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dunn/# fastml - 2015-11-28_20-39-46.txt

Created November 29, 2015 04:42
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fastml (homebrew/science/fastml) on OS X 10.11.1 - Homebrew build logs
Raw
# fastml - 2015-11-28_20-39-46.txt
Homebrew build logs for homebrew/science/fastml on OS X 10.11.1
Build date: 2015-11-28 20:39:46
Raw
00.config.out
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew.git
HEAD: 5e11e3bc588dd8153fb7e1fe4f832754e3bb61df
Last commit: 10 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit haswell
OS X: 10.11.1-x86_64
Xcode: 7.1.1
CLT: 7.1.0.0.1.1444952191
Clang: 7.0 build 700
X11: 2.7.8 => /opt/X11
System Ruby: 2.0.0-p645
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/local/bin/ruby => /usr/local/Cellar/ruby/2.2.3/bin/ruby
Java: 1.8.0_66, 1.8.0_20
Raw
00.doctor.out
Your system is ready to brew.
Raw
00.tap.out
Formula: fastml
Tap: homebrew/homebrew-science
Path: /usr/local/Library/Taps/homebrew/homebrew-science/fastml.rb
Raw
01.make
2015-11-28 20:39:46 -0800
make
install
cd libs;make all
cd phylogeny && make all
making depend
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o AddLog.o AddLog.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiProp.o NNiProp.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiSep.o NNiSep.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Nni.o Nni.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o aaJC.o aaJC.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTrees.o allTrees.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o alphabet.o alphabet.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o amino.o amino.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlpha.o bestAlpha.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestHKYparam.o bestHKYparam.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bootstrap.o bootstrap.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM.o bblEM.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMfixRoot.o bblEMfixRoot.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProprtional.o bblEMProprtional.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMSeperate.o bblEMSeperate.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o clustalFormat.o clustalFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codon.o codon.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonJC.o codonJC.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeCounts.o computeCounts.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeDownAlg.o computeDownAlg.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeMarginalAlg.o computeMarginalAlg.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePijComponent.o computePijComponent.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlg.o computeUpAlg.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ConversionUtils.o ConversionUtils.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o countTableComponent.o countTableComponent.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o datMatrixHolder.o datMatrixHolder.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceTable.o distanceTable.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distribution.o distribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o errorMsg.o errorMsg.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastStartTree.o fastStartTree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastaFormat.o fastaFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o findRateOfGene.o findRateOfGene.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromQtoPt.o fromQtoPt.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistribution.o gammaDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaUtilities.o gammaUtilities.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistribution.o generalGammaDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o getRandomWeights.o getRandomWeights.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o goldmanYangModel.o goldmanYangModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o hky.o hky.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateWithDependence.o simulateWithDependence.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o KH_calculation.o KH_calculation.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist.o likeDist.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistfixRoot.o likeDistfixRoot.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistProp.o likeDistProp.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistPropEB.o likeDistPropEB.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation.o likelihoodComputation.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logFile.o logFile.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o maseFormat.o maseFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o molphyFormat.o molphyFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nexusFormat.o nexusFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nj.o nj.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o njConstrain.o njConstrain.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucJC.o nucJC.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucleotide.o nucleotide.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o numRec.o numRec.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Parameters.o Parameters.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipFormat.o phylipFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pijAccelerator.o pijAccelerator.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o readDatMatrix.o readDatMatrix.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o readTree.o readTree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o recognizeFormat.o recognizeFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModel.o replacementModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o searchStatus.o searchStatus.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequence.o sequence.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequenceContainer.o sequenceContainer.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateTree.o simulateTree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o siteSpecificRate.o siteSpecificRate.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o someUtil.o someUtil.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o split.o split.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitMap.o splitMap.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitTreeUtil.o splitTreeUtil.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcess.o stochasticProcess.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatComponent.o suffStatComponent.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o talRandom.o talRandom.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tree.o tree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeIt.o treeIt.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeUtil.o treeUtil.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniDistribution.o uniDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniformDistribution.o uniformDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GLaguer.o GLaguer.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o posteriorDistance.o posteriorDistance.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o doubleRep.o doubleRep.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logRep.o logRep.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indel.o indel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indelModel.o indelModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mulAlphabet.o mulAlphabet.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModelSSRV.o replacementModelSSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o matrixUtils.o matrixUtils.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaUtilities.o betaUtilities.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistribution.o betaDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o geneticCodeHolder.o geneticCodeHolder.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o samplingSequences.o samplingSequences.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2USSRV.o bblEM2USSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestParamUSSRV.o bestParamUSSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2USSRV.o likeDist2USSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ussrvModel.o ussrvModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o normalDist.o normalDist.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tamura92.o tamura92.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestTamura92param.o bestTamura92param.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o extremeValDistribution.o extremeValDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusCategory.o distributionPlusCategory.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumps.o simulateJumps.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeJumps.o computeJumps.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqeuncesFilter.o seqeuncesFilter.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mixtureDistribution.o mixtureDistribution.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gainLossAlphabet.o gainLossAlphabet.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o wYangModel.o wYangModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonUtils.o codonUtils.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2Codon.o likeDist2Codon.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o unObservableData.o unObservableData.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateModel.o threeStateModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateAlphabet.o threeStateAlphabet.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2codon.o bblEM2codon.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndK.o bestAlphaAndK.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gtrModel.o gtrModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestGtrModelParams.o bestGtrModelParams.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o integerAlphabet.o integerAlphabet.cpp
ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o
ar: creating archive libEvolTree.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(aaJC.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(codonJC.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(nucJC.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(suffStatComponent.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(treeIt.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(cmdline2EvolObjs.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(doubleRep.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(logRep.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(generalGammaDistributionPlusInvariant.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(gammaDistributionPlusInvariant.o) has no symbols
a - AddLog.o
a - NNiProp.o
a - NNiSep.o
a - Nni.o
a - aaJC.o
a - allTrees.o
a - allTreesSeparateModel.o
a - alphabet.o
a - amino.o
a - bestAlpha.o
a - bestAlphaManyTrees.o
a - bestHKYparam.o
a - bootstrap.o
a - bblEM.o
a - bblEMfixRoot.o
a - bblEMProprtional.o
a - bblEMProportionalEB.o
a - bblLSProportionalEB.o
a - bblEMSeperate.o
a - chebyshevAccelerator.o
a - clustalFormat.o
a - codon.o
a - codonJC.o
a - computeCounts.o
a - computeDownAlg.o
a - computeMarginalAlg.o
a - computePijComponent.o
a - computeUpAlg.o
a - computeUpAlgFactors.o
a - computeSubstitutionCounts.o
a - computePosteriorExpectationOfSubstitutions.o
a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o
a - ConversionUtils.o
a - countTableComponent.o
a - datMatrixHolder.o
a - distanceTable.o
a - distribution.o
a - errorMsg.o
a - evaluateCharacterFreq.o
a - fastStartTree.o
a - fastaFormat.o
a - findRateOfGene.o
a - fromCountTableComponentToDistance.o
a - fromCountTableComponentToDistancefixRoot.o
a - fromCountTableComponentToDistanceProp.o
a - fromCountTableComponentToDistancePropEB.o
a - fromQtoPt.o
a - generalGammaDistributionFixedCategories.o
a - gammaDistribution.o
a - gammaUtilities.o
a - generalGammaDistribution.o
a - getRandomWeights.o
a - goldmanYangModel.o
a - granthamChemicalDistances.o
a - hky.o
a - simulateWithDependence.o
a - KH_calculation.o
a - likeDist.o
a - likeDistfixRoot.o
a - likeDistProp.o
a - likeDistPropEB.o
a - likelihoodComputation.o
a - likelihoodComputationFactors.o
a - logFile.o
a - maseFormat.o
a - molphyFormat.o
a - nexusFormat.o
a - nj.o
a - njConstrain.o
a - nucJC.o
a - nucleotide.o
a - numRec.o
a - Parameters.o
a - phylipFormat.o
a - pijAccelerator.o
a - readDatMatrix.o
a - readTree.o
a - recognizeFormat.o
a - replacementModel.o
a - searchStatus.o
a - seqContainerTreeMap.o
a - sequence.o
a - sequenceContainer.o
a - simulateTree.o
a - siteSpecificRate.o
a - someUtil.o
a - split.o
a - splitMap.o
a - splitTreeUtil.o
a - stochasticProcess.o
a - suffStatComponent.o
a - talRandom.o
a - tree.o
a - treeIt.o
a - treeUtil.o
a - uniDistribution.o
a - uniformDistribution.o
a - cmdline2EvolObjs.o
a - generalGammaDistributionLaguerre.o
a - gammaDistributionLaguerre.o
a - GLaguer.o
a - givenRatesMLDistance.o
a - distanceBasedSeqs2Tree.o
a - posteriorDistance.o
a - pairwiseGammaDistance.o
a - doubleRep.o
a - logRep.o
a - indel.o
a - indelModel.o
a - mulAlphabet.o
a - replacementModelSSRV.o
a - stochasticProcessSSRV.o
a - bestAlphaAndNu.o
a - C_evalParamUSSRV.o
a - matrixUtils.o
a - betaOmegaDistribution.o
a - betaUtilities.o
a - betaDistribution.o
a - geneticCodeHolder.o
a - samplingSequences.o
a - bblEM2USSRV.o
a - bestParamUSSRV.o
a - likeDist2USSRV.o
a - ussrvModel.o
a - likelihoodComputation2USSRV.o
a - fromCountTableComponentToDistance2USSRV.o
a - normalDist.o
a - tamura92.o
a - bestTamura92param.o
a - phylipSequentialFormat.o
a - simulateCodonsJumps.o
a - simulateJumpsAbstract.o
a - ssrvDistanceSeqs2Tree.o
a - multipleStochasticProcess.o
a - distributionPlusInvariant.o
a - extremeValDistribution.o
a - gammaDistributionFixedCategories.o
a - generalGammaDistributionPlusInvariant.o
a - gammaDistributionPlusInvariant.o
a - distributionPlusCategory.o
a - simulateJumps.o
a - computeJumps.o
a - seqeuncesFilter.o
a - optGammaMixtureLS.o
a - mixtureDistribution.o
a - suffStatGammaMixture.o
a - GamMixtureOptimizer.o
a - optGammaMixtureEM.o
a - gainLossAlphabet.o
a - wYangModel.o
a - codonUtils.o
a - likelihoodComputation2Codon.o
a - likeDist2Codon.o
a - unObservableData.o
a - likelihoodComputationGL.o
a - threeStateModel.o
a - threeStateAlphabet.o
a - oneTwoMoreModel.o
a - betaDistributionFixedCategories.o
a - betaDistributionFixedCategoriesWithOmegaUniform.o
a - bblEM2codon.o
a - bestAlphaAndK.o
a - fromCountTableComponentToDistance2Codon.o
a - gtrModel.o
a - bestGtrModelParams.o
a - simulateRateShiftJumps.o
a - integerAlphabet.o
ranlib libEvolTree.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(aaJC.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(codonJC.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(nucJC.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(suffStatComponent.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(treeIt.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(cmdline2EvolObjs.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(doubleRep.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(logRep.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(generalGammaDistributionPlusInvariant.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libEvolTree.a(gammaDistributionPlusInvariant.o) has no symbols
cd programs;make install
cd fastml && make install
cd gainLoss && make install
cd indelCoder && make install
making depend
making depend
making depend
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoder.o indelCoder.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderOptions.o indelCoderOptions.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o fastml.o fastml.cpp
In file included from fastml.cpp:1:
In file included from ./mainbb.h:4:
In file included from ./bb_options.h:13:
In file included from ../../libs/phylogeny/definitions.h:18:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/vector:264:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__config:23:
/usr/include/unistd.h:508:6: error: conflicting types for 'getopt'
int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt);
^
../../libs/phylogeny/getopt.h:147:12: note: previous declaration is here
extern int getopt ();
^
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbAlg.o bbAlg.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss.o gainLoss.cpp
1 error generated.
make[2]: *** [fastml.o] Error 1
make[2]: *** Waiting for unfinished jobs....
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderProject.o indelCoderProject.cpp
In file included from bbAlg.cpp:1:
In file included from ./bbAlg.h:5:
In file included from ./bbNodeOrderAlg.h:5:
In file included from ./bb_options.h:10:
../../libs/phylogeny/getopt.h:147:12: error: conflicting types for 'getopt'
extern int getopt ();
^
/usr/include/unistd.h:508:6: note: previous declaration is here
int getopt(int, char * const [], const char *) __DARWIN_ALIAS(getopt);
^
1 error generated.
make[2]: *** [bbAlg.o] Error 1
make[1]: *** [fastml.install] Error 2
make[1]: *** Waiting for unfinished jobs....
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptions.o gainLossOptions.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossUtils.o gainLossUtils.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderUtils.o indelCoderUtils.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o character.o character.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gaps.o gaps.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossModel.o gainLossModel.cpp
ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o
ar: creating archive libindelCoder.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libindelCoder.a(gaps.o) has no symbols
a - indelCoder.o
a - indelCoderOptions.o
a - indelCoderProject.o
a - indelCoderUtils.o
a - character.o
a - gaps.o
ranlib libindelCoder.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libindelCoder.a(gaps.o) has no symbols
g++ -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder
cp indelCoder ../../bin/indelCoder
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o siteSpecificGL.o siteSpecificGL.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossProject.o gainLossProject.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptimizer.o gainLossOptimizer.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o rate4siteGL.o rate4siteGL.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCountsGL.o computeCountsGL.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCorrelations.o computeCorrelations.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss4site.o gainLoss4site.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateOnePos.o simulateOnePos.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bblLS.o bblLS.cpp
g++ -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp
ar rv libgainLoss.a gainLossOptions.o gainLoss.o gainLossUtils.o optimizeGainLossModel.o optimizeGainLossModelVV.o ../../libs/phylogeny/likelihoodComputationGL.o gainLossModel.o siteSpecificGL.o computePosteriorExpectationOfChange.o gainLossProject.o gainLossOptimizer.o ancestralReconstructStates.o rate4siteGL.o computeCountsGL.o computeCorrelations.o gainLoss4site.o simulateChangesAlongTree.o simulateOnePos.o bblLS.o sankoffReconstructGL.o
ar: creating archive libgainLoss.a
a - gainLossOptions.o
a - gainLoss.o
a - gainLossUtils.o
a - optimizeGainLossModel.o
a - optimizeGainLossModelVV.o
a - ../../libs/phylogeny/likelihoodComputationGL.o
a - gainLossModel.o
a - siteSpecificGL.o
a - computePosteriorExpectationOfChange.o
a - gainLossProject.o
a - gainLossOptimizer.o
a - ancestralReconstructStates.o
a - rate4siteGL.o
a - computeCountsGL.o
a - computeCorrelations.o
a - gainLoss4site.o
a - simulateChangesAlongTree.o
a - simulateOnePos.o
a - bblLS.o
a - sankoffReconstructGL.o
ranlib libgainLoss.a
g++ -L../../libs/phylogeny gainLoss.o libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss
cp gainLoss ../../bin/gainLoss
make: *** [programs.install] Error 2
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew.git
HEAD: 5e11e3bc588dd8153fb7e1fe4f832754e3bb61df
Last commit: 10 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit haswell
OS X: 10.11.1-x86_64
Xcode: 7.1.1
CLT: 7.1.0.0.1.1444952191
GCC-4.2: build 0
Clang: 7.0 build 700
X11: 2.7.8 => /opt/X11
System Ruby: 2.0.0-p645
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.8.0_66, 1.8.0_20
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/10.11
HOMEBREW_VERBOSE: 1
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Library/ENV/4.3:/usr/bin:/bin:/usr/sbin:/sbin
Raw
01.make.cc
g++ called with: -MM -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp computeSubstitutionCounts.cpp computePosteriorExpectationOfSubstitutions.cpp computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp sequence.cpp sequenceContainer.cpp simulateTree.cpp siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp uniformDistribution.cpp cmdline2EvolObjs.cpp generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp simulateCodonsJumps.cpp simulateJumpsAbstract.cpp ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp extremeValDistribution.cpp gammaDistributionFixedCategories.cpp generalGammaDistributionPlusInvariant.cpp gammaDistributionPlusInvariant.cpp distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp optGammaMixtureLS.cpp mixtureDistribution.cpp suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -pipe -w -Os -march=native -MM -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp computeSubstitutionCounts.cpp computePosteriorExpectationOfSubstitutions.cpp computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp sequence.cpp sequenceContainer.cpp simulateTree.cpp siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp uniformDistribution.cpp cmdline2EvolObjs.cpp generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp simulateCodonsJumps.cpp simulateJumpsAbstract.cpp ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp extremeValDistribution.cpp gammaDistributionFixedCategories.cpp generalGammaDistributionPlusInvariant.cpp gammaDistributionPlusInvariant.cpp distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp optGammaMixtureLS.cpp mixtureDistribution.cpp suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiProp.o NNiProp.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiProp.o NNiProp.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Nni.o Nni.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Nni.o Nni.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o AddLog.o AddLog.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o AddLog.o AddLog.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiSep.o NNiSep.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o NNiSep.o NNiSep.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o aaJC.o aaJC.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o aaJC.o aaJC.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTrees.o allTrees.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTrees.o allTrees.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o alphabet.o alphabet.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o alphabet.o alphabet.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o amino.o amino.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o amino.o amino.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlpha.o bestAlpha.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlpha.o bestAlpha.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestHKYparam.o bestHKYparam.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestHKYparam.o bestHKYparam.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bootstrap.o bootstrap.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bootstrap.o bootstrap.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM.o bblEM.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM.o bblEM.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMfixRoot.o bblEMfixRoot.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMfixRoot.o bblEMfixRoot.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProprtional.o bblEMProprtional.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProprtional.o bblEMProprtional.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMSeperate.o bblEMSeperate.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEMSeperate.o bblEMSeperate.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o clustalFormat.o clustalFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o clustalFormat.o clustalFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codon.o codon.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codon.o codon.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonJC.o codonJC.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonJC.o codonJC.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeCounts.o computeCounts.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeCounts.o computeCounts.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeDownAlg.o computeDownAlg.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeDownAlg.o computeDownAlg.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeMarginalAlg.o computeMarginalAlg.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeMarginalAlg.o computeMarginalAlg.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePijComponent.o computePijComponent.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePijComponent.o computePijComponent.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlg.o computeUpAlg.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlg.o computeUpAlg.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ConversionUtils.o ConversionUtils.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ConversionUtils.o ConversionUtils.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o countTableComponent.o countTableComponent.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o countTableComponent.o countTableComponent.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o datMatrixHolder.o datMatrixHolder.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o datMatrixHolder.o datMatrixHolder.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceTable.o distanceTable.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceTable.o distanceTable.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distribution.o distribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distribution.o distribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o errorMsg.o errorMsg.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o errorMsg.o errorMsg.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastStartTree.o fastStartTree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastStartTree.o fastStartTree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastaFormat.o fastaFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fastaFormat.o fastaFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o findRateOfGene.o findRateOfGene.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o findRateOfGene.o findRateOfGene.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromQtoPt.o fromQtoPt.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromQtoPt.o fromQtoPt.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistribution.o gammaDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistribution.o gammaDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaUtilities.o gammaUtilities.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaUtilities.o gammaUtilities.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistribution.o generalGammaDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistribution.o generalGammaDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o getRandomWeights.o getRandomWeights.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o getRandomWeights.o getRandomWeights.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o goldmanYangModel.o goldmanYangModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o goldmanYangModel.o goldmanYangModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o hky.o hky.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o hky.o hky.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateWithDependence.o simulateWithDependence.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateWithDependence.o simulateWithDependence.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o KH_calculation.o KH_calculation.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o KH_calculation.o KH_calculation.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist.o likeDist.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist.o likeDist.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistfixRoot.o likeDistfixRoot.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistfixRoot.o likeDistfixRoot.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistProp.o likeDistProp.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistProp.o likeDistProp.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistPropEB.o likeDistPropEB.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDistPropEB.o likeDistPropEB.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation.o likelihoodComputation.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation.o likelihoodComputation.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logFile.o logFile.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logFile.o logFile.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o maseFormat.o maseFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o maseFormat.o maseFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o molphyFormat.o molphyFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o molphyFormat.o molphyFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nexusFormat.o nexusFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nexusFormat.o nexusFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nj.o nj.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nj.o nj.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o njConstrain.o njConstrain.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o njConstrain.o njConstrain.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucJC.o nucJC.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucJC.o nucJC.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucleotide.o nucleotide.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o nucleotide.o nucleotide.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o numRec.o numRec.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o numRec.o numRec.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Parameters.o Parameters.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o Parameters.o Parameters.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipFormat.o phylipFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipFormat.o phylipFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pijAccelerator.o pijAccelerator.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pijAccelerator.o pijAccelerator.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o readDatMatrix.o readDatMatrix.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o readDatMatrix.o readDatMatrix.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o readTree.o readTree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o readTree.o readTree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o recognizeFormat.o recognizeFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o recognizeFormat.o recognizeFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModel.o replacementModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModel.o replacementModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o searchStatus.o searchStatus.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o searchStatus.o searchStatus.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequence.o sequence.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequence.o sequence.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequenceContainer.o sequenceContainer.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o sequenceContainer.o sequenceContainer.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateTree.o simulateTree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateTree.o simulateTree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o siteSpecificRate.o siteSpecificRate.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o siteSpecificRate.o siteSpecificRate.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o someUtil.o someUtil.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o someUtil.o someUtil.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o split.o split.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o split.o split.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitMap.o splitMap.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitMap.o splitMap.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitTreeUtil.o splitTreeUtil.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o splitTreeUtil.o splitTreeUtil.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcess.o stochasticProcess.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcess.o stochasticProcess.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatComponent.o suffStatComponent.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatComponent.o suffStatComponent.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o talRandom.o talRandom.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o talRandom.o talRandom.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tree.o tree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tree.o tree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeIt.o treeIt.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeIt.o treeIt.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeUtil.o treeUtil.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o treeUtil.o treeUtil.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniDistribution.o uniDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniDistribution.o uniDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniformDistribution.o uniformDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o uniformDistribution.o uniformDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GLaguer.o GLaguer.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GLaguer.o GLaguer.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o posteriorDistance.o posteriorDistance.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o posteriorDistance.o posteriorDistance.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o doubleRep.o doubleRep.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o doubleRep.o doubleRep.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logRep.o logRep.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o logRep.o logRep.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indel.o indel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indel.o indel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indelModel.o indelModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o indelModel.o indelModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mulAlphabet.o mulAlphabet.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mulAlphabet.o mulAlphabet.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModelSSRV.o replacementModelSSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o replacementModelSSRV.o replacementModelSSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o matrixUtils.o matrixUtils.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o matrixUtils.o matrixUtils.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaUtilities.o betaUtilities.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaUtilities.o betaUtilities.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistribution.o betaDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistribution.o betaDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o geneticCodeHolder.o geneticCodeHolder.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o geneticCodeHolder.o geneticCodeHolder.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o samplingSequences.o samplingSequences.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o samplingSequences.o samplingSequences.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2USSRV.o bblEM2USSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2USSRV.o bblEM2USSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestParamUSSRV.o bestParamUSSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestParamUSSRV.o bestParamUSSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2USSRV.o likeDist2USSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2USSRV.o likeDist2USSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ussrvModel.o ussrvModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ussrvModel.o ussrvModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o normalDist.o normalDist.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o normalDist.o normalDist.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tamura92.o tamura92.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o tamura92.o tamura92.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestTamura92param.o bestTamura92param.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestTamura92param.o bestTamura92param.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o extremeValDistribution.o extremeValDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o extremeValDistribution.o extremeValDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusCategory.o distributionPlusCategory.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o distributionPlusCategory.o distributionPlusCategory.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumps.o simulateJumps.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateJumps.o simulateJumps.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeJumps.o computeJumps.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o computeJumps.o computeJumps.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqeuncesFilter.o seqeuncesFilter.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o seqeuncesFilter.o seqeuncesFilter.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mixtureDistribution.o mixtureDistribution.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o mixtureDistribution.o mixtureDistribution.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gainLossAlphabet.o gainLossAlphabet.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gainLossAlphabet.o gainLossAlphabet.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o wYangModel.o wYangModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o wYangModel.o wYangModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonUtils.o codonUtils.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o codonUtils.o codonUtils.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2Codon.o likeDist2Codon.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likeDist2Codon.o likeDist2Codon.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o unObservableData.o unObservableData.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o unObservableData.o unObservableData.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateModel.o threeStateModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateModel.o threeStateModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateAlphabet.o threeStateAlphabet.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o threeStateAlphabet.o threeStateAlphabet.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2codon.o bblEM2codon.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bblEM2codon.o bblEM2codon.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndK.o bestAlphaAndK.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestAlphaAndK.o bestAlphaAndK.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gtrModel.o gtrModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o gtrModel.o gtrModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestGtrModelParams.o bestGtrModelParams.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o bestGtrModelParams.o bestGtrModelParams.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o integerAlphabet.o integerAlphabet.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -c -o integerAlphabet.o integerAlphabet.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -MM -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 indelCoder.cpp indelCoderOptions.cpp indelCoderProject.cpp indelCoderUtils.cpp character.cpp gaps.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -pipe -w -Os -march=native -MM -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 indelCoder.cpp indelCoderOptions.cpp indelCoderProject.cpp indelCoderUtils.cpp character.cpp gaps.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++ called with: -MM -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 gainLossOptions.cpp gainLoss.cpp gainLossUtils.cpp optimizeGainLossModel.cpp optimizeGainLossModelVV.cpp ../../libs/phylogeny/likelihoodComputationGL.cpp gainLossModel.cpp siteSpecificGL.cpp computePosteriorExpectationOfChange.cpp gainLossProject.cpp gainLossOptimizer.cpp ancestralReconstructStates.cpp rate4siteGL.cpp computeCountsGL.cpp computeCorrelations.cpp gainLoss4site.cpp simulateChangesAlongTree.cpp simulateOnePos.cpp bblLS.cpp sankoffReconstructGL.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -pipe -w -Os -march=native -MM -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 gainLossOptions.cpp gainLoss.cpp gainLossUtils.cpp optimizeGainLossModel.cpp optimizeGainLossModelVV.cpp ../../libs/phylogeny/likelihoodComputationGL.cpp gainLossModel.cpp siteSpecificGL.cpp computePosteriorExpectationOfChange.cpp gainLossProject.cpp gainLossOptimizer.cpp ancestralReconstructStates.cpp rate4siteGL.cpp computeCountsGL.cpp computeCorrelations.cpp gainLoss4site.cpp simulateChangesAlongTree.cpp simulateOnePos.cpp bblLS.cpp sankoffReconstructGL.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++ called with: -MM -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 fastml.cpp bbAlg.cpp bbComputeDownAlg.cpp bbComputeUpAlg.cpp bbEvaluateSpecificAV.cpp bbfindBestAVDynProg.cpp bbNodeOrderAlg.cpp bb_options.cpp bbReport.cpp computeMarginalReconstruction.cpp jointNoGamma.cpp mainbb.cpp sequenceDataDiff.cpp suffStatComponentJointNoGamma.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -pipe -w -Os -march=native -MM -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 fastml.cpp bbAlg.cpp bbComputeDownAlg.cpp bbComputeUpAlg.cpp bbEvaluateSpecificAV.cpp bbfindBestAVDynProg.cpp bbNodeOrderAlg.cpp bb_options.cpp bbReport.cpp computeMarginalReconstruction.cpp jointNoGamma.cpp mainbb.cpp sequenceDataDiff.cpp suffStatComponentJointNoGamma.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoder.o indelCoder.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoder.o indelCoder.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderOptions.o indelCoderOptions.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderOptions.o indelCoderOptions.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o fastml.o fastml.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o fastml.o fastml.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbAlg.o bbAlg.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bbAlg.o bbAlg.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss.o gainLoss.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss.o gainLoss.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderProject.o indelCoderProject.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderProject.o indelCoderProject.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptions.o gainLossOptions.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptions.o gainLossOptions.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossUtils.o gainLossUtils.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossUtils.o gainLossUtils.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderUtils.o indelCoderUtils.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o indelCoderUtils.o indelCoderUtils.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o character.o character.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o character.o character.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gaps.o gaps.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gaps.o gaps.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossModel.o gainLossModel.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossModel.o gainLossModel.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -pipe -w -Os -march=native -L../../libs/phylogeny indelCoder.o libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o siteSpecificGL.o siteSpecificGL.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o siteSpecificGL.o siteSpecificGL.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossProject.o gainLossProject.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossProject.o gainLossProject.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptimizer.o gainLossOptimizer.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLossOptimizer.o gainLossOptimizer.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o rate4siteGL.o rate4siteGL.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o rate4siteGL.o rate4siteGL.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCountsGL.o computeCountsGL.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCountsGL.o computeCountsGL.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCorrelations.o computeCorrelations.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o computeCorrelations.o computeCorrelations.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss4site.o gainLoss4site.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o gainLoss4site.o gainLoss4site.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateOnePos.o simulateOnePos.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o simulateOnePos.o simulateOnePos.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bblLS.o bblLS.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o bblLS.o bblLS.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp
superenv removed: -O3 -Wall
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
superenv executed: clang++ -pipe -w -Os -march=native -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -ftemplate-depth-32 -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
g++ called with: -L../../libs/phylogeny gainLoss.o libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss
superenv added: -pipe -w -Os -march=native -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
superenv executed: clang++ -pipe -w -Os -march=native -L../../libs/phylogeny gainLoss.o libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss -isystem/usr/local/include -isystem/usr/include/libxml2 -isystem/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers -L/usr/local/lib -L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries -Wl,-headerpad_max_install_names
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