configure.ac:61: installing `config/missing' configure.ac:61: installing `config/install-sh' libGenome/Makefile.am: installing `config/depcomp' Makefile.am: installing `./INSTALL' Makefile.am: installing `./COPYING' configure: WARNING: doxygen not found - will not generate any doxygen documentation configure.ac:52: installing `config/missing' configure.ac:52: installing `config/install-sh' libMUSCLE/Makefile.am: installing `config/depcomp' Makefile.am: installing `./INSTALL' configure: WARNING: doxygen not found - will not generate any doxygen 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' 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' 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: 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' aligngivenpath.cpp:356: warning: unused variable 'uColB' 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' 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' 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' 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' ../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: 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: 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: 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 ../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 alpha.cpp: In function 'unsigned int muscle::GetAlphaSize(muscle::ALPHA)': alpha.cpp:86: warning: enumeration value 'ALPHA_Undefined' not handled in switch alpha.cpp: In function 'unsigned int muscle::GetAlphaSize(muscle::ALPHA)': alpha.cpp:86: warning: enumeration value 'ALPHA_Undefined' not handled in switch alpha.cpp: In function 'unsigned int muscle::GetAlphaSize(muscle::ALPHA)': alpha.cpp:86: warning: enumeration value 'ALPHA_Undefined' not handled in switch 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 ../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 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 '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 '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 anchoredpp.cpp: In function 'void muscle::AnchoredProfileProfile(muscle::MSA&, muscle::MSA&, muscle::MSA&)': anchoredpp.cpp:486: warning: unused variable 'uId' anchoredpp.cpp: In function 'void muscle::AnchoredProfileProfile(muscle::MSA&, muscle::MSA&, muscle::MSA&)': anchoredpp.cpp:486: warning: unused variable 'uId' 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' 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' 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' 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' 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 ../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: 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 anchors.cpp:108: warning: 'void muscle::ListBestCols(const muscle::MSA&, const muscle::SCORE*, const muscle::SCORE*, 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 anchors.cpp:108: warning: 'void muscle::ListBestCols(const muscle::MSA&, const muscle::SCORE*, const muscle::SCORE*, 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 anchors.cpp:108: warning: 'void muscle::ListBestCols(const muscle::MSA&, const muscle::SCORE*, const muscle::SCORE*, 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 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 'void muscle::BitTraceBack(char**, unsigned int, unsigned int, char, muscle::PWPath&)': bittraceback.cpp:149: warning: unused variable 'Bits' bittraceback.cpp: In function 'void muscle::BitTraceBack(char**, unsigned int, unsigned int, char, muscle::PWPath&)': bittraceback.cpp:149: warning: unused variable 'Bits' bittraceback.cpp: In function 'void muscle::BitTraceBack(char**, unsigned int, unsigned int, char, muscle::PWPath&)': bittraceback.cpp:149: warning: unused variable 'Bits' 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: 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: 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: 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 ../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/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor cluster.cpp: In member function 'void muscle::ClusterTree::Create(const muscle::DistFunc&)': cluster.cpp:269: warning: unused variable 'dMaxDist' ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor cluster.cpp: In member function 'void muscle::ClusterTree::Create(const muscle::DistFunc&)': cluster.cpp:269: warning: unused variable 'dMaxDist' cluster.cpp: In member function 'void muscle::ClusterTree::Create(const muscle::DistFunc&)': cluster.cpp:269: warning: unused variable 'dMaxDist' cluster.cpp: In member function 'void muscle::ClusterTree::Create(const muscle::DistFunc&)': cluster.cpp:269: warning: unused variable 'dMaxDist' ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor 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::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::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)': clust.cpp:206: warning: unused variable 'uClusterCount' 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::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 '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 '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::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 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 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 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 cluster.cpp:285: warning: 'uIndexClosest2' may be used uninitialized in this function cluster.cpp:284: warning: 'uIndexClosest1' may be used uninitialized in this function cluster.cpp:285: warning: 'uIndexClosest2' may be used uninitialized in this function cluster.cpp:284: warning: 'uIndexClosest1' may be used uninitialized in this function cluster.cpp:285: warning: 'uIndexClosest2' may be used uninitialized in this function cluster.cpp:284: warning: 'uIndexClosest1' may be used uninitialized in this function 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: 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: 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: 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: 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 color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer color.cpp:36: warning: missing braces around initializer ../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 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 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 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 ../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 diaglist.cpp: In member function 'void muscle::DiagList::FromPath(const muscle::PWPath&)': diaglist.cpp:53: warning: 'uStartPosA' may be used uninitialized in this function diaglist.cpp:54: warning: 'uStartPosB' may be used uninitialized in this function diaglist.cpp: In member function 'void muscle::DiagList::FromPath(const muscle::PWPath&)': diaglist.cpp:53: warning: 'uStartPosA' may be used uninitialized in this function diaglist.cpp:54: warning: 'uStartPosB' may be used uninitialized in this function diaglist.cpp: In member function 'void muscle::DiagList::FromPath(const muscle::PWPath&)': diaglist.cpp:53: warning: 'uStartPosA' may be used uninitialized in this function diaglist.cpp:54: warning: 'uStartPosB' may be used uninitialized in this function diaglist.cpp: In member function 'void muscle::DiagList::FromPath(const muscle::PWPath&)': diaglist.cpp:53: warning: 'uStartPosA' may be used uninitialized in this function diaglist.cpp:54: warning: 'uStartPosB' may be used uninitialized in this function 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' 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' 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' 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' ../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: 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: 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: 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 difftrees.cpp: In function 'void muscle::DiffTrees(const muscle::Tree&, const muscle::Tree&, muscle::Tree&, unsigned int*)': difftrees.cpp:163: warning: unused variable 'uLeafCount2' difftrees.cpp: In function 'void muscle::DiffTrees(const muscle::Tree&, const muscle::Tree&, muscle::Tree&, unsigned int*)': difftrees.cpp:163: warning: unused variable 'uLeafCount2' difftrees.cpp: In function 'void muscle::DiffTrees(const muscle::Tree&, const muscle::Tree&, muscle::Tree&, unsigned int*)': difftrees.cpp:163: warning: unused variable 'uLeafCount2' 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: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: 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: 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 ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../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 ../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 ../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' dpreglist.cpp: In function 'void muscle::DiagListToDPRegionList(const muscle::DiagList&, muscle::DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:84: warning: unused variable 'uDiagLengthMinusCaps' dpreglist.cpp: In function 'void muscle::DiagListToDPRegionList(const muscle::DiagList&, muscle::DPRegionList&, unsigned int, unsigned int)': dpreglist.cpp:84: warning: unused variable 'uDiagLengthMinusCaps' 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: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: 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: 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/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:15: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:22: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:28: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:36: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:41: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:49: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:63: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:70: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:79: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:88: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../libMUSCLE/enums.h:94: warning: missing braces around initializer ../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 ../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 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 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 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 ../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 ../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 ../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 estring.cpp:466: warning: 'bool muscle::CanMultiplyEstrings(const short int*, const short int*)' 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' 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' 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' 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: 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: At global scope: ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../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 ../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 fastdistkmer.cpp: In function 'void muscle::FastDistKmer(const muscle::SeqVect&, muscle::DistFunc&)': fastdistkmer.cpp:238: warning: unused variable 'KD' fastdistkmer.cpp: In function 'void muscle::FastDistKmer(const muscle::SeqVect&, muscle::DistFunc&)': fastdistkmer.cpp:238: warning: unused variable 'KD' fastdistkmer.cpp: In function 'void muscle::FastDistKmer(const muscle::SeqVect&, muscle::DistFunc&)': fastdistkmer.cpp:238: warning: unused variable 'KD' 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' fastdistmafft.cpp: In function 'void muscle::DistKmer6_6(const muscle::SeqVect&, muscle::DistFunc&)': fastdistmafft.cpp:241: warning: unused variable 'pName1' fastdistmafft.cpp: In function 'void muscle::DistKmer6_6(const muscle::SeqVect&, muscle::DistFunc&)': fastdistmafft.cpp:241: warning: unused variable 'pName1' 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 ../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: 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 ../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 ../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 ../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' fastdistnuc.cpp: In function 'void muscle::DistKmer4_6(const muscle::SeqVect&, muscle::DistFunc&)': fastdistnuc.cpp:226: warning: unused variable 'pName1' fastdistnuc.cpp: In function 'void muscle::DistKmer4_6(const muscle::SeqVect&, muscle::DistFunc&)': fastdistnuc.cpp:226: warning: unused variable 'pName1' 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: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: 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: 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: 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: 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 ../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 finddiagsn.cpp: In function 'char* muscle::TupleToStr(int)': finddiagsn.cpp:19: warning: comparison between signed and unsigned integer expressions finddiagsn.cpp: In function 'char* muscle::TupleToStr(int)': finddiagsn.cpp:19: warning: comparison between signed and unsigned integer expressions finddiagsn.cpp: In function 'char* muscle::TupleToStr(int)': finddiagsn.cpp:19: warning: comparison between signed and unsigned integer expressions ../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 ../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 ../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: 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: 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: 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 ../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 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 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 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 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: 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: 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 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: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: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: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 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 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 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 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 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 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 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 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 ../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: 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: 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: 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: 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' 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 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 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: 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' 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 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 glbalignss.cpp:224: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:286: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:224: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:286: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:224: warning: 'uInsertPos' may be used uninitialized in this function glbalignss.cpp:286: warning: 'uInsertPos' may be used uninitialized in this function 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 glbalndimer.cpp:17: warning: 'const char* muscle::LocalScoreToStr(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 glbalndimer.cpp:17: warning: 'const char* muscle::LocalScoreToStr(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 glbalndimer.cpp:17: warning: 'const char* muscle::LocalScoreToStr(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 glbalignss.cpp:14: warning: 'muscle::SCORE muscle::Subst(const muscle::Seq&, const muscle::Seq&, 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 glbalndimer.cpp:17: warning: 'const char* muscle::LocalScoreToStr(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 glbalignss.cpp:14: warning: 'muscle::SCORE muscle::Subst(const muscle::Seq&, const muscle::Seq&, 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 glbalignss.cpp:14: warning: 'muscle::SCORE muscle::Subst(const muscle::Seq&, const muscle::Seq&, 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 glbalignss.cpp:14: warning: 'muscle::SCORE muscle::Subst(const muscle::Seq&, const muscle::Seq&, unsigned int, 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 ../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 ../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 ../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 ../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 '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' 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 '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' makerootmsa.cpp: In function 'void muscle::MakeRootMSA(const muscle::SeqVect&, const muscle::Tree&, muscle::ProgNode*, muscle::MSA&)': makerootmsa.cpp:169: warning: unused variable 'uTreeNodeCount' 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: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: 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: 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: 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: 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 ../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 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' 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' 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::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' msa2.cpp: In function 'void muscle::MSAAppend(muscle::MSA&, const muscle::MSA&)': msa2.cpp:479: warning: unused variable 'uColCountCat' ../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: 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: 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 ../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 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 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 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 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 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 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 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 ../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 ../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 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::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::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::ObjScoreDP(const muscle::MSA&, const muscle::MSA&, muscle::SCORE*)': objscore2.cpp:316: warning: unused variable 'uColCount2' 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' objscore2.cpp: In function 'muscle::SCORE muscle::ObjScoreXP(const muscle::MSA&, const muscle::MSA&)': objscore2.cpp:495: warning: unused variable 'w' objscore2.cpp: In function 'muscle::SCORE muscle::ObjScoreXP(const muscle::MSA&, const muscle::MSA&)': objscore2.cpp:495: warning: unused variable 'w' objscore2.cpp: In function 'muscle::SCORE muscle::ObjScoreXP(const muscle::MSA&, const muscle::MSA&)': objscore2.cpp:495: warning: unused variable 'w' ../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: 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: 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 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 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 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 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: 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: 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 ../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 options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializeroptions.cpp:91: warning: missing braces around initializerr options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:91: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer options.cpp:133: warning: missing braces around initializer ../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 pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer ../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 pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer pam200mafft.cpp:34: warning: missing braces around initializer ../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 params.cpp: In function 'void muscle::SetPPScore(bool)': params.cpp:449: warning: enumeration value 'PPSCORE_Undefined' not handled in switch params.cpp: In function 'void muscle::SetPPScore(bool)': params.cpp:449: warning: enumeration value 'PPSCORE_Undefined' not handled in switch params.cpp: In function 'void muscle::SetPPScore(bool)': params.cpp:449: warning: enumeration value 'PPSCORE_Undefined' not handled in switch ../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: 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 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::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' 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' 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' 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 ../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 phy3.cpp:47: warning: 'void muscle::ListEIs(muscle::EdgeInfo**, 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 phy3.cpp:47: warning: 'void muscle::ListEIs(muscle::EdgeInfo**, 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 phy3.cpp:47: warning: 'void muscle::ListEIs(muscle::EdgeInfo**, 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 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 ../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 phy.cpp: In member function 'void muscle::Tree::RootUnrootedTree(muscle::ROOT)': phy.cpp:667: warning: unused variable 'dEdgeLength' phy.cpp: In member function 'void muscle::Tree::RootUnrootedTree(muscle::ROOT)': phy.cpp:667: warning: unused variable 'dEdgeLength' phy.cpp: In member function 'void muscle::Tree::RootUnrootedTree(muscle::ROOT)': phy.cpp:667: warning: unused variable 'dEdgeLength' 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: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: 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: 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 ../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::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 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 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 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: 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: 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 ../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/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../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 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' 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 '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' 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' 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: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: 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 ../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 ../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 ../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' progalign.cpp: In function 'muscle::ProgNode* muscle::ProgressiveAlignE(const muscle::SeqVect&, const muscle::Tree&, muscle::MSA&)': progalign.cpp:43: warning: unused variable 'uIterCount' progalign.cpp: In function 'muscle::ProgNode* muscle::ProgressiveAlignE(const muscle::SeqVect&, const muscle::Tree&, muscle::MSA&)': progalign.cpp:43: warning: unused variable 'uIterCount' 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: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: 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: 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 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' 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' 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' 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: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: 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: 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 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 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 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 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: 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: 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: 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 ../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 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' 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' 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' 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 ../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: At global scope: ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../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 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 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 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 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 ../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: 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' refinesubfams.cpp: In function 'bool muscle::RefineSubfams(muscle::MSA&, const muscle::Tree&, unsigned int)': refinesubfams.cpp:65: warning: unused variable 'uNodeCount' refinesubfams.cpp: In function 'bool muscle::RefineSubfams(muscle::MSA&, const muscle::Tree&, unsigned int)': refinesubfams.cpp:65: warning: unused variable 'uNodeCount' 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: 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: 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 ../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::AppendMSA(muscle::MSA&, const muscle::MSA&)': refinew.cpp:25: warning: unused variable 'uColCountCat' 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::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: 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' 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' 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' refinew.cpp:192: warning: unused variable 'uOutCols' ../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 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 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 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 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: 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: 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 ../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 ../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 setnewhandler.cpp:13: warning: ignoring #pragma omp critical setnewhandler.cpp:29: warning: ignoring #pragma omp critical setnewhandler.cpp:13: warning: ignoring #pragma omp critical setnewhandler.cpp:29: warning: ignoring #pragma omp critical setnewhandler.cpp:13: warning: ignoring #pragma omp critical setnewhandler.cpp:29: warning: ignoring #pragma omp critical 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 ../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 spfast.cpp: In function 'muscle::SCORE muscle::ObjScoreSPDimer(const muscle::MSA&)': spfast.cpp:254: warning: unused variable 'uSeqCount' spfast.cpp: In function 'muscle::SCORE muscle::ObjScoreSPDimer(const muscle::MSA&)': spfast.cpp:254: warning: unused variable 'uSeqCount' spfast.cpp: In function 'muscle::SCORE muscle::ObjScoreSPDimer(const muscle::MSA&)': spfast.cpp:254: warning: unused variable 'uSeqCount' 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: 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: 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: 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 ../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 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 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 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 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 ../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 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 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 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 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 ../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 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' 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' 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' 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: 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: 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 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: 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: 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: 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 traceback.cpp:70: warning: 'cPrevEdgeType' may be used uninitialized in this function traceback.cpp:70: warning: 'cPrevEdgeType' may be used uninitialized in this function 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: 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: 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 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: 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: 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: 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 tracebacksw.cpp:45: warning: 'cPrevEdgeType' may be used uninitialized in this function tracebacksw.cpp:45: warning: 'cPrevEdgeType' may be used uninitialized in this function 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 ../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: At global scope: ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../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 switchtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../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/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/msadist.h:26: warning: enumeration value 'DISTANCE_PWScoreDist' not handled in switch ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor../libMUSCLE/msadist.h:26: warning: enumeration value 'DISTANCE_ScoreDist' not handled in switchvirtual destructor ../libMUSCLE/msadist.h:26: warning: enumeration value 'DISTANCE_Edit' not handled in switch ../libMUSCLE/clustsetmsa.h: At global scope: ../libMUSCLE/clustsetmsa.h:16: warning: 'class muscle::ClustSetMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../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 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' 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' 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' 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 ../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: At global scope: ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:12: warning: 'class muscle::DistCalc' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:21: warning: 'class muscle::DistCalcDF' has virtual functions but non-virtual destructor ../libMUSCLE/distcalc.h:34: warning: 'class muscle::DistCalcMSA' has virtual functions but non-virtual destructor upgma2.cpp:363: warning: 'class muscle::DistCalcTest' has virtual functions but non-virtual destructor upgma2.cpp: In member function 'virtual void muscle::DistCalcTest::CalcDistRange(unsigned int, muscle::dist_t*) const': upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:363: warning: 'class muscle::DistCalcTest' has virtual functions but non-virtual destructor upgma2.cpp: In member function 'virtual void muscle::DistCalcTest::CalcDistRange(unsigned int, muscle::dist_t*) const': upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:363: warning: 'class muscle::DistCalcTest' has virtual functions but non-virtual destructor upgma2.cpp: In member function 'virtual void muscle::DistCalcTest::CalcDistRange(unsigned int, muscle::dist_t*) const': upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:363: warning: 'class muscle::DistCalcTest' has virtual functions but non-virtual destructor upgma2.cpp: In member function 'virtual void muscle::DistCalcTest::CalcDistRange(unsigned int, muscle::dist_t*) const': upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer upgma2.cpp:373: warning: missing braces around initializer usage.cpp:8: warning: ignoring #pragma omp critical usage.cpp:8: warning: ignoring #pragma omp critical usage.cpp:8: warning: ignoring #pragma omp critical usage.cpp:8: warning: ignoring #pragma omp critical ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used 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 ../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 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 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 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 ../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: 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: 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: 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 writescorefile.cpp: In function 'void muscle::WriteScoreFile(const muscle::MSA&)': writescorefile.cpp:29: warning: 'Score' may be used uninitialized in this function writescorefile.cpp: In function 'void muscle::WriteScoreFile(const muscle::MSA&)': writescorefile.cpp:29: warning: 'Score' may be used uninitialized in this function writescorefile.cpp: In function 'void muscle::WriteScoreFile(const muscle::MSA&)': writescorefile.cpp:29: warning: 'Score' may be used uninitialized in this function ../libMUSCLE/intmath.h:61: warning: 'double muscle::ScoreToDouble(muscle::SCORE)' defined but not used writescorefile.cpp: In function 'void muscle::WriteScoreFile(const muscle::MSA&)': writescorefile.cpp:29: warning: 'Score' 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: 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 ../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 ../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 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 ../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: *** [all-recursive] Error 1 ranlib: for architecture: ppc file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: ppc file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: ppc64 file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: ppc64 file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: i386 file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: i386 file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: x86_64 file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: x86_64 file: .libs/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: ppc file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: ppc file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: ppc64 file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: ppc64 file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: i386 file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: i386 file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols ranlib: for architecture: x86_64 file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-gotowt.o) has no symbols ranlib: for architecture: x86_64 file: /tmp/mauve_snapshot/build_scripts/build/lib/libMUSCLE-3.7.a(libMUSCLE_3_7_la-nwrec.o) has no symbols configure.ac:54: installing `config/missing' configure.ac:54: installing `config/install-sh' libMems/Makefile.am: installing `config/depcomp' configure: WARNING: doxygen not found - will not generate any doxygen 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 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 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 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 ../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 ../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 ../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 /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' /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' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../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 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 ../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 ../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 ../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 ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../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/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::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::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 In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': RepeatHash.cpp:63: 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/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': RepeatHash.cpp:63: 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/MatchFinder.h:18, from MatchFinder.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical ../libMems/UngappedLocalAlignment.h: In member function 'void mems::UngappedLocalAlignment::Move(int64) [with AbstractMatchImpl = mems::HybridAbstractMatch<2u, std::allocator, std::allocator >]': RepeatHash.cpp:63: 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 >]': RepeatHash.cpp:63: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../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 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 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 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/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::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:443: 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 >]': MatchFinder.cpp:443: 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 >]': MatchFinder.cpp:443: 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 >]': MatchFinder.cpp:443: 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/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used /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' /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' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../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 ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../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:438: warning: array subscript has type 'char' ../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::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:438: warning: array subscript has type 'char' 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:438: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector >&)': SortedMerList.cpp:548: warning: array subscript has type 'char' SortedMerList.cpp:560: warning: array subscript has type 'char' 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 uint64 mems::SortedMerList::GetSeedMer(gnSeqI) const': SortedMerList.cpp:743: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector >&)': SortedMerList.cpp:548: warning: array subscript has type 'char' SortedMerList.cpp:560: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual uint64 mems::SortedMerList::GetSeedMer(gnSeqI) const': SortedMerList.cpp:743: warning: comparison between signed and unsigned integer expressionsSortedMerList.cpp: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector >&)': SortedMerList.cpp:548: warning: array subscript has type 'char' SortedMerList.cpp:560: warning: array subscript has type 'char' 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:438: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual uint64 mems::SortedMerList::GetSeedMer(gnSeqI) const': SortedMerList.cpp:743: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::Create(const genome::gnSequence&, uint64)': SortedMerList.cpp:794: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::Create(const genome::gnSequence&, uint64)': SortedMerList.cpp:794: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::Create(const genome::gnSequence&, uint64)': SortedMerList.cpp:794: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::FillSML(gnSeqC*, gnSeqI, boolean, std::vector >&)': SortedMerList.cpp:548: warning: array subscript has type 'char' SortedMerList.cpp:560: warning: array subscript has type 'char' SortedMerList.cpp: In member function 'virtual uint64 mems::SortedMerList::GetSeedMer(gnSeqI) const': SortedMerList.cpp:743: warning: comparison between signed and unsigned integer expressions SortedMerList.cpp: In member function 'virtual void mems::SortedMerList::Create(const genome::gnSequence&, uint64)': SortedMerList.cpp:794: warning: comparison between signed and unsigned integer expressions 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 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 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 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 SortedMerList.cpp: In member function 'virtual gnSeqI mems::SortedMerList::UniqueMerCount()': SortedMerList.cpp:472: warning: 'prev_mer$mer' may be used uninitialized in this function SortedMerList.cpp: In member function 'virtual gnSeqI mems::SortedMerList::UniqueMerCount()': SortedMerList.cpp:472: warning: 'prev_mer$mer' may be used uninitialized in this function SortedMerList.cpp: In member function 'virtual gnSeqI mems::SortedMerList::UniqueMerCount()': SortedMerList.cpp:472: warning: 'prev_mer$mer' may be used uninitialized in this function SortedMerList.cpp: In member function 'virtual gnSeqI mems::SortedMerList::UniqueMerCount()': SortedMerList.cpp:472: warning: 'prev_mer$mer' may be used uninitialized in this function In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from FileSML.cpp:12: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from FileSML.cpp:12: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from FileSML.cpp:12: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from FileSML.cpp:12: ../libMems/Files.h:45: warning: ignoring #pragma omp critical 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/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/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/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 /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' /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' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/MatchFinder.h:18, from ../libMems/MemHash.h:20, from MemHash.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../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 ../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 ../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 ../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 ../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 ../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 ../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 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/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 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/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 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/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/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/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::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::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::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::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: 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 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' MemHash.cpp: In member function 'virtual mems::MatchHashEntry* mems::MemHash::AddHashEntry(mems::MatchHashEntry&)': MemHash.cpp:245: warning: unused variable 'submem' 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 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' MemHash.cpp: In member function 'virtual mems::MatchHashEntry* mems::MemHash::AddHashEntry(mems::MatchHashEntry&)': MemHash.cpp:245: warning: unused variable 'submem' ../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::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::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::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/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/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/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/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/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/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/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 >]': FileSML.cpp:678: 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 >]': FileSML.cpp:678: 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 >]': FileSML.cpp:678: 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 >]': FileSML.cpp:678: 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 >]': MemHash.cpp:329: 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 >]': MemHash.cpp:329: 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 >]': MemHash.cpp:329: 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 >]': MemHash.cpp:329: 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/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used FileSML.cpp: In member function 'virtual boolean mems::FileSML::Read(std::vector >&, gnSeqI, gnSeqI)': FileSML.cpp:403: warning: 'tmp_mer$mer' may be used uninitialized in this function ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used FileSML.cpp: In member function 'virtual boolean mems::FileSML::Read(std::vector >&, gnSeqI, gnSeqI)': FileSML.cpp:403: warning: 'tmp_mer$mer' may be used uninitialized in this function FileSML.cpp: In member function 'virtual boolean mems::FileSML::Read(std::vector >&, gnSeqI, gnSeqI)': FileSML.cpp:403: warning: 'tmp_mer$mer' may be used uninitialized in this function FileSML.cpp: In member function 'virtual boolean mems::FileSML::Read(std::vector >&, gnSeqI, gnSeqI)': FileSML.cpp:403: warning: 'tmp_mer$mer' may be used uninitialized in this function ../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/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 ../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 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 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 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 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 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 '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 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 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:202: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:188: 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:202: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: 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:202: 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 >]': MatchHashEntry.cpp:202: 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]': MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:188: 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:202: instantiated from here ../libMems/HybridAbstractMatch.h:166: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: instantiated from here ../libMems/HybridAbstractMatch.h:179: warning: comparison between signed and unsigned integer expressions MatchHashEntry.cpp:202: 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:202: 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 >]': MatchHashEntry.cpp:202: 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 ../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 ../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 /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' /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' /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' /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/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/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/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/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 ../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 ../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 ../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 ../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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../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/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/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/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::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::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::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/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/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/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/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/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/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/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/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:24: 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 >]': IntervalList.cpp:24: 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 >]': IntervalList.cpp:24: 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 >]': IntervalList.cpp:24: instantiated from here ../libMems/UngappedLocalAlignment.h:132: warning: comparison between signed and unsigned integer expressions /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' /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' /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' /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::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 '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::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 '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 '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: 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: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::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: 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::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:280: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:245: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:313: 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: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: 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: 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:384: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:400: 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:409: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:414: 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: 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:530: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:541: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:541: 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: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: 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:596: 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::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 '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:409: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:414: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:648: 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:657: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:530: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:671: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:541: 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::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: In member function 'bool mems::gnAlignedSequences::removeAlignedSeq(unsigned int)': gnAlignedSequences.cpp:737: 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 '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::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::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::constructNexusAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1259: warning: comparison between signed and unsigned integer expressions gnAlignedSequences.cpp:1257: warning: unused variable 'newFilter' nAlignedSequences.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::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::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::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::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 'bool mems::gnAlignedSequences::constructMSFAlignedSequenceList(std::ifstream&)': gnAlignedSequences.cpp:1211: 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::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::coordinates(std::string)': gnAlignedSequences.cpp:1558: 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 gnAlignedSequences.cpp: In member function 'bool mems::gnAlignedSequences::coordinates(std::string)': gnAlignedSequences.cpp:1558: 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 ../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/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/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 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 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 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/MatchList.h:25, from MatchList.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from MatchList.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from MatchList.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from MatchList.cpp:13: ../libMems/Files.h:45: warning: ignoring #pragma omp critical /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../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/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::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::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:25: 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 >]': MatchList.cpp:25: 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 >]': MatchList.cpp:25: 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 >]': MatchList.cpp:25: 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/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../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/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 ../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 ../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 ../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 ../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 ../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 ../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 ../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 ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/Files.h:45: warning: ignoring #pragma omp critical In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from Aligner.cpp:9: ../libMems/Files.h:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical In file included from Aligner.cpp:14: ../libMems/DistanceMatrix.h:212: warning: ignoring #pragma omp parallel ../libMems/DistanceMatrix.h:216: warning: ignoring #pragma omp critical In file included from Aligner.cpp:14: ../libMems/DistanceMatrix.h:212: warning: ignoring #pragma omp parallel ../libMems/DistanceMatrix.h:216: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical In file included from Aligner.cpp:14: ../libMems/DistanceMatrix.h:212: warning: ignoring #pragma omp parallel ../libMems/DistanceMatrix.h:216: warning: ignoring #pragma omp critical In file included from Aligner.cpp:14: ../libMems/DistanceMatrix.h:212: warning: ignoring #pragma omp parallel ../libMems/DistanceMatrix.h:216: warning: ignoring #pragma omp critical /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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 /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor /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/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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../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 ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/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 ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor../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 ../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 ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/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/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 ../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 ../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/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 ../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 ../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/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' ../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 ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' ../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 ../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 ../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 ../libMems/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor ../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/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char'atchComparator::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 ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' ../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 ../libMems/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor 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:77: warning: comparison between signed and unsigned integer expressions Aligner.cpp:127: warning: comparison between signed and unsigned integer expressions ../libMems/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' ../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 ../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 ../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 ../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 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 ../libMems/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor 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 ../libMems/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' Aligner.cpp:127: warning: comparison between signed and unsigned integer expressions ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' 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 ../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 Aligner.cpp:510: warning: comparison between signed and unsigned integer expressions 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 ../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 ../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::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::EliminateOverlaps(mems::MatchList&)': Aligner.cpp:77: warning: comparison between signed and unsigned integer expressions Aligner.cpp:127: warning: comparison between signed and unsigned integer expressions ../libMems/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor ../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 '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: 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 ../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 ../libMems/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' Aligner.cpp: In function 'boolean mems::checkCollinearity(mems::Match*, mems::Match*)': Aligner.cpp:269: warning: comparison between signed and unsigned integer expressionsay subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' 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::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: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 ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' 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 '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: In function 'void mems::transposeMatches(mems::MatchList&, uint, const std::vector >&)': Aligner.cpp:991: warning: comparison between signed and unsigned integer expressions Aligner.cpp:127: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1012: 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 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 ../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 '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::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: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: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 '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::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 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: 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 expressionsAligner.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 member function 'void mems::Aligner::AlignLCB(mems::MatchList&, mems::Interval&)': Aligner.cpp:1405: warning: comparison between signed and unsigned integer expressions ../libMems/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' Aligner.cpp:1403: warning: unused variable 'matchI' ../libMems/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' 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 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 Aligner.cpp:510: warning: comparison between signed and unsigned integer expressions Aligner.cpp: In member function 'void mems::Aligner::SearchWithinLCB(mems::MatchList&, std::vector >&, bool, bool)': Aligner.cpp:1495: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1478: warning: unused variable 'config_value' 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:1242: warning: comparison between signed and unsigned integer expressions 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: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::vector >&)': Aligner.cpp:1822: 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' ../libMems/Islands.h: In function 'char* mems::getCharmap()': ../libMems/Islands.h:98: warning: array subscript has type 'char' ../libMems/Islands.h:99: warning: array subscript has type 'char' ../libMems/Islands.h:100: warning: array subscript has type 'char' ../libMems/Islands.h:101: warning: array subscript has type 'char' ../libMems/Islands.h:102: warning: array subscript has type 'char' ../libMems/Islands.h:103: warning: array subscript has type 'char' ../libMems/Islands.h:104: warning: array subscript has type 'char' ../libMems/Islands.h:105: warning: array subscript has type 'char' ../libMems/Islands.h:106: warning: array subscript has type 'char' ../libMems/Islands.h:107: warning: array subscript has type 'char' ../libMems/Islands.h: In function 'void mems::findHssHomologyHMM(std::vector >&, mems::hss_list_t&, uint, uint, const Params&, boolean, boolean)': ../libMems/Islands.h:137: warning: array subscript has type 'char' ../libMems/Islands.h:137: warning: array subscript has type 'char' 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::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: 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::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 ../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 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:1126: 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 >&, 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:1403: warning: unused variable 'matchI' Aligner.cpp: In member function 'void mems::Aligner::SearchWithinLCB(mems::MatchList&, std::vector >&, bool, bool)': Aligner.cpp:1495: 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:1242: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2042: 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:2046: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2040: warning: unused variable 'prev_size' Aligner.cpp:1318: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1300: warning: unused variable 'galI' Aligner.cpp:2124: warning: comparison between signed and unsigned integer expressions 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:1403: warning: unused variable 'matchI' Aligner.cpp: In member function 'void mems::Aligner::SearchWithinLCB(mems::MatchList&, std::vector >&, bool, bool)': Aligner.cpp:1495: warning: comparison between signed and unsigned integer expressions Aligner.cpp:1478: warning: unused variable 'config_value' 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 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 Islands.cpp: In function 'void mems::findIslandsBetweenLCBs(mems::IntervalList&, uint, std::ostream&)': Islands.cpp:307: warning: comparison between signed and unsigned integer expressions 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 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 Islands.cpp: In function 'void mems::findIslandsBetweenLCBs(mems::IntervalList&, uint, std::ostream&)': Islands.cpp:307: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2139: warning: comparison between signed and unsigned integer expressions 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 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: In function 'void mems::filterMatches(std::vector >&, std::vector >&, 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:1242: warning: comparison between signed and unsigned integer expressions 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 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 >&, boolean, std::ostream*)': Aligner.cpp:1994: 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:1478: warning: unused variable 'config_value' Aligner.cpp:1300: warning: unused variable 'galI' 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: In member function 'void mems::Aligner::AlignLCB(mems::MatchList&, mems::Interval&)': Aligner.cpp:1405: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2124: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2139: warning: comparison between signed and unsigned integer expressions 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 ../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 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: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::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:1403: warning: unused variable 'matchI' 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::SearchWithinLCB(mems::MatchList&, std::vector >&, bool, bool)': Aligner.cpp:1495: 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/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 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 ../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 Aligner.cpp: In member function 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector >&, 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/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 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: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::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 >&, 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' ../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 Aligner.cpp:2124: warning: comparison between signed and unsigned integer expressions Aligner.cpp:2139: 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::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../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/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::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::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::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../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/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../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::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../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::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../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::Match]': ../libMems/Aligner.h:284: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::Match]': ../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/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/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/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/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/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/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/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:319: 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 >]': Islands.cpp:319: 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 >]': Islands.cpp:319: 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 >]': Islands.cpp:319: instantiated from here ../libMems/UngappedLocalAlignment.h:132: 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/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/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/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]': /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2334: instantiated from 'void std::partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2523: instantiated from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = int, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2606: instantiated from 'void std::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' Aligner.cpp:1873: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]': /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2334: instantiated from 'void std::partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2523: instantiated from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = int, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2606: instantiated from 'void std::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' Aligner.cpp:1873: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]': /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2334: instantiated from 'void std::partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2523: instantiated from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2606: instantiated from 'void std::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' Aligner.cpp:1873: instantiated from here ../libMems/AbstractMatch.h:308: warning: unused variable 'diff' ../libMems/AbstractMatch.h: In member function 'boolean mems::MatchStartComparator::operator()(const MatchType*, const MatchType*) const [with MatchType = mems::AbstractMatch]': /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2334: instantiated from 'void std::partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2523: instantiated from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >, _Size = long int, _Compare = mems::MatchStartComparator]' /Developer/SDKs/MacOSX10.4u.sdk/usr/include/c++/4.0.0/bits/stl_algo.h:2606: instantiated from 'void std::sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __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:2287: 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 >]': Aligner.cpp:2287: 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 >]': Aligner.cpp:2287: 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 >]': Aligner.cpp:2287: 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/Memory.h: At global scope: ../libMems/Memory.h:6: warning: 'debugging_memory' defined but not used ../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/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/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 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 ../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 ../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 ../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 ../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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical 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:45: warning: ignoring #pragma omp critical /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' /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' /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/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/SeedMasks.h: In function 'int64 getSeed(int, int)': ../libMems/SeedMasks.h:302: warning: unused variable 'i' ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../libMems/Files.h: In function 'void deleteRegisteredFiles()': ../libMems/Files.h:59: warning: comparison between signed and unsigned integer expressions ../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 MaskedMemHash.cpp: In member function 'virtual boolean mems::MaskedMemHash::HashMatch(std::list >&)': MaskedMemHash.cpp:56: 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 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/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::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::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:64: 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 >]': MaskedMemHash.cpp:64: 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 >]': MaskedMemHash.cpp:64: 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 >]': MaskedMemHash.cpp:64: 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/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used ../libMems/Match.h: At global scope: ../libMems/Match.h:28: warning: 'mems::seq_compare_start' defined but not used /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' /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' /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' /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/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/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/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/Memory.h: At global scope: ../libMems/Memory.h:6: warning: 'debugging_memory' defined but not used ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: 'debugging_memory' defined but not used ../libMems/Memory.h: At global scope: ../libMems/Memory.h:6: warning: 'debugging_memory' defined but not used 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:15bMUSCLE/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: /Developer/SDKs/MacOSX10.4u.sdk/usr/include/assert.h:87:1: warning: this is the location of the previous definition 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: /Developer/SDKs/MacOSX10.4u.sdk/usr/include/assert.h:84:1: warning: this is the location of the previous definition 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/AbstractMatch.h:21, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: /Developer/SDKs/MacOSX10.4u.sdk/usr/include/assert.h:87:1: warning: , from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: /Developer/SDKs/MacOSX10.4u.sdk/usr/include/assert.h:84:1: warning: this is the location of the previous definition /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' /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' /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' /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/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor ../libMems/GappedAligner.h: At global scope: ../libMems/GappedAligner.h:22: warning: 'class mems::GappedAligner' has virtual functions but non-virtual destructor ../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/MuscleInterface.h: At global scope: ../libMems/MuscleInterface.h:53: warning: 'class mems::MuscleInterface' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustset.h:11: warning: 'class muscle::ClustSet' has virtual functions but non-virtual destructor /tmp/mauve_snapshot/build_scripts/build/include/libMUSCLE-3.7/libMUSCLE/clustsetdf.h:14: warning: 'class muscle::ClustSetDF' has virtual functions but non-virtual destructor 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 '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 '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 '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 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: 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 expressionsMuscleInterface.cpp:450: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:461: 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: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: 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:551: warning: comparison between signed and unsigned integer expressions MuscleInterface.cpp:575: 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: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: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: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' 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 expression