems/Islands.h:26, from ../libMems/ProgressiveAligner.h:21, from GreedyBreakpointElimination.cpp:7: ../libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: ../libMems/Scoring.h:133: warning: array subscript has type ‘char’ ../libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from ../libMems/ProgressiveAligner.h:21, from GreedyBreakpointElimination.cpp:7: ../libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: ../libMems/Islands.h:135: warning: array subscript has type ‘char’ ../libMems/Islands.h:136: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ ../libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from GreedyBreakpointElimination.cpp:18: ../libMems/PairwiseMatchAdapter.h: In member function ‘virtual uint mems::PairwiseMatchAdapter::UsedSeq(uint) const’: ../libMems/PairwiseMatchAdapter.h:101: warning: comparison between signed and unsigned integer expressions ../libMems/PairwiseMatchAdapter.h:103: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In function ‘uint mems::RemoveLCBandCoalesce(size_t, uint, LcbVector&, std::vector >&, std::vector, std::allocator > >&, std::vector >&)’: GreedyBreakpointElimination.cpp:205: warning: suggest explicit braces to avoid ambiguous ‘else’ ../libMems/GreedyBreakpointElimination.h: In constructor ‘mems::EvenFasterSumOfPairsBreakpointScorer::EvenFasterSumOfPairsBreakpointScorer(double, double, boost::multi_array >, boost::multi_array >, std::vector >, mems::PairwiseLCBMatrix&, std::vector >&, std::vector >&, boost::multi_array >&, boost::multi_array >&, size_t, size_t, size_t, size_t)’: ../libMems/GreedyBreakpointElimination.h:552: warning: ‘mems::EvenFasterSumOfPairsBreakpointScorer::min_breakpoint_penalty’ will be initialized after ../libMems/GreedyBreakpointElimination.h:540: warning: ‘boost::multi_array > mems::EvenFasterSumOfPairsBreakpointScorer::bp_weights’ GreedyBreakpointElimination.cpp:338: warning: when initialized here ../libMems/GreedyBreakpointElimination.h:572: warning: ‘mems::EvenFasterSumOfPairsBreakpointScorer::tm_lcb_id_array’ will be initialized after ../libMems/GreedyBreakpointElimination.h:556: warning: ‘const size_t mems::EvenFasterSumOfPairsBreakpointScorer::seqI_count’ GreedyBreakpointElimination.cpp:338: warning: when initialized here ../libMems/GreedyBreakpointElimination.h:577: warning: ‘mems::EvenFasterSumOfPairsBreakpointScorer::seqI_last’ will be initialized after ../libMems/GreedyBreakpointElimination.h:576: warning: ‘const size_t mems::EvenFasterSumOfPairsBreakpointScorer::seqJ_first’ GreedyBreakpointElimination.cpp:338: warning: when initialized here GreedyBreakpointElimination.cpp: In member function ‘bool mems::EvenFasterSumOfPairsBreakpointScorer::remove(std::pair&, bool, boost::multi_array >&, boost::multi_array >&, bool, std::vector, std::allocator > >&, size_t&)’: GreedyBreakpointElimination.cpp:561: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:563: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:567: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:661: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:677: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:710: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In member function ‘bool mems::EvenFasterSumOfPairsBreakpointScorer::validate()’: GreedyBreakpointElimination.cpp:824: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:824: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In member function ‘bool mems::SimpleBreakpointScorer::isValid(size_t, double)’: GreedyBreakpointElimination.cpp:902: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In member function ‘void mems::SimpleBreakpointScorer::remove(uint, std::vector, std::allocator > >&)’: GreedyBreakpointElimination.cpp:933: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In member function ‘bool mems::GreedyRemovalScorer::isValid(size_t, double)’: GreedyBreakpointElimination.cpp:963: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In member function ‘void mems::GreedyRemovalScorer::remove(uint, std::vector, std::allocator > >&)’: GreedyBreakpointElimination.cpp:983: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:979: warning: unused variable ‘bp_removed’ ../libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/GappedAlignment.h:114: instantiated from here ../libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions ../libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions ../libMems/MatchList.h:557: instantiated from here ../libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ GreedyBreakpointElimination.cpp: In function ‘uint mems::RemoveLCBandCoalesce(size_t, uint, LcbVector&, std::vector >&, std::vector, std::allocator > >&, std::vector >&) [with LcbVector = std::vector, std::allocator > >]’: GreedyBreakpointElimination.cpp:666: instantiated from here GreedyBreakpointElimination.cpp:164: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:166: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:177: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:182: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:666: instantiated from here GreedyBreakpointElimination.cpp:199: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:199: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:201: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:201: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:203: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:203: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:205: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:205: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:224: warning: suggest parentheses around comparison in operand of != GreedyBreakpointElimination.cpp:666: instantiated from here GreedyBreakpointElimination.cpp:250: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:255: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In function ‘void mems::undoLcbRemoval(uint, LcbVector&, std::vector, std::allocator > >&) [with LcbVector = std::vector, std::allocator > >]’: GreedyBreakpointElimination.cpp:731: instantiated from here GreedyBreakpointElimination.cpp:277: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:286: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:288: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:309: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:315: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In function ‘uint mems::RemoveLCBandCoalesce(size_t, uint, LcbVector&, std::vector >&, std::vector, std::allocator > >&, std::vector >&) [with LcbVector = std::vector >]’: GreedyBreakpointElimination.cpp:913: instantiated from here GreedyBreakpointElimination.cpp:164: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:166: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:177: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:182: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:199: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:199: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:201: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:201: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:203: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:203: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:205: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:205: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:224: warning: suggest parentheses around comparison in operand of != GreedyBreakpointElimination.cpp:250: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:255: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp: In function ‘void mems::undoLcbRemoval(uint, LcbVector&, std::vector, std::allocator > >&) [with LcbVector = std::vector >]’: GreedyBreakpointElimination.cpp:914: instantiated from here GreedyBreakpointElimination.cpp:277: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:286: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:288: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:309: warning: comparison between signed and unsigned integer expressions GreedyBreakpointElimination.cpp:315: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: ../libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ ../libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ ../libMems/CompactGappedAlignment.h:813: instantiated from here ../libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions ../libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SingleStartComparator]’ GreedyBreakpointElimination.cpp:852: instantiated from here ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: ../libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ ../libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ ../libMems/ProgressiveAligner.h:521: instantiated from here ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions ../libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions ../libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: GreedyBreakpointElimination.cpp:993: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used ../libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used ../libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used HomologyHMM/homologymain.cc: In function ‘void run(std::string&, std::string&, const Params&)’: HomologyHMM/homologymain.cc:39: warning: unused variable ‘pViterbiDP’ dmSML/aPOSIXaio.c: In function ‘QueryLastCompletePAIO’: dmSML/aPOSIXaio.c:115: warning: passing argument 1 of ‘aio_suspend’ from incompatible pointer type dmSML/util.c: In function ‘removeFile’: dmSML/util.c:126: warning: assignment discards qualifiers from pointer target type dmSML/util.c:128: warning: assignment discards qualifiers from pointer target type dmSML/util.c:129: warning: implicit declaration of function ‘system’ dmSML/dmsort.c: In function ‘Translate32’: dmSML/dmsort.c:498: warning: array subscript has type ‘char’ dmSML/dmsort.c: In function ‘RestructureReadSMLBins’: dmSML/dmsort.c:617: warning: array subscript has type ‘char’ dmSML/dmsort.c:662: warning: array subscript has type ‘char’ dmSML/dmsort.c:544: warning: unused variable ‘config_value’ dmSML/dmsort.c: In function ‘dmSML’: dmSML/dmsort.c:1849: warning: unused variable ‘buffer_size’ dmSML/dmsort.c:1848: warning: unused variable ‘working_mb’ dmSML/dmsort.c: At top level: dmSML/dmsort.c:212: warning: ‘ComputeNNNNNBinNumber’ defined but not used dmSML/dmsort.c:239: warning: ‘ComputeAsciiBinNumber’ defined but not used dmSML/dmsort.c: In function ‘InitdmSML’: dmSML/dmsort.c:778: warning: ‘desired_ws_size’ may be used uninitialized in this function In file included from dmSML/sml.c:6: ../libMems/SeedMasks.h: In function ‘getSeed’: ../libMems/SeedMasks.h:302: warning: unused variable ‘i’ dmSML/sml.c: At top level: ../libMems/dmSML/sml.h:41: warning: ‘DNA_TABLE’ defined but not used ../libMems/dmSML/sml.h:45: warning: ‘seed_mask’ defined but not used ../libMems/dmSML/sml.h:46: warning: ‘mask_length’ defined but not used ../libMems/dmSML/sml.h:47: warning: ‘mask_weight’ defined but not used configure.ac:10: installing `config/config.guess' configure.ac:10: installing `config/config.sub' configure.ac:12: installing `config/install-sh' configure.ac:12: installing `config/missing' src/Makefile.am: installing `config/depcomp' Makefile.am: installing `./INSTALL' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from mauveAligner.cpp:20: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning mauveAligner.cpp:47:1: warning: "NELEMS" redefined In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SlotAllocator.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:22, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from mauveAligner.cpp:21: /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/threadstorage.h:22:1: warning: this is the location of the previous definition In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from mauveAligner.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:21, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from mauveAligner.cpp:20: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from mauveAligner.cpp:21: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from mauveAligner.cpp:23: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from mauveAligner.cpp:23: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from mauveAligner.cpp:23: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from mauveAligner.cpp:29: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from mauveAligner.cpp:29: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from mauveAligner.cpp:31: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h: In function ‘void mems::SingleCopyDistanceMatrix(MatchVector&, std::vector >&, NumericMatrix&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:241: warning: suggest explicit braces to avoid ambiguous ‘else’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:246: warning: suggest explicit braces to avoid ambiguous ‘else’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h: In function ‘void mems::TransformDistanceIdentity(NumericMatrix&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:277: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:278: warning: comparison between signed and unsigned integer expressions mauveAligner.cpp: In function ‘int doAlignment(int, char**)’: mauveAligner.cpp:507: warning: comparison between signed and unsigned integer expressions mauveAligner.cpp:508: warning: comparison between signed and unsigned integer expressions mauveAligner.cpp:728: warning: comparison between signed and unsigned integer expressions mauveAligner.cpp:733: warning: comparison between signed and unsigned integer expressions mauveAligner.cpp:145: warning: unused variable ‘detail_list_out’ mauveAligner.cpp: In function ‘void print_usage(const char*)’: mauveAligner.cpp:911: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In function ‘void mems::LoadMFASequences(MatchListType&, const std::string&, std::ostream*) [with MatchListType = mems::MatchList]’: mauveAligner.cpp:454: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:394: warning: unused variable ‘total_len’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In member function ‘void mems::GenericMatchList::CreateMemorySMLs(uint, std::ostream*, int) [with MatchPtrType = mems::Match*]’: mauveAligner.cpp:456: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:424: warning: unused variable ‘success’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In member function ‘void mems::GenericMatchList::LoadSMLs(uint, std::ostream*, int, bool, bool) [with MatchPtrType = mems::Match*]’: mauveAligner.cpp:465: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:275: warning: unused variable ‘default_seed’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadList(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: mauveAligner.cpp:506: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:181: warning: unused variable ‘cur_iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: mauveAligner.cpp:918: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from scoreAlignment.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:18, from scoreAlignment.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from scoreAlignment.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp: In function ‘int main(int, char**)’: scoreAlignment.cpp:195: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp:230: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp:272: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp:274: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp:291: warning: comparisons like X<=Y<=Z do not have their mathematical meaning scoreAlignment.cpp:325: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp:374: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: scoreAlignment.cpp:135: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: scoreAlignment.cpp:465: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions scoreAlignment.cpp: In function ‘int main(int, char**)’: scoreAlignment.cpp:209: warning: ‘calc_baseJ’ may be used uninitialized in this function scoreAlignment.cpp:208: warning: ‘calc_baseI’ may be used uninitialized in this function /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from uniqueMerCount.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from uniqueMerCount.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:21, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from uniqueMerCount.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from toRawSequence.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnFASSource.h:25, from mfa2xmfa.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/gnAlignedSequences.h:32, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Interval.h:19, from addUnalignedIntervals.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from addUnalignedIntervals.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: addUnalignedIntervals.cpp:22: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: addUnalignedIntervals.cpp:33: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/gnAlignedSequences.h:32, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Interval.h:19, from toMultiFastA.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from toMultiFastA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadList(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: toMultiFastA.cpp:23: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:181: warning: unused variable ‘cur_iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: toMultiFastA.cpp:53: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from getAlignmentWindows.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from getAlignmentWindows.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from getAlignmentWindows.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from getAlignmentWindows.cpp:14: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from getAlignmentWindows.cpp:14: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from getAlignmentWindows.cpp:14: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from getAlignmentWindows.cpp:14: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from getAlignmentWindows.cpp:14: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ getAlignmentWindows.cpp: In function ‘int main(int, const char**)’: getAlignmentWindows.cpp:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: getAlignmentWindows.cpp:52: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: getAlignmentWindows.cpp:136: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h: In member function ‘void PhyloTree::readTree(std::istream&) [with T = TreeNode]’: uniquifyTrees.cpp:219: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h:160: warning: unused variable ‘already_read_name’ /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from toGrimmFormat.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from toGrimmFormat.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from toGrimmFormat.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from toGrimmFormat.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from toGrimmFormat.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from toGrimmFormat.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions toGrimmFormat.cpp: In function ‘int main(int, char**)’: toGrimmFormat.cpp:27: warning: comparison between signed and unsigned integer expressions toGrimmFormat.cpp:62: warning: comparison between signed and unsigned integer expressions toGrimmFormat.cpp:66: warning: comparison between signed and unsigned integer expressions toGrimmFormat.cpp:66: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadList(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: toGrimmFormat.cpp:49: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:181: warning: unused variable ‘cur_iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: toGrimmFormat.cpp:84: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from mauveToXMFA.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from mauveToXMFA.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from mauveToXMFA.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadList(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: mauveToXMFA.cpp:31: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:181: warning: unused variable ‘cur_iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: mauveToXMFA.cpp:34: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from stripGapColumns.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from stripGapColumns.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from stripGapColumns.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: stripGapColumns.cpp:27: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: stripGapColumns.cpp:74: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from progressiveMauve.cpp:20: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from progressiveMauve.cpp:19: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:21, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from progressiveMauve.cpp:20: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from progressiveMauve.cpp:21: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from progressiveMauve.cpp:26: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from progressiveMauve.cpp:26: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from progressiveMauve.cpp:26: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from progressiveMauve.cpp:26: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from progressiveMauve.cpp:26: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from progressiveMauve.cpp:33: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HomologyHMM/parameters.h: In function ‘Params getAdaptedHoxdMatrixParameters(double)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HomologyHMM/parameters.h:62: warning: unused variable ‘s’ progressiveMauve.cpp: In member function ‘option* OptionList::getOptions()’: progressiveMauve.cpp:80: warning: comparison between signed and unsigned integer expressions progressiveMauve.cpp: In function ‘void getDefaultSmlFileNames(const std::vector, std::allocator >, std::allocator, std::allocator > > >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, int, int)’: progressiveMauve.cpp:222: warning: comparison between signed and unsigned integer expressions progressiveMauve.cpp: In function ‘int doAlignment(int, char**)’: progressiveMauve.cpp:502: warning: comparison between signed and unsigned integer expressions progressiveMauve.cpp:394: warning: unused variable ‘create_LCBs’ progressiveMauve.cpp:398: warning: unused variable ‘lcb_match_input_format’ progressiveMauve.cpp:402: warning: unused variable ‘detail_list_out’ progressiveMauve.cpp:405: warning: unused variable ‘seq_name_arg’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:120: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:122: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:231: warning: unused variable ‘iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: progressiveMauve.cpp:371: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In function ‘void mems::LoadMFASequences(MatchListType&, const std::string&, std::ostream*) [with MatchListType = mems::MatchList]’: progressiveMauve.cpp:377: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:394: warning: unused variable ‘total_len’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In member function ‘void mems::GenericMatchList::CreateMemorySMLs(uint, std::ostream*, int) [with MatchPtrType = mems::Match*]’: progressiveMauve.cpp:438: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:424: warning: unused variable ‘success’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In member function ‘void mems::GenericMatchList::LoadSMLs(uint, std::ostream*, int, bool, bool) [with MatchPtrType = mems::Match*]’: progressiveMauve.cpp:445: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:275: warning: unused variable ‘default_seed’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::SparseAbstractMatch, std::allocator >]’: progressiveMauve.cpp:758: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::CropRight(gnSeqI, uint) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: progressiveMauve.cpp:758: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:620: warning: unused variable ‘pre_lend’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:621: warning: unused variable ‘pre_lend0’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: progressiveMauve.cpp:758: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from UniqueMatchFinder.h:16, from UniqueMatchFinder.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from UniqueMatchFinder.h:16, from UniqueMatchFinder.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from UniqueMatchFinder.h:16, from UniqueMatchFinder.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from UniqueMatchFinder.h:16, from UniqueMatchFinder.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: UniqueMatchFinder.cpp:60: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' extractBCITrees.cpp: In function ‘int main(int, char**)’: extractBCITrees.cpp:210: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h: In member function ‘void PhyloTree::readTree(std::istream&) [with T = TreeNode]’: extractBCITrees.cpp:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h:160: warning: unused variable ‘already_read_name’ /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/gnAlignedSequences.h:32, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Interval.h:19, from createBackboneMFA.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from createBackboneMFA.cpp:2: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadList(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: createBackboneMFA.cpp:23: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:181: warning: unused variable ‘cur_iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: createBackboneMFA.cpp:56: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from repeatoire.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:18, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:23, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from repeatoire.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from repeatoire.cpp:10: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HomologyHMM/parameters.h: In function ‘Params getAdaptedHoxdMatrixParameters(double)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HomologyHMM/parameters.h:62: warning: unused variable ‘s’ In file included from repeatoire.cpp:18: SeedMatchEnumerator.h: In member function ‘void SeedMatchEnumerator::SetDirection(mems::Match&)’: SeedMatchEnumerator.h:132: warning: comparison between signed and unsigned integer expressions SeedMatchEnumerator.h:138: warning: comparison between signed and unsigned integer expressions repeatoire.cpp: In function ‘void supersetLinkExtension(GappedMatchRecord*&, int, int&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, bool)’: repeatoire.cpp:640: warning: unused variable ‘ik_parity’ repeatoire.cpp:596: warning: unused variable ‘changed’ repeatoire.cpp: In function ‘void neighborhoodListLookup(GappedMatchRecord*, MatchPositionLookupTable&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, int, uint, uint, mems::bitset_t&, mems::bitset_t&, GappedMatchRecord*)’: repeatoire.cpp:846: warning: suggest explicit braces to avoid ambiguous ‘else’ repeatoire.cpp: In function ‘void processSupersetMatches(GappedMatchRecord*&, std::vector >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type>, std::allocator >, std::vector >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> > >&, int, int&, bool)’: repeatoire.cpp:1118: warning: unused variable ‘changed’ repeatoire.cpp: In function ‘int ExtendMatch(GappedMatchRecord*&, std::vector >&, Params&, unsigned int, int, std::vector >&, int, int, int)’: repeatoire.cpp:1170: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1179: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1195: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1207: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1221: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1246: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1273: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1348: warning: unused variable ‘cgalen’ repeatoire.cpp:1349: warning: unused variable ‘resultlen’ repeatoire.cpp:1147: warning: unused variable ‘novel_hss_regions_support’ repeatoire.cpp:1148: warning: unused variable ‘danger_zone_active’ repeatoire.cpp:1327: warning: unused variable ‘boundaries_improved’ repeatoire.cpp:1339: warning: unused variable ‘isnovel’ repeatoire.cpp: In function ‘int main(int, char**)’: repeatoire.cpp:2259: warning: unused variable ‘changed’ repeatoire.cpp:2147: warning: unused variable ‘e’ repeatoire.cpp:2071: warning: unused variable ‘score’ repeatoire.cpp:2512: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:2585: warning: unused variable ‘endI’ repeatoire.cpp:2688: warning: comparison between signed and unsigned integer expressions repeatoire.cpp:1667: warning: unused variable ‘debug_extension’ repeatoire.cpp:1913: warning: unused variable ‘all_components_overlap’ repeatoire.cpp:1915: warning: unused variable ‘prev_overlaps’ repeatoire.cpp:1916: warning: unused variable ‘mi_multiplicity’ repeatoire.cpp:1917: warning: unused variable ‘mi2_multiplicity’ repeatoire.cpp:1918: warning: unused variable ‘num_components’ repeatoire.cpp:1919: warning: unused variable ‘overlap_size’ repeatoire.cpp:1920: warning: unused variable ‘hit_match’ repeatoire.cpp:1997: warning: unused variable ‘curr_extensions’ repeatoire.cpp:1998: warning: unused variable ‘max_extensions’ repeatoire.cpp:2506: warning: unused variable ‘e’ repeatoire.cpp:2509: warning: unused variable ‘alignment_count’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:120: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:122: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:231: warning: unused variable ‘iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = GappedMatchRecord, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: MatchRecord.h:341: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::Interval, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: repeatoire.cpp:1318: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::WriteXMLAlignment(std::ostream&) const [with MatchType = GappedMatchRecord]’: repeatoire.cpp:1648: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:336: warning: unused variable ‘length’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In member function ‘void mems::GenericMatchList::LoadSMLs(uint, std::ostream*, int, bool, bool) [with MatchPtrType = mems::Match*]’: repeatoire.cpp:1850: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:275: warning: unused variable ‘default_seed’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::MatchStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::MatchStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]’ MatchRecord.h:293: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = MatchRecord]’: repeatoire.cpp:2715: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = CompactMatchRecord]’: repeatoire.cpp:2715: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::CropRight(gnSeqI, uint) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: repeatoire.cpp:2715: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:620: warning: unused variable ‘pre_lend’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:621: warning: unused variable ‘pre_lend0’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: repeatoire.cpp:2715: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from alignmentProjector.cpp:11: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from alignmentProjector.cpp:11: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from alignmentProjector.cpp:11: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from alignmentProjector.cpp:11: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from alignmentProjector.cpp:16: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from alignmentProjector.cpp:16: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from alignmentProjector.cpp:16: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:21, from alignmentProjector.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:21, from alignmentProjector.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: alignmentProjector.cpp:50: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h: In function ‘void mems::LoadMFASequences(MatchListType&, const std::string&, std::ostream*) [with MatchListType = mems::MatchList]’: alignmentProjector.cpp:55: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:394: warning: unused variable ‘total_len’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: alignmentProjector.cpp:100: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from stripSubsetLCBs.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from stripSubsetLCBs.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from stripSubsetLCBs.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from stripSubsetLCBs.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from stripSubsetLCBs.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from stripSubsetLCBs.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from stripSubsetLCBs.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: stripSubsetLCBs.cpp:57: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: stripSubsetLCBs.cpp:137: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from projectAndStrip.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from projectAndStrip.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from projectAndStrip.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from projectAndStrip.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from projectAndStrip.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from projectAndStrip.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from projectAndStrip.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from projectAndStrip.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from projectAndStrip.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ projectAndStrip.cpp: In function ‘int main(int, char**)’: projectAndStrip.cpp:51: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: projectAndStrip.cpp:56: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: projectAndStrip.cpp:143: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from makeBadgerMatrix.cpp:10: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from makeBadgerMatrix.cpp:10: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from makeBadgerMatrix.cpp:10: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from makeBadgerMatrix.cpp:10: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from makeBadgerMatrix.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from makeBadgerMatrix.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from makeBadgerMatrix.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: makeBadgerMatrix.cpp:58: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: makeBadgerMatrix.cpp:115: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from randomGeneSample.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from randomGeneSample.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from randomGeneSample.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from randomGeneSample.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from randomGeneSample.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from randomGeneSample.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from randomGeneSample.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from randomGeneSample.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from randomGeneSample.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ randomGeneSample.cpp: In function ‘int main(int, char**)’: randomGeneSample.cpp:125: warning: comparison between signed and unsigned integer expressions randomGeneSample.cpp:129: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:120: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:122: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:231: warning: unused variable ‘iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: randomGeneSample.cpp:55: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::GenericInterval, std::allocator > > >, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: randomGeneSample.cpp:136: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::CropRight(gnSeqI, uint) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: randomGeneSample.cpp:164: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:620: warning: unused variable ‘pre_lend’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:621: warning: unused variable ‘pre_lend0’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: randomGeneSample.cpp:164: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from getOrthologList.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from getOrthologList.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from getOrthologList.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from getOrthologList.cpp:12: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from getOrthologList.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from getOrthologList.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from getOrthologList.cpp:17: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from getOrthologList.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from getOrthologList.cpp:18: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ In file included from getOrthologList.cpp:25: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h: In function ‘void mems::SingleCopyDistanceMatrix(MatchVector&, std::vector >&, NumericMatrix&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:241: warning: suggest explicit braces to avoid ambiguous ‘else’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:246: warning: suggest explicit braces to avoid ambiguous ‘else’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h: In function ‘void mems::TransformDistanceIdentity(NumericMatrix&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:277: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DistanceMatrix.h:278: warning: comparison between signed and unsigned integer expressions getOrthologList.cpp: In function ‘int main(int, char**)’: getOrthologList.cpp:180: warning: comparison between signed and unsigned integer expressions getOrthologList.cpp:146: warning: unused variable ‘bbI’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:120: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:122: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:231: warning: unused variable ‘iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: getOrthologList.cpp:91: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In constructor ‘mems::CompactGappedAlignment::CompactGappedAlignment(MatchType&) [with MatchType = mems::GenericInterval, std::allocator > > >, BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: getOrthologList.cpp:213: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:55: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h: In member function ‘void mems::CompactGappedAlignment::CropRight(gnSeqI, uint) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’: getOrthologList.cpp:316: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:620: warning: unused variable ‘pre_lend’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:621: warning: unused variable ‘pre_lend0’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: getOrthologList.cpp:316: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:18, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:16, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:18, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:18, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:23, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:23, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:23, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:24, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:24, from bbFilter.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ bbFilter.cpp: In function ‘int main(int, char**)’: bbFilter.cpp:86: warning: comparison between signed and unsigned integer expressions bbFilter.cpp:167: warning: unused variable ‘prev_in_sI’ bbFilter.cpp:170: warning: unused variable ‘prev_in_k’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:120: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:122: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:231: warning: unused variable ‘iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: bbFilter.cpp:261: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:16, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:18, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:23, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:23, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:23, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:26, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:24, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h: In function ‘void mems::computeMatchScores(const std::string&, const std::string&, const mems::PairwiseScoringScheme&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:133: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Scoring.h:134: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:24, from bbAnalyze.cpp:4: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findHssHomologyHMM(std::vector, std::allocator >, std::allocator, std::allocator > > >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:135: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:136: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:137: warning: array subscript has type ‘char’ bbAnalyze.cpp: In function ‘void featureIntersect(std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, uint, std::vector >, std::allocator > > >&, genome::gnSequence*)’: bbAnalyze.cpp:106: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp:110: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp:113: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp: In function ‘void featureNearestNeighbors(const std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, const mems::bitset_t&, uint, std::vector, std::allocator > >&, genome::gnSequence*, const std::vector, std::allocator >, std::allocator, std::allocator > > >&)’: bbAnalyze.cpp:323: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp:329: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp:288: warning: unused variable ‘seq_count’ bbAnalyze.cpp: In function ‘void findVariableSegmentsWithFlankingBB(const std::vector >&, const std::vector >&, std::vector, std::allocator > >&, size_t, size_t, bool)’: bbAnalyze.cpp:486: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp: In function ‘void classifyCoordinateRanges(const std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, genome::gnSequence*, std::vector >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&, std::vector >, std::allocator > > >&)’: bbAnalyze.cpp:670: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp:674: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp:677: warning: comparison between signed and unsigned integer expressions bbAnalyze.cpp: In function ‘int main(int, char**)’: bbAnalyze.cpp:1218: warning: unused variable ‘c1’ bbAnalyze.cpp:1219: warning: unused variable ‘c2’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::findBigGaps(const MatchVector&, std::vector >&, mems::hss_array_t&, size_t) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:120: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:391: warning: suggest parentheses around comparison in operand of ^ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h: In function ‘void mems::HssColsToIslandCols(const MatchVector&, std::vector >&, mems::hss_array_t&, mems::hss_array_t&) [with MatchVector = std::vector, std::allocator > > >*, std::allocator, std::allocator > > >*> >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Backbone.h:122: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Islands.h:231: warning: unused variable ‘iv’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h: In member function ‘void PhyloTree::readTree(std::istream&) [with T = TreeNode]’: bbAnalyze.cpp:989: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h:160: warning: unused variable ‘already_read_name’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: bbAnalyze.cpp:999: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h: In function ‘void mems::EliminateOverlaps_v2(MatchVector&, const std::vector >&, bool) [with MatchVector = std::vector >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = std::vector >]’ bbAnalyze.cpp:1051: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:316: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:317: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:320: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:324: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = std::vector >]’ bbAnalyze.cpp:1051: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:369: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:406: instantiated from ‘void mems::EliminateOverlaps_v2(MatchVector&, bool) [with MatchVector = std::vector >]’ bbAnalyze.cpp:1051: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:305: warning: unused variable ‘seq_count’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SingleStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]’: /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SingleStartComparator]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SingleStartComparator]’ bbAnalyze.cpp:1048: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:341: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:342: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::MatchProjectionAdapter*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/ProgressiveAligner.h:521: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: bbAnalyze.cpp:1410: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' strip: Warning: 'src' is not an ordinary file strip: Warning: 'src/.deps' is not an ordinary file strip: Warning: 'src/.svn' is not an ordinary file configure.ac:9: installing `config/config.guess' configure.ac:9: installing `config/config.sub' configure.ac:11: installing `config/install-sh' configure.ac:11: installing `config/missing' src/Makefile.am: installing `config/depcomp' Makefile.am: installing `./INSTALL' Makefile.am: installing `./COPYING' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:19, from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning sgEvolver.cpp:227:1: warning: "NELEMS" redefined In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SlotAllocator.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:22, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/threadstorage.h:22:1: warning: this is the location of the previous definition In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from sgEvolver.cpp:13: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemorySML.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAMemorySML.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:17, from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:19, from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from Alignment.h:9, from Mutator.h:13, from sgEvolver.cpp:15: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions sgEvolver.cpp: In function ‘int main(int, char**)’: sgEvolver.cpp:431: warning: comparison between signed and unsigned integer expressions sgEvolver.cpp:435: warning: comparison between signed and unsigned integer expressions sgEvolver.cpp:273: warning: unused variable ‘m_argc’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h: In member function ‘void PhyloTree::readTree(std::istream&) [with T = TreeNode]’: sgEvolver.cpp:416: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/PhyloTree.h:160: warning: unused variable ‘already_read_name’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: sgEvolver.cpp:497: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:19, from Alignment.h:9, from Mutator.h:13, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/gnAlignedSequences.h:32, from Mutator.h:8, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemorySML.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAMemorySML.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:17, from Alignment.h:9, from Mutator.h:13, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from Alignment.h:9, from Mutator.h:13, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:19, from Alignment.h:9, from Mutator.h:13, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from Alignment.h:9, from Mutator.h:13, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from Alignment.h:9, from Mutator.h:13, from Mutator.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: Mutator.cpp:188: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:19, from Alignment.h:9, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/gnAlignedSequences.h:32, from Alignment.h:8, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemorySML.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAMemorySML.h:17, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:17, from Alignment.h:9, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from Alignment.h:9, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:19, from Alignment.h:9, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from Alignment.h:9, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from Alignment.h:9, from Alignment.cpp:5: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions Alignment.cpp: In member function ‘void Alignment::applyInversions(const PhyloTree&)’: Alignment.cpp:563: warning: unused variable ‘cc_left’ Alignment.cpp:564: warning: unused variable ‘cc_right’ Alignment.cpp:565: warning: unused variable ‘cn_left’ Alignment.cpp:566: warning: unused variable ‘cn_right’ Alignment.cpp: In member function ‘void Alignment::writeAlignment(std::ostream&, const PhyloTree&, boolean) const’: Alignment.cpp:605: warning: unused variable ‘seq_count’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ GisSplayTree.h: In member function ‘typename GisSplayTree::size_type GisSplayTree::erase(typename GisSplayTree::size_type, typename GisSplayTree::size_type) [with Key = SourceInterval, Allocator = std::allocator]’: Alignment.cpp:166: instantiated from here GisSplayTree.h:491: warning: unused variable ‘left_ins’ GisSplayTree.h: In static member function ‘static typename GisSplayTree::size_type GisSplayTree::checkNodeLengths(typename GisSplayTree::GisNode*) [with Key = SourceInterval, Allocator = std::allocator]’: GisSplayTree.h:293: instantiated from ‘void GisSplayTree::checkTree() const [with Key = SourceInterval, Allocator = std::allocator]’ Alignment.cpp:88: instantiated from here GisSplayTree.h:325: warning: comparison between signed and unsigned integer expressions GisSplayTree.h:327: warning: comparison between signed and unsigned integer expressions GisSplayTree.h: In static member function ‘static typename GisSplayTree::size_type GisSplayTree::checkNodeSeqLengths(typename GisSplayTree::GisNode*) [with Key = SourceInterval, Allocator = std::allocator]’: GisSplayTree.h:294: instantiated from ‘void GisSplayTree::checkTree() const [with Key = SourceInterval, Allocator = std::allocator]’ Alignment.cpp:88: instantiated from here GisSplayTree.h:352: warning: comparison between signed and unsigned integer expressions GisSplayTree.h:354: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions GisSplayTree.h: In member function ‘void GisSplayTree::insert(InputIterator, InputIterator, typename GisSplayTree::size_type) [with InputIterator = GisSplayTree >::__generic_iterator, Key = SourceInterval, Allocator = std::allocator]’: GisSplayTree.h:207: instantiated from ‘GisSplayTree::GisSplayTree(const GisSplayTree&) [with Key = SourceInterval, Allocator = std::allocator]’ /usr/include/c++/4.3/bits/stl_uninitialized.h:79: instantiated from ‘static _ForwardIterator std::__uninitialized_copy< >::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = GisSplayTree >*, _ForwardIterator = GisSplayTree >*, bool = false]’ /usr/include/c++/4.3/bits/stl_uninitialized.h:122: instantiated from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = GisSplayTree >*, _ForwardIterator = GisSplayTree >*]’ /usr/include/c++/4.3/bits/stl_uninitialized.h:262: instantiated from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = GisSplayTree >*, _ForwardIterator = GisSplayTree >*, _Tp = GisSplayTree >]’ /usr/include/c++/4.3/bits/vector.tcc:170: instantiated from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = GisSplayTree >, _Alloc = std::allocator > >]’ Alignment.cpp:104: instantiated from here GisSplayTree.h:465: warning: unused variable ‘cur_point’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: Alignment.cpp:675: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions Alignment.cpp: In member function ‘void Alignment::applyInversions(const PhyloTree&)’: Alignment.cpp:361: warning: ‘right_lcb’ may be used uninitialized in this function Alignment.cpp:361: warning: ‘left_lcb’ may be used uninitialized in this function /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from scoreAlignment2.cpp:19: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from scoreAlignment2.cpp:19: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from scoreAlignment2.cpp:19: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from scoreAlignment2.cpp:19: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:18, from scoreAlignment2.cpp:24: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h: In function ‘boolean mems::getInterveningCoordinates(std::vector >&, mems::Match*, mems::Match*, uint, int64&, int64&)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:50: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAligner.h:51: warning: comparison between signed and unsigned integer expressions In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:15, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:26, from scoreAlignment2.cpp:24: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h: In member function ‘bool mems::LCBLeftComparator::operator()(const mems::LCB&, const mems::LCB&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:38: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/LCB.h:39: warning: comparison between signed and unsigned integer expressions In file included from scoreAlignment2.cpp:24: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::LabeledMemComparator::operator()(const mems::LabeledMem&, const mems::LabeledMem&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:58: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:59: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h: In member function ‘boolean mems::PlacementMatchComparator::operator()(const mems::PlacementMatch&, const mems::PlacementMatch&) const’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:103: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:104: warning: comparison between signed and unsigned integer expressions scoreAlignment2.cpp: In function ‘void constructCoordList(uint, uint, mems::IntervalList&, std::vector >&, std::vector >&)’: scoreAlignment2.cpp:57: warning: comparison between signed and unsigned integer expressions scoreAlignment2.cpp:66: warning: comparison between signed and unsigned integer expressions scoreAlignment2.cpp: In function ‘void compareAlignments(mems::IntervalList&, mems::IntervalList&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, std::vector >&)’: scoreAlignment2.cpp:267: warning: unused variable ‘cur_count’ scoreAlignment2.cpp: In function ‘size_t findLcb(std::vector >&, int64)’: scoreAlignment2.cpp:392: warning: comparison between signed and unsigned integer expressions scoreAlignment2.cpp: In function ‘void computeLCBaccuracy(mems::IntervalList&, mems::IntervalList&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, std::vector >&)’: scoreAlignment2.cpp:652: warning: unused variable ‘found’ scoreAlignment2.cpp:572: warning: unused variable ‘corI’ scoreAlignment2.cpp:573: warning: unused variable ‘calcI’ scoreAlignment2.cpp: In function ‘void computeIndelAccuracy(mems::IntervalList&, mems::IntervalList&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, std::vector >&)’: scoreAlignment2.cpp:926: warning: unused variable ‘indel_sp_perfectpos’ scoreAlignment2.cpp: In function ‘int main(int, char**)’: scoreAlignment2.cpp:1159: warning: unused variable ‘comp_filter’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::UngappedLocalAlignment, std::allocator > >]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Aligner.h:284: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:308: warning: unused variable ‘diff’ scoreAlignment2.cpp: In function ‘bool findFirstCorrectlyAlignedPair(const FwdIt&, const FwdIt&, const FwdIt&, const FwdIt&, FwdIt&, FwdIt&, int) [with FwdIt = __gnu_cxx::__normal_iterator > >]’: scoreAlignment2.cpp:604: instantiated from here scoreAlignment2.cpp:334: warning: suggest parentheses around && within || /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h: In member function ‘void mems::GenericIntervalList::ReadStandardAlignment(std::istream&) [with MatchType = mems::GenericInterval, std::allocator > > >]’: scoreAlignment2.cpp:1145: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:525: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:537: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h: In member function ‘boolean mems::SSC::operator()(const typename boost::remove_pointer::type&, const typename boost::remove_pointer::type&) const [with MatchType = mems::AbstractMatch]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:370: instantiated from ‘boolean mems::SSC::operator()(const typename boost::add_pointer::type&, const typename boost::add_pointer::type&) const [with MatchType = mems::AbstractMatch]’ /usr/include/c++/4.3/bits/stl_algo.h:128: instantiated from ‘const _Tp& std::__median(const _Tp&, const _Tp&, const _Tp&, _Compare) [with _Tp = mems::AbstractMatch*, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:1952: instantiated from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::SSC]’ /usr/include/c++/4.3/bits/stl_algo.h:4820: instantiated from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator > >, _Compare = mems::SSC]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GreedyBreakpointElimination.h:169: instantiated from ‘void mems::IdentifyBreakpoints(MatchVector&, std::vector >&) [with MatchVector = std::vector >]’ scoreAlignment2.cpp:514: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:378: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractMatch.h:379: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: scoreAlignment2.cpp:1187: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions scoreAlignment2.cpp: In function ‘bool findFirstCorrectlyAlignedPair(const FwdIt&, const FwdIt&, const FwdIt&, const FwdIt&, FwdIt&, FwdIt&, int) [with FwdIt = __gnu_cxx::__normal_iterator > >]’: scoreAlignment2.cpp:385: warning: control reaches end of non-void function /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnDefs.h: In function ‘void markAllCorrectlyAlignedLcbs(const __gnu_cxx::__normal_iterator > >&, const __gnu_cxx::__normal_iterator > >&, const __gnu_cxx::__normal_iterator > >&, const __gnu_cxx::__normal_iterator > >&, std::vector >&, boost::dynamic_bitset >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnDefs.h:210: warning: ‘next_act.aligned_coords_s::pos2’ may be used uninitialized in this function scoreAlignment2.cpp:451: note: ‘next_act.aligned_coords_s::pos2’ was declared here /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnDefs.h: In function ‘void computeLCBaccuracy(mems::IntervalList&, mems::IntervalList&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, std::vector >&)’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnDefs.h:210: warning: ‘next_act.aligned_coords_s::pos2’ may be used uninitialized in this function scoreAlignment2.cpp:451: note: ‘next_act.aligned_coords_s::pos2’ was declared here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SubstitutionMatrix.h:67: warning: ‘mems::PairwiseScoringScheme& mems::getDefaultScoringScheme()’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from mfaToMultiFiles.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/DNAFileSML.h:16, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from maf2xmfa.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:16: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:17: warning: ignoring #pragma warning /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/FileSML.h:18: warning: ignoring #pragma warning In file included from /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnSequence.h:31, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:19, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from maf2xmfa.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h: In member function ‘boolean genome::gnCompare::LessThan(gnSeqC, gnSeqC, boolean) const’: /tmp/mauve_snapshot/build_scripts/build/include/libGenome-1.3/libGenome/gnCompare.h:142: warning: array subscript has type ‘char’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SortedMerList.h:24, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:20, from maf2xmfa.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h: In function ‘int64 getSeed(int, int)’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SeedMasks.h:302: warning: unused variable ‘i’ In file included from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:25, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchFinder.h:18, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MemHash.h:20, from /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h:23, from maf2xmfa.cpp:1: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h: In function ‘void deleteRegisteredFiles()’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions maf2xmfa.cpp: In function ‘int main(int, char**)’: maf2xmfa.cpp:62: warning: comparison between signed and unsigned integer expressions maf2xmfa.cpp:72: warning: comparison between signed and unsigned integer expressions maf2xmfa.cpp:48: warning: unused variable ‘read_state’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h: In member function ‘void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/GappedAlignment.h:114: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:124: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/SparseAbstractMatch.h:126: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/MatchList.h:557: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:188: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h: In member function ‘void mems::HybridAbstractMatch::swap(mems::HybridAbstractMatch*) [with unsigned int FIXED_SEQ_COUNT = 2u, int64Alloc = std::allocator, uintAlloc = std::allocator]’: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/AbstractGappedAlignment.h:68: instantiated from ‘void mems::AbstractGappedAlignment::swap(mems::AbstractGappedAlignment*) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:113: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment*) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:106: instantiated from ‘void mems::CompactGappedAlignment::swap(mems::CompactGappedAlignment&) [with BaseType = mems::AbstractGappedAlignment, std::allocator > >]’ /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/CompactGappedAlignment.h:813: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:107: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:108: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:109: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:112: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:113: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/HybridAbstractMatch.h:114: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h: In member function ‘void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]’: maf2xmfa.cpp:118: instantiated from here /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h: At global scope: /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Memory.h:6: warning: ‘debugging_memory’ defined but not used /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/Match.h:28: warning: ‘mems::seq_compare_start’ defined but not used /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/libpthread.a(sem_open.o): In function `sem_open': /usr/src/packages/BUILD/glibc-2.9/nptl/sem_open.c:330: warning: the use of `mktemp' is dangerous, better use `mkstemp' strip: Warning: 'src' is not an ordinary file strip:src/simujobgen.pl: File format not recognized strip:src/rbplocalization.R: File format not recognized strip: Warning: 'src/.deps' is not an ordinary file strip:src/scoregen.pl: File format not recognized strip: Warning: 'src/.svn' is not an ordinary file strip:src/simujobrun.pl: File format not recognized strip:src/Rgradientgen.pl: File format not recognized strip:src/simujobparams.pm: File format not recognized