Running phase: unpackPhase unpacking source archive /nix/store/3l71fvys70y7fhpcqdzni4ridd686bpi-rate4site-3.0.0.orig.tar.gz source root is rate4site-3.0.0 setting SOURCE_DATE_EPOCH to timestamp 1380939582 of file "rate4site-3.0.0/src/rate4site/Makefile.in" Running phase: patchPhase Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase patching script interpreter paths in ./configure ./configure: interpreter directive changed from "#! /bin/sh" to "/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/sh" configure flags: --disable-dependency-tracking --prefix=/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0 checking for a BSD-compatible install... /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none ./configure: line 3620: test: syntax error: `-std=gnu++98' unexpected checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /nix/store/yhr4ps9rdmb55pgqaq246vlh7xfac1dx-gnugrep-3.12/bin/grep checking for egrep... /nix/store/yhr4ps9rdmb55pgqaq246vlh7xfac1dx-gnugrep-3.12/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking string usability... yes checking string presence... yes checking for string... yes checking iostream usability... yes checking iostream presence... yes checking for iostream... yes checking for size_t... yes checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) none checking for ranlib... ranlib checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/phylogeny/Makefile config.status: creating src/rate4site/Makefile config.status: creating config.h config.status: executing depfiles commands Running phase: buildPhase build flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash make all-recursive make[1]: Entering directory '/build/rate4site-3.0.0' Making all in src/phylogeny make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o alphabet.o alphabet.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o sequenceContainer.o sequenceContainer.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o sequence.o sequence.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o mulAlphabet.o mulAlphabet.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o someUtil.o someUtil.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o logFile.o logFile.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gainLossAlphabet.o gainLossAlphabet.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o pijAccelerator.o pijAccelerator.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o replacementModel.o replacementModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o distribution.o distribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o readTree.o readTree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o errorMsg.o errorMsg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nucleotide.o nucleotide.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o amino.o amino.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o geneticCodeHolder.o geneticCodeHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o codon.o codon.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o doubleRep.o doubleRep.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o uniDistribution.o uniDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o generalGammaDistribution.o generalGammaDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o readDatMatrix.o readDatMatrix.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o datMatrixHolder.o datMatrixHolder.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nucJC.o nucJC.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o aaJC.o aaJC.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gtrModel.o gtrModel.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromQtoPt.o fromQtoPt.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o distanceTable.o distanceTable.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nj.o nj.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o njConstrain.o njConstrain.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o numRec.o numRec.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o uniformDistribution.o uniformDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePijComponent.o computePijComponent.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o stochasticProcess.o stochasticProcess.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o suffStatComponent.o suffStatComponent.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o unObservableData.o unObservableData.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likeDist.o likeDist.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o countTableComponent.o countTableComponent.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fastStartTree.o fastStartTree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestAlpha.o bestAlpha.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gammaDistribution.o gammaDistribution.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o siteSpecificRate.o siteSpecificRate.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputation.o likelihoodComputation.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o recognizeFormat.o recognizeFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblEM.o bblEM.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o hky.o hky.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestGtrModelParams.o bestGtrModelParams.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o tamura92.o tamura92.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestHKYparam.o bestHKYparam.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestTamura92param.o bestTamura92param.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o talRandom.o talRandom.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeCounts.o computeCounts.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeDownAlg.o computeDownAlg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeUpAlg.o computeUpAlg.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gammaUtilities.o gammaUtilities.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o treeUtil.o treeUtil.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o matrixUtils.o matrixUtils.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateJumps.o simulateJumps.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o treeIt.o treeIt.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o tree.o tree.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likeDistPropEB.o likeDistPropEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o phylipFormat.o phylipFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o maseFormat.o maseFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o clustalFormat.o clustalFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fastaFormat.o fastaFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o molphyFormat.o molphyFormat.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o getRandomWeights.o getRandomWeights.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nexusFormat.o nexusFormat.cpp rm -f libphylo.a ar cru libphylo.a alphabet.o sequenceContainer.o sequence.o mulAlphabet.o someUtil.o logFile.o gainLossAlphabet.o pijAccelerator.o replacementModel.o distribution.o readTree.o errorMsg.o nucleotide.o amino.o geneticCodeHolder.o codon.o doubleRep.o evaluateCharacterFreq.o uniDistribution.o generalGammaDistribution.o readDatMatrix.o datMatrixHolder.o chebyshevAccelerator.o nucJC.o aaJC.o gtrModel.o fromQtoPt.o distanceTable.o nj.o njConstrain.o numRec.o uniformDistribution.o computePijComponent.o stochasticProcess.o suffStatComponent.o unObservableData.o likeDist.o countTableComponent.o fastStartTree.o likelihoodComputationFactors.o bestAlpha.o gammaDistribution.o siteSpecificRate.o likelihoodComputation.o recognizeFormat.o bblEM.o hky.o bestGtrModelParams.o tamura92.o bestHKYparam.o bestTamura92param.o talRandom.o computeSubstitutionCounts.o fromCountTableComponentToDistance.o computeCounts.o computeDownAlg.o computeUpAlg.o computeUpAlgFactors.o gammaUtilities.o seqContainerTreeMap.o treeUtil.o matrixUtils.o simulateCodonsJumps.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o multipleStochasticProcess.o simulateJumps.o simulateJumpsAbstract.o treeIt.o likelihoodComputationGL.o tree.o bblEMProportionalEB.o fromCountTableComponentToDistancePropEB.o likeDistPropEB.o bblLSProportionalEB.o phylipFormat.o maseFormat.o clustalFormat.o fastaFormat.o phylipSequentialFormat.o molphyFormat.o getRandomWeights.o nexusFormat.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libphylo.a make[2]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny' Making all in src/rate4site make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site' g++ -DHAVE_CONFIG_H -I. -I../.. -DDOUBLEREP -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4site-rate4siteOptions.o `test -f 'rate4siteOptions.cpp' || echo './'`rate4siteOptions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -DDOUBLEREP -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4site-rate4site.o `test -f 'rate4site.cpp' || echo './'`rate4site.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4siteOptions.o rate4siteOptions.cpp g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4site.o rate4site.cpp sed -e 's|__pkgdatadir__|/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/share/rate4site|g;s|__examplesdir__||g;s|__sysconfdir__|/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/etc|g;s|__bindir__|/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/bin|g;s|__PACKAGE_VERSION__|3.0.0|g' "rate4site.cpp" | \ pod2man --utf8 -c 'User Commands' -r "3.0.0" -name RATE4SITE > "rate4site.1" g++ -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a g++ -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a make[2]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' make[2]: Entering directory '/build/rate4site-3.0.0' make[2]: Leaving directory '/build/rate4site-3.0.0' make[1]: Leaving directory '/build/rate4site-3.0.0' Running phase: installPhase install flags: -j48 SHELL=/nix/store/9ipfvwnqp1q8ijnmi5sxvlx9r8w34lw3-bash-5.3p15/bin/bash install Making install in src/phylogeny make[1]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/mkdir -p '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/lib' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c -m 644 libphylo.a '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/lib' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/mkdir -p '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/include/libphylo' ( cd '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/lib' && ranlib libphylo.a ) /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c -m 644 replacementMatrixSource/mitochondriaAscidian.code replacementMatrixSource/mitochondriaProtozoan.code replacementMatrixSource/nuclearCiliate.code replacementMatrixSource/mitochondriaEchinoderm.code replacementMatrixSource/mitochondriaVertebrate.code replacementMatrixSource/nuclearEuplotid.code replacementMatrixSource/mitochondriaFlatworm.code replacementMatrixSource/mitochondriaYeast.code replacementMatrixSource/nuclearStandard.code replacementMatrixSource/mitochondriaInvertebrate.code replacementMatrixSource/nuclearBlepharisma.code cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q adrianCodon.dat.q LG.dat.q replacementMatrixSource/cpREV45.dat replacementMatrixSource/dayhoff.dat replacementMatrixSource/jones.dat replacementMatrixSource/mtREV24.dat replacementMatrixSource/wag.dat getopt.h errorMsg.h definitions.h doubleRep.h ConversionUtils.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h pijAccelerator.h replacementModel.h distribution.h '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/include/libphylo' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c -m 644 readTree.h nucleotide.h amino.h geneticCodeHolder.h codon.h evaluateCharacterFreq.h uniDistribution.h generalGammaDistribution.h readDatMatrix.h datMatrixHolder.h chebyshevAccelerator.h nucJC.h aaJC.h gtrModel.h fromQtoPt.h trivialAccelerator.h distanceMethod.h distanceTable.h nj.h njConstrain.h distances2Tree.h numRec.h uniformDistribution.h checkcovFanctors.h likelihoodComputation.h computePijComponent.h stochasticProcess.h suffStatComponent.h unObservableData.h likeDist.h countTableComponent.h jcDistance.h fastStartTree.h checkcovFanctorsWithFactors.h likelihoodComputationFactors.h bestAlpha.h gammaDistribution.h siteSpecificRate.h recognizeFormat.h bblEM.h '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/include/libphylo' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c -m 644 bestGtrModelParams.h tamura92.h bestHKYparam.h hky.h bestTamura92param.h talRandom.h computeSubstitutionCounts.h fromCountTableComponentToDistance.h computeCounts.h computeDownAlg.h computeUpAlg.h gammaUtilities.h seqContainerTreeMap.h treeUtil.h matrixUtils.h computePosteriorExpectationOfSubstitutions.h computePosteriorExpectationOfSubstitutions_nonReversibleSp.h multipleStochasticProcess.h simulateJumps.h simulateJumpsAbstract.h simulateCodonsJumps.h treeIt.h likelihoodComputationGL.h tree.h bblEMProportionalEB.h fromCountTableComponentToDistancePropEB.h likeDistPropEB.h bblLSProportionalEB.h phylipFormat.h maseFormat.h clustalFormat.h fastaFormat.h phylipSequentialFormat.h molphyFormat.h getRandomWeights.h nexusFormat.h '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/include/libphylo' make[2]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny' make[1]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny' Making install in src/rate4site make[1]: Entering directory '/build/rate4site-3.0.0/src/rate4site' make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/mkdir -p '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/bin' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/mkdir -p '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/share/man/man1' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c rate4site rate4site_doublerep '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/bin' /nix/store/3qgy8q2j64v2m9jy3a5jmssacbblhd4r-coreutils-9.11/bin/install -c -m 644 rate4site.1 '/nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/share/man/man1' make[2]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' make[1]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' make[1]: Entering directory '/build/rate4site-3.0.0' make[2]: Entering directory '/build/rate4site-3.0.0' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/build/rate4site-3.0.0' make[1]: Leaving directory '/build/rate4site-3.0.0' Running phase: fixupPhase shrinking RPATHs of ELF executables and libraries in /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0 shrinking /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/bin/rate4site shrinking /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/bin/rate4site_doublerep checking for references to /build/ in /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0... gzipping man pages under /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/share/man/ patching script interpreter paths in /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0 stripping (with command strip and flags -S -p) in /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/lib /nix/store/xvcrgp9bsqnrj0qpfzz8b8akz785v0ri-rate4site-3.0.0/bin