Project file 'C:\build_temp\repeatoire\projects\repeatoire.vcproj' could not be loaded.
The project is either missing from disk or access was denied.
One or more projects in the solution could not be loaded for the following reason(s):

The project file or web has been moved, renamed or is not on your computer.

These projects will be labeled as unavailable in Solution Explorer. Expand the project node to show the reason the project could not be loaded.------ Rebuild All started: Project: libMUSCLE, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'libMUSCLE', configuration 'Release OpenMP|x64'
Compiling...
aligngivenpath.cpp
writescorefile.cpp
vtml2.cpp
validateids.cpp
usage.cpp
upgma2.cpp
typetostr.cpp
treefrommsa.cpp
tracebacksw.cpp
tracebackopt.cpp
traceback.cpp
tomhydro.cpp
threewaywt.cpp
textfile.cpp
termgaps.cpp
sw.cpp
subfams.cpp
subfam.cpp
stabilize.cpp
sptest.cpp
Compiling...
spfast.cpp
setnewhandler.cpp
setgscweights.cpp
setblosumweights.cpp
seqvect.cpp
seq.cpp
scorepp.cpp
scorehistory.cpp
scoregaps.cpp
scoredist.cpp
savebest.cpp
refinew.cpp
refinevert.cpp
refinetreee.cpp
refinetree.cpp
refinesubfams.cpp
refinehoriz.cpp
refine.cpp
realigndiffse.cpp
realigndiffs.cpp
Compiling...
readmx.cpp
pwpath.cpp
progressivealign.cpp
progress.cpp
progalign.cpp
profilefrommsa.cpp
profile.cpp
profdb.cpp
ppscore.cpp
posgap.cpp
phytofile.cpp
physeq.cpp
phyfromfile.cpp
phyfromclust.cpp
phy4.cpp
phy3.cpp
phy2.cpp
phy.cpp
params.cpp
pam200mafft.cpp
Compiling...
outweights.cpp
options.cpp
onexception.cpp
objscoreda.cpp
objscore2.cpp
objscore.cpp
nwsmall.cpp
nwrec.cpp
nwdasmall.cpp
nwdasimple2.cpp
nwdasimple.cpp
nucmx.cpp
muscleout.cpp
muscle.cpp
msf.cpp
msadistkimura.cpp
msa2.cpp
msa.cpp
mpam200.cpp
mhack.cpp
Compiling...
maketree.cpp
makerootmsab.cpp
makerootmsa.cpp
main.cpp
local.cpp
intmath.cpp
hydro.cpp
html.cpp
henikoffweightpb.cpp
henikoffweight.cpp
gotowt.cpp
gonnet.cpp
globalswin32.cpp
globalsother.cpp
globalslinux.cpp
globals.cpp
glbalndimer.cpp
glbalignss.cpp
glbalignspn.cpp
glbalignsp.cpp
Compiling...
glbalignsimple.cpp
glbalignle.cpp
glbaligndiag.cpp
glbalign352.cpp
glbalign.cpp
finddiagsn.cpp
finddiags.cpp
fastscorepath2.cpp
fastdistnuc.cpp
fastdistmafft.cpp
fastdistkmer.cpp
fastdistkbit.cpp
fastdistjones.cpp
fastdist.cpp
fastclust.cpp
fasta2.cpp
fasta.cpp
estring.cpp
enumtostr.cpp
enumopts.cpp
Compiling...
edgelist.cpp
drawtree.cpp
dpreglist.cpp
dosp.cpp
domuscle.cpp
distpwkimura.cpp
distfunc.cpp
distcalc.cpp
difftreese.cpp
difftrees.cpp
diffpaths.cpp
diffobjscore.cpp
diaglist.cpp
cons.cpp
color.cpp
clwwt.cpp
cluster.cpp
clust.cpp
blosumla.cpp
blosum62.cpp
Compiling...
bittraceback.cpp
anchors.cpp
anchoredpp.cpp
alpha.cpp
aln.cpp
aligntwoprofs.cpp
aligntwomsas.cpp
aligngivenpathsw.cpp
Creating library...
writescorefile.obj : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Build log was saved at "file://c:\build_temp\muscle\projects\x64\Release OpenMP\BuildLog.htm"
libMUSCLE - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: libGenome, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'libGenome', configuration 'Release OpenMP|x64'
Compiling...
gnABISource.cpp
gnTranslator.cpp
gnStringTools.cpp
gnStringSpec.cpp
gnSourceSpec.cpp
gnSourceQualifier.cpp
gnSourceHeader.cpp
gnSourceFactory.cpp
gnSequence.cpp
gnSEQSource.cpp
gnRAWSource.cpp
gnPosSpecificTranslator.cpp
gnLocation.cpp
gnGenomeSpec.cpp
gnGBKSource.cpp
gnFragmentSpec.cpp
gnFilter.cpp
gnFileSource.cpp
gnFileContig.cpp
gnFeature.cpp
Compiling...
gnFastTranslator.cpp
gnFASSource.cpp
gnException.cpp
gnDefs.cpp
gnContigSpec.cpp
gnCompare.cpp
gnBaseFeature.cpp
Creating library...
gnTranslator.obj : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Build log was saved at "file://c:\build_temp\libGenome\projects\x64\Release OpenMP\BuildLog.htm"
libGenome - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: libMems, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'libMems', configuration 'Release OpenMP|x64'
Compiling...
algebras.cc
SuperInterval.cpp
ProgressiveAligner.cpp
PairwiseMatchFinder.cpp
GreedyBreakpointElimination.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4267: 'initializing' : conversion from 'size_t' to 'uint', possible loss of data
        ..\libMems\GreedyBreakpointElimination.cpp(191) : see reference to function template instantiation 'std::pair<_Ty1,_Ty2>::pair<size_t,int>(const std::pair<size_t,int> &)' being compiled
        with
        [
            _Ty1=uint,
            _Ty2=uint
        ]
        ..\libMems\GreedyBreakpointElimination.cpp(666) : see reference to function template instantiation 'uint mems::RemoveLCBandCoalesce<std::vector<_Ty>>(size_t,uint,LcbVector &,std::vector<double> &,std::vector<std::pair<_Ty1,_Ty2>> &,std::vector<uint32> &)' being compiled
        with
        [
            _Ty=mems::TrackingLCB<mems::TrackingMatch *>,
            LcbVector=std::vector<mems::TrackingLCB<mems::TrackingMatch *>>,
            _Ty1=uint,
            _Ty2=uint
        ]
Backbone.cpp
MuscleInterface.cpp
..\libMems\MuscleInterface.cpp(730) : warning C4244: '=' : conversion from 'int' to 'muscle::SCORE', possible loss of data
..\libMems\MuscleInterface.cpp(732) : warning C4244: '=' : conversion from 'int' to 'muscle::SCORE', possible loss of data
Islands.cpp
Aligner.cpp
RepeatHash.cpp
MemHash.cpp
MatchFinder.cpp
MaskedMemHash.cpp
RepeatMatchList.cpp
RepeatMatch.cpp
MatchHashEntry.cpp
gnAlignedSequences.cpp
GappedAlignment.cpp
SortedMerList.cpp
MemorySML.cpp
Compiling...
FileSML.cpp
DNAMemorySML.cpp
DNAFileSML.cpp
homologymain.cc
homology.cc
Compiling...
twister.c
util.c
timing.c
sorting.c
sml.c
dmsort.c
buffer.c
awin32aio.c
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 1 of type 'HANDLE'
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 2 of type 'char *'
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 4 of type 'OVERLAPPED *'
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 5 of type 'void (__cdecl *)(DWORD,DWORD,LPOVERLAPPED)'
asyncio.c
aPOSIXaio.c
alinuxaio.c
alibc.c
Creating library...
SuperInterval.obj : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Build log was saved at "file://c:\build_temp\libMems\projects\x64\Release OpenMP\BuildLog.htm"
libMems - 0 error(s), 7 warning(s)
------ Rebuild All started: Project: muscle, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'muscle', configuration 'Release OpenMP|x64'
Compiling...
writescorefile.cpp
vtml2.cpp
validateids.cpp
usage.cpp
upgma2.cpp
typetostr.cpp
treefrommsa.cpp
tracebacksw.cpp
tracebackopt.cpp
traceback.cpp
tomhydro.cpp
threewaywt.cpp
textfile.cpp
termgaps.cpp
sw.cpp
subfams.cpp
subfam.cpp
stabilize.cpp
sptest.cpp
spfast.cpp
Compiling...
setnewhandler.cpp
setgscweights.cpp
setblosumweights.cpp
seqvect.cpp
seq.cpp
scorepp.cpp
scorehistory.cpp
scoregaps.cpp
scoredist.cpp
savebest.cpp
refinew.cpp
refinevert.cpp
refinetreee.cpp
refinetree.cpp
refinesubfams.cpp
refinehoriz.cpp
refine.cpp
realigndiffse.cpp
realigndiffs.cpp
readmx.cpp
Compiling...
pwpath.cpp
progressivealign.cpp
progress.cpp
progalign.cpp
profilefrommsa.cpp
profile.cpp
profdb.cpp
ppscore.cpp
posgap.cpp
phytofile.cpp
physeq.cpp
phyfromfile.cpp
phyfromclust.cpp
phy4.cpp
phy3.cpp
phy2.cpp
phy.cpp
params.cpp
pam200mafft.cpp
outweights.cpp
Compiling...
options.cpp
onexception.cpp
objscoreda.cpp
objscore2.cpp
objscore.cpp
nwsmall.cpp
nwrec.cpp
nwdasmall.cpp
nwdasimple2.cpp
nwdasimple.cpp
nucmx.cpp
muscleout.cpp
muscle.cpp
msf.cpp
msadistkimura.cpp
msa2.cpp
msa.cpp
mpam200.cpp
mhack.cpp
maketree.cpp
Compiling...
makerootmsab.cpp
makerootmsa.cpp
main.cpp
local.cpp
intmath.cpp
hydro.cpp
html.cpp
henikoffweightpb.cpp
henikoffweight.cpp
gotowt.cpp
gonnet.cpp
globalswin32.cpp
globalsother.cpp
globalslinux.cpp
globals.cpp
glbalndimer.cpp
glbalignss.cpp
glbalignspn.cpp
glbalignsp.cpp
glbalignsimple.cpp
Compiling...
glbalignle.cpp
glbaligndiag.cpp
glbalign352.cpp
glbalign.cpp
finddiagsn.cpp
finddiags.cpp
fastscorepath2.cpp
fastdistnuc.cpp
fastdistmafft.cpp
fastdistkmer.cpp
fastdistkbit.cpp
fastdistjones.cpp
fastdist.cpp
fastclust.cpp
fasta2.cpp
fasta.cpp
estring.cpp
enumtostr.cpp
enumopts.cpp
edgelist.cpp
Compiling...
drawtree.cpp
dpreglist.cpp
dosp.cpp
domuscle.cpp
distpwkimura.cpp
distfunc.cpp
distcalc.cpp
difftreese.cpp
difftrees.cpp
diffpaths.cpp
diffobjscore.cpp
diaglist.cpp
cons.cpp
color.cpp
clwwt.cpp
cluster.cpp
clust.cpp
blosumla.cpp
blosum62.cpp
bittraceback.cpp
Compiling...
anchors.cpp
anchoredpp.cpp
alpha.cpp
aln.cpp
aligntwoprofs.cpp
aligntwomsas.cpp
aligngivenpathsw.cpp
aligngivenpath.cpp
Compiling manifest to resources...
Linking...
LINK : warning LNK4075: ignoring '/INCREMENTAL' due to '/LTCG' specification
Generating code
Finished generating code
Embedding manifest...
LINK : warning LNK4075: ignoring '/INCREMENTAL' due to '/LTCG' specification
Generating code
Finished generating code
Build log was saved at "file://c:\build_temp\muscle\projects\x64\Release OpenMP\BuildLog.htm"
muscle - 0 error(s), 2 warning(s)
------ Rebuild All started: Project: stripSubsetLCBs, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'stripSubsetLCBs', configuration 'Release OpenMP|x64'
Compiling...
stripSubsetLCBs.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
stripSubsetLCBs - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: getOrthologList, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'getOrthologList', configuration 'Release OpenMP|x64'
Compiling...
getOrthologList.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
getOrthologList - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: bbAnalyze, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'bbAnalyze', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
bbAnalyze.cpp
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
bbAnalyze - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: scoreProcrastAlignment, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'scoreProcrastAlignment', configuration 'Release OpenMP|x64'
Compiling...
scoreProcrastAlignment.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4244: 'initializing' : conversion from 'const uint64' to 'uint', possible loss of data
        ..\src\scoreProcrastAlignment.cpp(180) : see reference to function template instantiation 'std::pair<_Ty1,_Ty2>::pair<uint64,uint64>(const std::pair<_Ty1,uint64> &)' being compiled
        with
        [
            _Ty1=size_t,
            _Ty2=uint
        ]
Compiling...
getopt1.c
getopt.c
Linking...
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
scoreProcrastAlignment - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: extractBCITrees, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'extractBCITrees', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
extractBCITrees.cpp
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
extractBCITrees - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: calculateBackboneCoverage2, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'calculateBackboneCoverage2', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
calculateBackboneCoverage2.cpp
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
calculateBackboneCoverage2 - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: checkForLGT, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'checkForLGT', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
checkForLGT.cpp
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
checkForLGT - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: sortContigs, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'sortContigs', configuration 'Release OpenMP|x64'
Compiling...
sortContigs.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
sortContigs - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: toEvoHighwayFormat, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'toEvoHighwayFormat', configuration 'Release OpenMP|x64'
Compiling...
toEvoHighwayFormat.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
toEvoHighwayFormat - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: toGrimmFormat, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'toGrimmFormat', configuration 'Release OpenMP|x64'
Compiling...
toGrimmFormat.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
toGrimmFormat - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: extractSubalignments, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'extractSubalignments', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
extractSubalignments.cpp
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
extractSubalignments - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: uniquifyTrees, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'uniquifyTrees', configuration 'Release OpenMP|x64'
Compiling...
uniquifyTrees.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
uniquifyTrees - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: progressiveMauve, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'progressiveMauve', configuration 'Release OpenMP|x64'
Compiling...
UniqueMatchFinder.cpp
progressiveMauve.cpp
Compiling...
getopt1.c
getopt.c
Linking...
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
progressiveMauve - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: scoreAlignment2, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'scoreAlignment2', configuration 'Release OpenMP|x64'
Compiling...
scoreAlignment2.cpp
c:\build_temp\sgevolver\src\scorealignment2.cpp(385) : warning C4715: 'findFirstCorrectlyAlignedPair<std::_Vector_iterator<aligned_coords_s,std::allocator<aligned_coords_s> > >' : not all control paths return a value
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\sgEvolver\projects\x64\Release OpenMP\BuildLog.htm"
scoreAlignment2 - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: unalign, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'unalign', configuration 'Release OpenMP|x64'
Compiling...
unalign.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
unalign - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: sgEvolver, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'sgEvolver', configuration 'Release OpenMP|x64'
Compiling...
twister.c
getopt1.c
getopt.c
Generating Code...
Compiling...
sgEvolver.cpp
..\src\sgEvolver.cpp(227) : warning C4005: 'NELEMS' : macro redefinition
        C:\build_temp\muscle\libMUSCLE/threadstorage.h(22) : see previous definition of 'NELEMS'
Mutator.cpp
gnStringSource.cpp
gnGapSource.cpp
Alignment.cpp
Generating Code...
Linking...
mems64omp.lib(gnAlignedSequences.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\sgEvolver\projects\x64\Release OpenMP\BuildLog.htm"
sgEvolver - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: uniqueMerCount, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'uniqueMerCount', configuration 'Release OpenMP|x64'
Compiling...
uniqueMerCount.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(DNAFileSML.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
uniqueMerCount - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: transposeCoordinates, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'transposeCoordinates', configuration 'Release OpenMP|x64'
Compiling...
transposeCoordinates.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(Aligner.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
transposeCoordinates - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: scoreALU, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'scoreALU', configuration 'Release OpenMP|x64'
Compiling...
scoreALU.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
genome64omp.lib(gnException.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
scoreALU - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: scoreAlignment, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'scoreAlignment', configuration 'Release OpenMP|x64'
Compiling...
scoreAlignment.cpp
..\src\scoreAlignment.cpp(205) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(207) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(219) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(220) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(291) : warning C4804: '<=' : unsafe use of type 'bool' in operation
..\src\scoreAlignment.cpp(315) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(316) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(385) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(386) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\xtree(618) : warning C4800: 'boolean' : forcing value to bool 'true' or 'false' (performance warning)
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\xtree(611) : while compiling class template member function 'std::pair<_Ty1,_Ty2> std::_Tree<_Traits>::insert(const std::pair<const _Kty,_Ty> &)'
        with
        [
            _Ty1=std::_Tree<std::_Tmap_traits<std::pair<uint64,uint64>,uint,IntervalCompare,std::allocator<std::pair<const std::pair<uint64,uint64>,uint>>,false>>::iterator,
            _Ty2=bool,
            _Traits=std::_Tmap_traits<std::pair<uint64,uint64>,uint,IntervalCompare,std::allocator<std::pair<const std::pair<uint64,uint64>,uint>>,false>,
            _Kty=std::pair<uint64,uint64>,
            _Ty=uint
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\map(82) : see reference to class template instantiation 'std::_Tree<_Traits>' being compiled
        with
        [
            _Traits=std::_Tmap_traits<std::pair<uint64,uint64>,uint,IntervalCompare,std::allocator<std::pair<const std::pair<uint64,uint64>,uint>>,false>
        ]
        ..\src\scoreAlignment.cpp(48) : see reference to class template instantiation 'std::map<_Kty,_Ty,_Pr>' being compiled
        with
        [
            _Kty=std::pair<uint64,uint64>,
            _Ty=uint,
            _Pr=IntervalCompare
        ]
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
scoreAlignment - 0 error(s), 10 warning(s)
------ Rebuild All started: Project: mauveAligner, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'mauveAligner', configuration 'Release OpenMP|x64'
Compiling...
mauveAligner.cpp
..\src\mauveAligner.cpp(47) : warning C4005: 'NELEMS' : macro redefinition
        C:\build_temp\muscle\libMUSCLE/threadstorage.h(22) : see previous definition of 'NELEMS'
Compiling...
getopt1.c
getopt.c
Linking...
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
mauveAligner - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: extractBackbone, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'extractBackbone', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
extractBackbone.cpp
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
extractBackbone - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: calculateBackboneCoverage, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'calculateBackboneCoverage', configuration 'Release OpenMP|x64'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
calculateBackboneCoverage.cpp
..\src\calculateBackboneCoverage.cpp(25) : warning C4005: 'NELEMS' : macro redefinition
        C:\build_temp\muscle\libMUSCLE/threadstorage.h(22) : see previous definition of 'NELEMS'
Linking...
mems64omp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
calculateBackboneCoverage - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: rootTrees, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'rootTrees', configuration 'Release OpenMP|x64'
Compiling...
rootTrees.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
rootTrees - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: xmfa2maf, Configuration: Release OpenMP x64 ------
Deleting intermediate and output files for project 'xmfa2maf', configuration 'Release OpenMP|x64'
Compiling...
xmfa2maf.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
genome64omp.lib(gnException.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\x64\Release OpenMP\BuildLog.htm"
xmfa2maf - 0 error(s), 0 warning(s)
========== Rebuild All: 29 succeeded, 0 failed, 0 skipped ==========


Project file 'C:\build_temp\repeatoire\projects\repeatoire.vcproj' could not be loaded.
The project is either missing from disk or access was denied.
One or more projects in the solution could not be loaded for the following reason(s):

The project file or web has been moved, renamed or is not on your computer.

These projects will be labeled as unavailable in Solution Explorer. Expand the project node to show the reason the project could not be loaded.------ Rebuild All started: Project: libMUSCLE, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'libMUSCLE', configuration 'Release OpenMP|Win32'
Compiling...
aligngivenpath.cpp
writescorefile.cpp
vtml2.cpp
validateids.cpp
usage.cpp
upgma2.cpp
typetostr.cpp
treefrommsa.cpp
tracebacksw.cpp
tracebackopt.cpp
traceback.cpp
tomhydro.cpp
threewaywt.cpp
textfile.cpp
termgaps.cpp
sw.cpp
subfams.cpp
subfam.cpp
stabilize.cpp
sptest.cpp
Compiling...
spfast.cpp
setnewhandler.cpp
setgscweights.cpp
setblosumweights.cpp
seqvect.cpp
seq.cpp
scorepp.cpp
scorehistory.cpp
scoregaps.cpp
scoredist.cpp
savebest.cpp
refinew.cpp
refinevert.cpp
refinetreee.cpp
refinetree.cpp
refinesubfams.cpp
refinehoriz.cpp
refine.cpp
realigndiffse.cpp
realigndiffs.cpp
Compiling...
readmx.cpp
pwpath.cpp
progressivealign.cpp
progress.cpp
progalign.cpp
profilefrommsa.cpp
profile.cpp
profdb.cpp
ppscore.cpp
posgap.cpp
phytofile.cpp
physeq.cpp
phyfromfile.cpp
phyfromclust.cpp
phy4.cpp
phy3.cpp
phy2.cpp
phy.cpp
params.cpp
pam200mafft.cpp
Compiling...
outweights.cpp
options.cpp
onexception.cpp
objscoreda.cpp
objscore2.cpp
objscore.cpp
nwsmall.cpp
nwrec.cpp
nwdasmall.cpp
nwdasimple2.cpp
nwdasimple.cpp
nucmx.cpp
muscleout.cpp
muscle.cpp
msf.cpp
msadistkimura.cpp
msa2.cpp
msa.cpp
mpam200.cpp
mhack.cpp
Compiling...
maketree.cpp
makerootmsab.cpp
makerootmsa.cpp
main.cpp
local.cpp
intmath.cpp
hydro.cpp
html.cpp
henikoffweightpb.cpp
henikoffweight.cpp
gotowt.cpp
gonnet.cpp
globalswin32.cpp
globalsother.cpp
globalslinux.cpp
globals.cpp
glbalndimer.cpp
glbalignss.cpp
glbalignspn.cpp
glbalignsp.cpp
Compiling...
glbalignsimple.cpp
glbalignle.cpp
glbaligndiag.cpp
glbalign352.cpp
glbalign.cpp
finddiagsn.cpp
finddiags.cpp
fastscorepath2.cpp
fastdistnuc.cpp
fastdistmafft.cpp
fastdistkmer.cpp
fastdistkbit.cpp
fastdistjones.cpp
fastdist.cpp
fastclust.cpp
fasta2.cpp
fasta.cpp
estring.cpp
enumtostr.cpp
enumopts.cpp
Compiling...
edgelist.cpp
drawtree.cpp
dpreglist.cpp
dosp.cpp
domuscle.cpp
distpwkimura.cpp
distfunc.cpp
distcalc.cpp
difftreese.cpp
difftrees.cpp
diffpaths.cpp
diffobjscore.cpp
diaglist.cpp
cons.cpp
color.cpp
clwwt.cpp
cluster.cpp
clust.cpp
blosumla.cpp
blosum62.cpp
Compiling...
bittraceback.cpp
anchors.cpp
anchoredpp.cpp
alpha.cpp
aln.cpp
aligntwoprofs.cpp
aligntwomsas.cpp
aligngivenpathsw.cpp
Creating library...
writescorefile.obj : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Build log was saved at "file://c:\build_temp\muscle\projects\Release OpenMP\BuildLog.htm"
libMUSCLE - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: libGenome, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'libGenome', configuration 'Release OpenMP|Win32'
Compiling...
gnABISource.cpp
gnTranslator.cpp
gnStringTools.cpp
gnStringSpec.cpp
gnSourceSpec.cpp
gnSourceQualifier.cpp
gnSourceHeader.cpp
gnSourceFactory.cpp
gnSequence.cpp
gnSEQSource.cpp
gnRAWSource.cpp
gnPosSpecificTranslator.cpp
gnLocation.cpp
gnGenomeSpec.cpp
gnGBKSource.cpp
gnFragmentSpec.cpp
gnFilter.cpp
gnFileSource.cpp
gnFileContig.cpp
gnFeature.cpp
Compiling...
gnFastTranslator.cpp
gnFASSource.cpp
gnException.cpp
gnDefs.cpp
gnContigSpec.cpp
gnCompare.cpp
gnBaseFeature.cpp
Creating library...
gnTranslator.obj : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Build log was saved at "file://c:\build_temp\libGenome\projects\Release OpenMP\BuildLog.htm"
libGenome - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: libMems, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'libMems', configuration 'Release OpenMP|Win32'
Compiling...
algebras.cc
SuperInterval.cpp
ProgressiveAligner.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(739) : warning C4267: '=' : conversion from 'size_t' to 'unsigned int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(757) : see reference to function template instantiation '_OutIt std::_Transform<_InIt1,unsigned int*,unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),std::forward_iterator_tag,std::forward_iterator_tag>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,_InItCats,_InOutItCat,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=unsigned int *,
            _InIt1=unsigned int *,
            _InIt2=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),
            _InItCats=std::forward_iterator_tag,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(872) : see reference to function template instantiation '_OutIt std::_Transform<unsigned int*,_InIt2,_OutIt,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,std::random_access_iterator_tag,std::random_access_iterator_tag,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _InIt1=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(419) : see reference to function template instantiation '__w64 unsigned int *std::transform<__w64 unsigned int*,__w64 unsigned int*,__w64 unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2)' being compiled
        with
        [
            _InIt1=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _OutIt=__w64 unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(402) : while compiling class template member function 'boost::multi_array<T,NumDims> &boost::multi_array<T,NumDims>::resize(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=double,
            NumDims=2,
            NumRanges=2
        ]
        c:\build_temp\libMems\libMems/GreedyBreakpointElimination.h(540) : see reference to class template instantiation 'boost::multi_array<T,NumDims>' being compiled
        with
        [
            T=double,
            NumDims=2
        ]
PairwiseMatchFinder.cpp
GreedyBreakpointElimination.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4267: 'initializing' : conversion from 'size_t' to 'uint', possible loss of data
        ..\libMems\GreedyBreakpointElimination.cpp(191) : see reference to function template instantiation 'std::pair<_Ty1,_Ty2>::pair<size_t,int>(const std::pair<_Ty1,int> &)' being compiled
        with
        [
            _Ty1=uint,
            _Ty2=uint
        ]
        ..\libMems\GreedyBreakpointElimination.cpp(666) : see reference to function template instantiation 'uint mems::RemoveLCBandCoalesce<std::vector<_Ty>>(size_t,uint,LcbVector &,std::vector<double> &,std::vector<std::pair<_Ty1,_Ty2>> &,std::vector<node_id_t> &)' being compiled
        with
        [
            _Ty=mems::TrackingLCB<mems::TrackingMatch *>,
            LcbVector=std::vector<mems::TrackingLCB<mems::TrackingMatch *>>,
            _Ty1=uint,
            _Ty2=uint
        ]
Backbone.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4244: 'initializing' : conversion from 'const uint64' to 'uint', possible loss of data
        ..\libMems\Backbone.cpp(457) : see reference to function template instantiation 'std::pair<_Ty1,_Ty2>::pair<uint64,uint64>(const std::pair<uint64,uint64> &)' being compiled
        with
        [
            _Ty1=uint,
            _Ty2=uint
        ]
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4244: 'initializing' : conversion from 'const uint64' to 'uint', possible loss of data
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(739) : warning C4267: '=' : conversion from 'size_t' to 'unsigned int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(757) : see reference to function template instantiation '_OutIt std::_Transform<_InIt1,unsigned int*,unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),std::forward_iterator_tag,std::forward_iterator_tag>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,_InItCats,_InOutItCat,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=unsigned int *,
            _InIt1=unsigned int *,
            _InIt2=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),
            _InItCats=std::forward_iterator_tag,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(872) : see reference to function template instantiation '_OutIt std::_Transform<unsigned int*,_InIt2,_OutIt,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,std::random_access_iterator_tag,std::random_access_iterator_tag,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _InIt1=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(419) : see reference to function template instantiation '__w64 unsigned int *std::transform<__w64 unsigned int*,__w64 unsigned int*,__w64 unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2)' being compiled
        with
        [
            _InIt1=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _OutIt=__w64 unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(402) : while compiling class template member function 'boost::multi_array<T,NumDims> &boost::multi_array<T,NumDims>::resize(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=std::vector<std::pair<uint,uint>>,
            NumDims=3,
            NumRanges=3
        ]
        ..\libMems\Backbone.cpp(276) : see reference to class template instantiation 'boost::multi_array<T,NumDims>' being compiled
        with
        [
            T=std::vector<std::pair<uint,uint>>,
            NumDims=3
        ]
MuscleInterface.cpp
..\libMems\MuscleInterface.cpp(730) : warning C4244: '=' : conversion from 'int' to 'muscle::SCORE', possible loss of data
..\libMems\MuscleInterface.cpp(732) : warning C4244: '=' : conversion from 'int' to 'muscle::SCORE', possible loss of data
Islands.cpp
Aligner.cpp
RepeatHash.cpp
MemHash.cpp
MatchFinder.cpp
MaskedMemHash.cpp
RepeatMatchList.cpp
RepeatMatch.cpp
MatchHashEntry.cpp
gnAlignedSequences.cpp
GappedAlignment.cpp
SortedMerList.cpp
MemorySML.cpp
Compiling...
FileSML.cpp
DNAMemorySML.cpp
DNAFileSML.cpp
homologymain.cc
homology.cc
Compiling...
twister.c
util.c
timing.c
sorting.c
sml.c
dmsort.c
buffer.c
awin32aio.c
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 1 of type 'HANDLE'
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 2 of type 'char *'
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 4 of type 'OVERLAPPED *'
..\libMems\dmSML\awin32aio.c(132) : warning C4313: 'printf' : '%d' in format string conflicts with argument 5 of type 'void (__stdcall *)(DWORD,DWORD,LPOVERLAPPED)'
asyncio.c
aPOSIXaio.c
alinuxaio.c
alibc.c
Creating library...
SuperInterval.obj : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Build log was saved at "file://c:\build_temp\libMems\projects\Release OpenMP\BuildLog.htm"
libMems - 0 error(s), 11 warning(s)
------ Rebuild All started: Project: muscle, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'muscle', configuration 'Release OpenMP|Win32'
Compiling...
writescorefile.cpp
vtml2.cpp
validateids.cpp
usage.cpp
upgma2.cpp
typetostr.cpp
treefrommsa.cpp
tracebacksw.cpp
tracebackopt.cpp
traceback.cpp
tomhydro.cpp
threewaywt.cpp
textfile.cpp
termgaps.cpp
sw.cpp
subfams.cpp
subfam.cpp
stabilize.cpp
sptest.cpp
spfast.cpp
Compiling...
setnewhandler.cpp
setgscweights.cpp
setblosumweights.cpp
seqvect.cpp
seq.cpp
scorepp.cpp
scorehistory.cpp
scoregaps.cpp
scoredist.cpp
savebest.cpp
refinew.cpp
refinevert.cpp
refinetreee.cpp
refinetree.cpp
refinesubfams.cpp
refinehoriz.cpp
refine.cpp
realigndiffse.cpp
realigndiffs.cpp
readmx.cpp
Compiling...
pwpath.cpp
progressivealign.cpp
progress.cpp
progalign.cpp
profilefrommsa.cpp
profile.cpp
profdb.cpp
ppscore.cpp
posgap.cpp
phytofile.cpp
physeq.cpp
phyfromfile.cpp
phyfromclust.cpp
phy4.cpp
phy3.cpp
phy2.cpp
phy.cpp
params.cpp
pam200mafft.cpp
outweights.cpp
Compiling...
options.cpp
onexception.cpp
objscoreda.cpp
objscore2.cpp
objscore.cpp
nwsmall.cpp
nwrec.cpp
nwdasmall.cpp
nwdasimple2.cpp
nwdasimple.cpp
nucmx.cpp
muscleout.cpp
muscle.cpp
msf.cpp
msadistkimura.cpp
msa2.cpp
msa.cpp
mpam200.cpp
mhack.cpp
maketree.cpp
Compiling...
makerootmsab.cpp
makerootmsa.cpp
main.cpp
local.cpp
intmath.cpp
hydro.cpp
html.cpp
henikoffweightpb.cpp
henikoffweight.cpp
gotowt.cpp
gonnet.cpp
globalswin32.cpp
globalsother.cpp
globalslinux.cpp
globals.cpp
glbalndimer.cpp
glbalignss.cpp
glbalignspn.cpp
glbalignsp.cpp
glbalignsimple.cpp
Compiling...
glbalignle.cpp
glbaligndiag.cpp
glbalign352.cpp
glbalign.cpp
finddiagsn.cpp
finddiags.cpp
fastscorepath2.cpp
fastdistnuc.cpp
fastdistmafft.cpp
fastdistkmer.cpp
fastdistkbit.cpp
fastdistjones.cpp
fastdist.cpp
fastclust.cpp
fasta2.cpp
fasta.cpp
estring.cpp
enumtostr.cpp
enumopts.cpp
edgelist.cpp
Compiling...
drawtree.cpp
dpreglist.cpp
dosp.cpp
domuscle.cpp
distpwkimura.cpp
distfunc.cpp
distcalc.cpp
difftreese.cpp
difftrees.cpp
diffpaths.cpp
diffobjscore.cpp
diaglist.cpp
cons.cpp
color.cpp
clwwt.cpp
cluster.cpp
clust.cpp
blosumla.cpp
blosum62.cpp
bittraceback.cpp
Compiling...
anchors.cpp
anchoredpp.cpp
alpha.cpp
aln.cpp
aligntwoprofs.cpp
aligntwomsas.cpp
aligngivenpathsw.cpp
aligngivenpath.cpp
Compiling manifest to resources...
Linking...
LINK : warning LNK4075: ignoring '/INCREMENTAL' due to '/LTCG' specification
Generating code
Finished generating code
Embedding manifest...
LINK : warning LNK4075: ignoring '/INCREMENTAL' due to '/LTCG' specification
Generating code
Finished generating code
Build log was saved at "file://c:\build_temp\muscle\projects\Release OpenMP\BuildLog.htm"
muscle - 0 error(s), 2 warning(s)
------ Rebuild All started: Project: stripSubsetLCBs, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'stripSubsetLCBs', configuration 'Release OpenMP|Win32'
Compiling...
stripSubsetLCBs.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
stripSubsetLCBs - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: getOrthologList, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'getOrthologList', configuration 'Release OpenMP|Win32'
Compiling...
getOrthologList.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(739) : warning C4267: '=' : conversion from 'size_t' to 'unsigned int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(757) : see reference to function template instantiation '_OutIt std::_Transform<_InIt1,unsigned int*,unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),std::forward_iterator_tag,std::forward_iterator_tag>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,_InItCats,_InOutItCat,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=unsigned int *,
            _InIt1=unsigned int *,
            _InIt2=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),
            _InItCats=std::forward_iterator_tag,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(872) : see reference to function template instantiation '_OutIt std::_Transform<unsigned int*,_InIt2,_OutIt,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,std::random_access_iterator_tag,std::random_access_iterator_tag,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _InIt1=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(419) : see reference to function template instantiation '__w64 unsigned int *std::transform<__w64 unsigned int*,__w64 unsigned int*,__w64 unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2)' being compiled
        with
        [
            _InIt1=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _OutIt=__w64 unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(402) : while compiling class template member function 'boost::multi_array<T,NumDims> &boost::multi_array<T,NumDims>::resize(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            NumRanges=3
        ]
        C:\build_temp\libMems\libMems/Backbone.h(105) : see reference to class template instantiation 'boost::multi_array<T,NumDims>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3
        ]
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(670) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(683) : see reference to function template instantiation '_OutIt std::_Transform<_InIt,int*,_Fn1,std::forward_iterator_tag>(_InIt,_InIt,_OutIt,_Fn1,_InOutItCat,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=int *,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> ,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(712) : see reference to function template instantiation '_OutIt std::_Transform<const boost::detail::multi_array::extent_range<Extent,SizeType>*,_OutIt,_Fn1>(_InIt,_InIt,_OutIt,_Fn1,std::random_access_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 int *,
            Extent=boost::detail::multi_array::extent_gen<NumRanges>::index,
            SizeType=boost::detail::multi_array::extent_gen<NumRanges>::size_type,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> 
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(380) : see reference to function template instantiation '__w64 int *std::transform<const boost::detail::multi_array::extent_range<Extent,SizeType>*,__w64 int*,boost::const_mem_fun_ref_t<S,T>>(_InIt,_InIt,_OutIt,_Fn1)' being compiled
        with
        [
            Extent=boost::detail::multi_array::extent_gen<NumRanges>::index,
            SizeType=boost::detail::multi_array::extent_gen<NumRanges>::size_type,
            S=__w64 unsigned int,
            T=boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> ,
            _OutIt=__w64 int *,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(367) : while compiling class template member function 'void boost::const_multi_array_ref<T,NumDims,TPtr>::init_from_extent_gen(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            TPtr=mems::hss_list_t *,
            NumRanges=3
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(417) : see reference to class template instantiation 'boost::const_multi_array_ref<T,NumDims,TPtr>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            TPtr=mems::hss_list_t *
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(113) : see reference to class template instantiation 'boost::multi_array_ref<T,NumDims>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3
        ]
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
getOrthologList - 0 error(s), 2 warning(s)
------ Rebuild All started: Project: bbAnalyze, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'bbAnalyze', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
bbAnalyze.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4244: 'initializing' : conversion from 'const uint64' to 'uint', possible loss of data
        ..\src\bbAnalyze.cpp(556) : see reference to function template instantiation 'std::pair<_Ty1,_Ty2>::pair<uint64,uint64>(const std::pair<uint64,uint64> &)' being compiled
        with
        [
            _Ty1=uint,
            _Ty2=uint
        ]
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\utility(44) : warning C4244: 'initializing' : conversion from 'const uint64' to 'uint', possible loss of data
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(739) : warning C4267: '=' : conversion from 'size_t' to 'unsigned int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(757) : see reference to function template instantiation '_OutIt std::_Transform<_InIt1,unsigned int*,unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),std::forward_iterator_tag,std::forward_iterator_tag>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,_InItCats,_InOutItCat,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=unsigned int *,
            _InIt1=unsigned int *,
            _InIt2=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),
            _InItCats=std::forward_iterator_tag,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(872) : see reference to function template instantiation '_OutIt std::_Transform<unsigned int*,_InIt2,_OutIt,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,std::random_access_iterator_tag,std::random_access_iterator_tag,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _InIt1=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(419) : see reference to function template instantiation '__w64 unsigned int *std::transform<__w64 unsigned int*,__w64 unsigned int*,__w64 unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2)' being compiled
        with
        [
            _InIt1=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _OutIt=__w64 unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(402) : while compiling class template member function 'boost::multi_array<T,NumDims> &boost::multi_array<T,NumDims>::resize(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            NumRanges=3
        ]
        C:\build_temp\libMems\libMems/Backbone.h(105) : see reference to class template instantiation 'boost::multi_array<T,NumDims>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3
        ]
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(670) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(683) : see reference to function template instantiation '_OutIt std::_Transform<_InIt,int*,_Fn1,std::forward_iterator_tag>(_InIt,_InIt,_OutIt,_Fn1,_InOutItCat,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=int *,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> ,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(712) : see reference to function template instantiation '_OutIt std::_Transform<const boost::detail::multi_array::extent_range<Extent,SizeType>*,_OutIt,_Fn1>(_InIt,_InIt,_OutIt,_Fn1,std::random_access_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 int *,
            Extent=boost::detail::multi_array::extent_gen<NumRanges>::index,
            SizeType=boost::detail::multi_array::extent_gen<NumRanges>::size_type,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> 
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(380) : see reference to function template instantiation '__w64 int *std::transform<const boost::detail::multi_array::extent_range<Extent,SizeType>*,__w64 int*,boost::const_mem_fun_ref_t<S,T>>(_InIt,_InIt,_OutIt,_Fn1)' being compiled
        with
        [
            Extent=boost::detail::multi_array::extent_gen<NumRanges>::index,
            SizeType=boost::detail::multi_array::extent_gen<NumRanges>::size_type,
            S=__w64 unsigned int,
            T=boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> ,
            _OutIt=__w64 int *,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(367) : while compiling class template member function 'void boost::const_multi_array_ref<T,NumDims,TPtr>::init_from_extent_gen(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            TPtr=mems::hss_list_t *,
            NumRanges=3
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(417) : see reference to class template instantiation 'boost::const_multi_array_ref<T,NumDims,TPtr>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            TPtr=mems::hss_list_t *
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(113) : see reference to class template instantiation 'boost::multi_array_ref<T,NumDims>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3
        ]
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
bbAnalyze - 0 error(s), 4 warning(s)
------ Rebuild All started: Project: scoreProcrastAlignment, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'scoreProcrastAlignment', configuration 'Release OpenMP|Win32'
Compiling...
scoreProcrastAlignment.cpp
Compiling...
getopt1.c
getopt.c
Linking...
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
scoreProcrastAlignment - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: extractBCITrees, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'extractBCITrees', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
extractBCITrees.cpp
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
extractBCITrees - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: calculateBackboneCoverage2, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'calculateBackboneCoverage2', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
calculateBackboneCoverage2.cpp
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
calculateBackboneCoverage2 - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: checkForLGT, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'checkForLGT', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
checkForLGT.cpp
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
checkForLGT - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: sortContigs, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'sortContigs', configuration 'Release OpenMP|Win32'
Compiling...
sortContigs.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
sortContigs - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: toEvoHighwayFormat, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'toEvoHighwayFormat', configuration 'Release OpenMP|Win32'
Compiling...
toEvoHighwayFormat.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
toEvoHighwayFormat - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: toGrimmFormat, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'toGrimmFormat', configuration 'Release OpenMP|Win32'
Compiling...
toGrimmFormat.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
toGrimmFormat - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: extractSubalignments, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'extractSubalignments', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
extractSubalignments.cpp
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
extractSubalignments - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: uniquifyTrees, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'uniquifyTrees', configuration 'Release OpenMP|Win32'
Compiling...
uniquifyTrees.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
uniquifyTrees - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: progressiveMauve, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'progressiveMauve', configuration 'Release OpenMP|Win32'
Compiling...
UniqueMatchFinder.cpp
progressiveMauve.cpp
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(739) : warning C4267: '=' : conversion from 'size_t' to 'unsigned int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(757) : see reference to function template instantiation '_OutIt std::_Transform<_InIt1,unsigned int*,unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),std::forward_iterator_tag,std::forward_iterator_tag>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,_InItCats,_InOutItCat,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=unsigned int *,
            _InIt1=unsigned int *,
            _InIt2=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &),
            _InItCats=std::forward_iterator_tag,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(872) : see reference to function template instantiation '_OutIt std::_Transform<unsigned int*,_InIt2,_OutIt,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2,std::random_access_iterator_tag,std::random_access_iterator_tag,std::_Range_checked_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _InIt1=unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(419) : see reference to function template instantiation '__w64 unsigned int *std::transform<__w64 unsigned int*,__w64 unsigned int*,__w64 unsigned int*,__w64 const unsigned int&(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)>(_InIt1,_InIt1,_InIt2,_OutIt,_Fn2)' being compiled
        with
        [
            _InIt1=__w64 unsigned int *,
            _InIt2=__w64 unsigned int *,
            _OutIt=__w64 unsigned int *,
            _Fn2=__w64 const unsigned int &(__cdecl *)(__w64 const unsigned int &,__w64 const unsigned int &)
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(402) : while compiling class template member function 'boost::multi_array<T,NumDims> &boost::multi_array<T,NumDims>::resize(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            NumRanges=3
        ]
        C:\build_temp\libMems\libMems/Backbone.h(105) : see reference to class template instantiation 'boost::multi_array<T,NumDims>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3
        ]
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(670) : warning C4267: '=' : conversion from 'size_t' to 'int', possible loss of data
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(683) : see reference to function template instantiation '_OutIt std::_Transform<_InIt,int*,_Fn1,std::forward_iterator_tag>(_InIt,_InIt,_OutIt,_Fn1,_InOutItCat,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=int *,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> ,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>,
            _InOutItCat=std::forward_iterator_tag
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\algorithm(712) : see reference to function template instantiation '_OutIt std::_Transform<const boost::detail::multi_array::extent_range<Extent,SizeType>*,_OutIt,_Fn1>(_InIt,_InIt,_OutIt,_Fn1,std::random_access_iterator_tag,std::_Range_checked_iterator_tag)' being compiled
        with
        [
            _OutIt=__w64 int *,
            Extent=boost::detail::multi_array::extent_gen<NumRanges>::index,
            SizeType=boost::detail::multi_array::extent_gen<NumRanges>::size_type,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> 
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(380) : see reference to function template instantiation '__w64 int *std::transform<const boost::detail::multi_array::extent_range<Extent,SizeType>*,__w64 int*,boost::const_mem_fun_ref_t<S,T>>(_InIt,_InIt,_OutIt,_Fn1)' being compiled
        with
        [
            Extent=boost::detail::multi_array::extent_gen<NumRanges>::index,
            SizeType=boost::detail::multi_array::extent_gen<NumRanges>::size_type,
            S=__w64 unsigned int,
            T=boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>,
            _InIt=const boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type> ,
            _OutIt=__w64 int *,
            _Fn1=boost::const_mem_fun_ref_t<__w64 unsigned int,boost::detail::multi_array::extent_range<boost::detail::multi_array::extent_gen<NumRanges>::index,boost::detail::multi_array::extent_gen<NumRanges>::size_type>>
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(367) : while compiling class template member function 'void boost::const_multi_array_ref<T,NumDims,TPtr>::init_from_extent_gen(const boost::detail::multi_array::extent_gen<NumRanges> &)'
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            TPtr=mems::hss_list_t *,
            NumRanges=3
        ]
        C:\boost\include\boost-1_37\boost/multi_array/multi_array_ref.hpp(417) : see reference to class template instantiation 'boost::const_multi_array_ref<T,NumDims,TPtr>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3,
            TPtr=mems::hss_list_t *
        ]
        C:\boost\include\boost-1_37\boost/multi_array.hpp(113) : see reference to class template instantiation 'boost::multi_array_ref<T,NumDims>' being compiled
        with
        [
            T=mems::hss_list_t,
            NumDims=3
        ]
Compiling...
getopt1.c
getopt.c
Linking...
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
progressiveMauve - 0 error(s), 2 warning(s)
------ Rebuild All started: Project: scoreAlignment2, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'scoreAlignment2', configuration 'Release OpenMP|Win32'
Compiling...
scoreAlignment2.cpp
c:\build_temp\sgevolver\src\scorealignment2.cpp(385) : warning C4715: 'findFirstCorrectlyAlignedPair<std::_Vector_iterator<aligned_coords_s,std::allocator<aligned_coords_s> > >' : not all control paths return a value
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\sgEvolver\projects\Release OpenMP\BuildLog.htm"
scoreAlignment2 - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: unalign, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'unalign', configuration 'Release OpenMP|Win32'
Compiling...
unalign.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
unalign - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: sgEvolver, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'sgEvolver', configuration 'Release OpenMP|Win32'
Compiling...
twister.c
getopt1.c
getopt.c
Generating Code...
Compiling...
sgEvolver.cpp
..\src\sgEvolver.cpp(227) : warning C4005: 'NELEMS' : macro redefinition
        C:\build_temp\muscle\libMUSCLE/threadstorage.h(22) : see previous definition of 'NELEMS'
Mutator.cpp
gnStringSource.cpp
gnGapSource.cpp
Alignment.cpp
Generating Code...
Linking...
memsomp.lib(gnAlignedSequences.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\sgEvolver\projects\Release OpenMP\BuildLog.htm"
sgEvolver - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: uniqueMerCount, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'uniqueMerCount', configuration 'Release OpenMP|Win32'
Compiling...
uniqueMerCount.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(DNAFileSML.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
uniqueMerCount - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: transposeCoordinates, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'transposeCoordinates', configuration 'Release OpenMP|Win32'
Compiling...
transposeCoordinates.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(Aligner.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
transposeCoordinates - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: scoreALU, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'scoreALU', configuration 'Release OpenMP|Win32'
Compiling...
scoreALU.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
genomeomp.lib(gnException.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
scoreALU - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: scoreAlignment, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'scoreAlignment', configuration 'Release OpenMP|Win32'
Compiling...
scoreAlignment.cpp
..\src\scoreAlignment.cpp(205) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(207) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(219) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(220) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(291) : warning C4804: '<=' : unsafe use of type 'bool' in operation
..\src\scoreAlignment.cpp(315) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(316) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(385) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
..\src\scoreAlignment.cpp(386) : warning C4146: unary minus operator applied to unsigned type, result still unsigned
C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\xtree(618) : warning C4800: 'boolean' : forcing value to bool 'true' or 'false' (performance warning)
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\xtree(611) : while compiling class template member function 'std::pair<_Ty1,_Ty2> std::_Tree<_Traits>::insert(const std::pair<const _Kty,_Ty> &)'
        with
        [
            _Ty1=std::_Tree<std::_Tmap_traits<std::pair<uint64,uint64>,uint,IntervalCompare,std::allocator<std::pair<const std::pair<uint64,uint64>,uint>>,false>>::iterator,
            _Ty2=bool,
            _Traits=std::_Tmap_traits<std::pair<uint64,uint64>,uint,IntervalCompare,std::allocator<std::pair<const std::pair<uint64,uint64>,uint>>,false>,
            _Kty=std::pair<uint64,uint64>,
            _Ty=uint
        ]
        C:\Program Files (x86)\Microsoft Visual Studio 8\VC\INCLUDE\map(82) : see reference to class template instantiation 'std::_Tree<_Traits>' being compiled
        with
        [
            _Traits=std::_Tmap_traits<std::pair<uint64,uint64>,uint,IntervalCompare,std::allocator<std::pair<const std::pair<uint64,uint64>,uint>>,false>
        ]
        ..\src\scoreAlignment.cpp(48) : see reference to class template instantiation 'std::map<_Kty,_Ty,_Pr>' being compiled
        with
        [
            _Kty=std::pair<uint64,uint64>,
            _Ty=uint,
            _Pr=IntervalCompare
        ]
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
scoreAlignment - 0 error(s), 10 warning(s)
------ Rebuild All started: Project: mauveAligner, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'mauveAligner', configuration 'Release OpenMP|Win32'
Compiling...
mauveAligner.cpp
..\src\mauveAligner.cpp(47) : warning C4005: 'NELEMS' : macro redefinition
        C:\build_temp\muscle\libMUSCLE/threadstorage.h(22) : see previous definition of 'NELEMS'
Compiling...
getopt1.c
getopt.c
Linking...
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
mauveAligner - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: extractBackbone, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'extractBackbone', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
extractBackbone.cpp
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
extractBackbone - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: calculateBackboneCoverage, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'calculateBackboneCoverage', configuration 'Release OpenMP|Win32'
Compiling...
getopt1.c
getopt.c
Generating Code...
Compiling...
calculateBackboneCoverage.cpp
..\src\calculateBackboneCoverage.cpp(25) : warning C4005: 'NELEMS' : macro redefinition
        C:\build_temp\muscle\libMUSCLE/threadstorage.h(22) : see previous definition of 'NELEMS'
Linking...
memsomp.lib(GappedAlignment.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
calculateBackboneCoverage - 0 error(s), 1 warning(s)
------ Rebuild All started: Project: rootTrees, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'rootTrees', configuration 'Release OpenMP|Win32'
Compiling...
rootTrees.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
rootTrees - 0 error(s), 0 warning(s)
------ Rebuild All started: Project: xmfa2maf, Configuration: Release OpenMP Win32 ------
Deleting intermediate and output files for project 'xmfa2maf', configuration 'Release OpenMP|Win32'
Compiling...
xmfa2maf.cpp
Compiling...
getopt1.c
getopt.c
Generating Code...
Linking...
genomeomp.lib(gnException.obj) : MSIL .netmodule or module compiled with /GL found; restarting link with /LTCG; add /LTCG to the link command line to improve linker performance
Generating code
Finished generating code
Embedding manifest...
Build log was saved at "file://c:\build_temp\mauveAligner\projects\Release OpenMP\BuildLog.htm"
xmfa2maf - 0 error(s), 0 warning(s)
========== Rebuild All: 29 succeeded, 0 failed, 0 skipped ==========