rate4site-3.0.0
checks.x86_64-linux.pkgs-rate4site
· build #95
· raw
unpackPhase
1unpacking source archive /nix/store/3l71fvys70y7fhpcqdzni4ridd686bpi-rate4site-3.0.0.orig.tar.gz2source root is rate4site-3.0.03setting SOURCE_DATE_EPOCH to timestamp 1380939582 of file "rate4site-3.0.0/src/rate4site/Makefile.in"configurePhase
4patching script interpreter paths in ./configure5./configure: interpreter directive changed from "#! /bin/sh" to "/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/sh"6configure flags: --disable-dependency-tracking --prefix=/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.07checking for a BSD-compatible install... /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/install -c8checking whether build environment is sane... yes9checking for a thread-safe mkdir -p... /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/mkdir -p10checking for gawk... gawk11checking whether make sets $(MAKE)... yes12checking for gcc... gcc13checking whether the C compiler works... yes14checking for C compiler default output file name... a.out15checking for suffix of executables... 16checking whether we are cross compiling... no17checking for suffix of object files... o18checking whether we are using the GNU C compiler... yes19checking whether gcc accepts -g... yes20checking for gcc option to accept ISO C89... none needed21checking for style of include used by make... GNU22checking dependency style of gcc... none23./configure: line 3620: test: syntax error: `-std=gnu++98' unexpected24checking whether we are using the GNU C++ compiler... yes25checking whether g++ accepts -g... yes26checking dependency style of g++... none27checking how to run the C++ preprocessor... g++ -E28checking for grep that handles long lines and -e... /nix/store/3668q0d9zhc5n9l2pnyvpd44kz9bjsjm-gnugrep-3.12/bin/grep29checking for egrep... /nix/store/3668q0d9zhc5n9l2pnyvpd44kz9bjsjm-gnugrep-3.12/bin/grep -E30checking for ANSI C header files... yes31checking for sys/types.h... yes32checking for sys/stat.h... yes33checking for stdlib.h... yes34checking for string.h... yes35checking for memory.h... yes36checking for strings.h... yes37checking for inttypes.h... yes38checking for stdint.h... yes39checking for unistd.h... yes40checking string usability... yes41checking string presence... yes42checking for string... yes43checking iostream usability... yes44checking iostream presence... yes45checking for iostream... yes46checking for size_t... yes47checking whether we are using the GNU C++ compiler... (cached) yes48checking whether g++ accepts -g... (cached) yes49checking dependency style of g++... (cached) none50checking whether we are using the GNU C++ compiler... (cached) yes51checking whether g++ accepts -g... (cached) yes52checking dependency style of g++... (cached) none53checking for ranlib... ranlib54checking whether ln -s works... yes55checking whether make sets $(MAKE)... (cached) yes56configure: creating ./config.status57config.status: creating Makefile58config.status: creating src/phylogeny/Makefile59config.status: creating src/rate4site/Makefile60config.status: creating config.h61config.status: executing depfiles commandsbuildPhase
62build flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/bash63make all-recursive64make[1]: Entering directory '/build/rate4site-3.0.0'65Making all in src/phylogeny66make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny'67g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o alphabet.o alphabet.cpp68g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o sequenceContainer.o sequenceContainer.cpp69g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o sequence.o sequence.cpp70g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o mulAlphabet.o mulAlphabet.cpp71g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o someUtil.o someUtil.cpp72g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o logFile.o logFile.cpp73g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gainLossAlphabet.o gainLossAlphabet.cpp74g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o pijAccelerator.o pijAccelerator.cpp75g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o replacementModel.o replacementModel.cpp76g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o distribution.o distribution.cpp77g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o readTree.o readTree.cpp78g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o errorMsg.o errorMsg.cpp79g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nucleotide.o nucleotide.cpp80g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o amino.o amino.cpp81g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o geneticCodeHolder.o geneticCodeHolder.cpp82g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o codon.o codon.cpp83g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o doubleRep.o doubleRep.cpp84g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp85g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o uniDistribution.o uniDistribution.cpp86g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o generalGammaDistribution.o generalGammaDistribution.cpp87g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o readDatMatrix.o readDatMatrix.cpp88g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o datMatrixHolder.o datMatrixHolder.cpp89g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp90g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nucJC.o nucJC.cpp91g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o aaJC.o aaJC.cpp92g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gtrModel.o gtrModel.cpp93g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromQtoPt.o fromQtoPt.cpp94g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o distanceTable.o distanceTable.cpp95g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nj.o nj.cpp96g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o njConstrain.o njConstrain.cpp97g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o numRec.o numRec.cpp98g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o uniformDistribution.o uniformDistribution.cpp99g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePijComponent.o computePijComponent.cpp100g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o stochasticProcess.o stochasticProcess.cpp101g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o suffStatComponent.o suffStatComponent.cpp102g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o unObservableData.o unObservableData.cpp103g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likeDist.o likeDist.cpp104g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o countTableComponent.o countTableComponent.cpp105g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fastStartTree.o fastStartTree.cpp106g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp107g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestAlpha.o bestAlpha.cpp108g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gammaDistribution.o gammaDistribution.cpp109g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o siteSpecificRate.o siteSpecificRate.cpp110g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputation.o likelihoodComputation.cpp111g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o recognizeFormat.o recognizeFormat.cpp112g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblEM.o bblEM.cpp113g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o hky.o hky.cpp114g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestGtrModelParams.o bestGtrModelParams.cpp115g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o tamura92.o tamura92.cpp116g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestHKYparam.o bestHKYparam.cpp117g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestTamura92param.o bestTamura92param.cpp118g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o talRandom.o talRandom.cpp119g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp120g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp121g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeCounts.o computeCounts.cpp122g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeDownAlg.o computeDownAlg.cpp123g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeUpAlg.o computeUpAlg.cpp124g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp125g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gammaUtilities.o gammaUtilities.cpp126g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp127g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o treeUtil.o treeUtil.cpp128g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o matrixUtils.o matrixUtils.cpp129g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp130g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp131g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp132g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp133g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateJumps.o simulateJumps.cpp134g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp135g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o treeIt.o treeIt.cpp136g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp137g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o tree.o tree.cpp138g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp139g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp140g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likeDistPropEB.o likeDistPropEB.cpp141g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp142g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o phylipFormat.o phylipFormat.cpp143g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o maseFormat.o maseFormat.cpp144g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o clustalFormat.o clustalFormat.cpp145g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fastaFormat.o fastaFormat.cpp146g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp147g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o molphyFormat.o molphyFormat.cpp148g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o getRandomWeights.o getRandomWeights.cpp149g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nexusFormat.o nexusFormat.cpp150rm -f libphylo.a151ar 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 152ar: `u' modifier ignored since `D' is the default (see `U')153ranlib libphylo.a154make[2]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny'155Making all in src/rate4site156make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site'157g++ -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.cpp158g++ -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.cpp159g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4siteOptions.o rate4siteOptions.cpp160g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4site.o rate4site.cpp161sed -e 's|__pkgdatadir__|/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/share/rate4site|g;s|__examplesdir__||g;s|__sysconfdir__|/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/etc|g;s|__bindir__|/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/bin|g;s|__PACKAGE_VERSION__|3.0.0|g' "rate4site.cpp" | \162pod2man --utf8 -c 'User Commands' -r "3.0.0" -name RATE4SITE > "rate4site.1"163g++ -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a 164g++ -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a 165make[2]: Leaving directory '/build/rate4site-3.0.0/src/rate4site'166make[2]: Entering directory '/build/rate4site-3.0.0'167make[2]: Leaving directory '/build/rate4site-3.0.0'168make[1]: Leaving directory '/build/rate4site-3.0.0'installPhase
169install flags: -j48 SHELL=/nix/store/10dxp0qxqxxsyiljrh2kp0xqhz6arhcx-bash-5.3p15/bin/bash install170Making install in src/phylogeny171make[1]: Entering directory '/build/rate4site-3.0.0/src/phylogeny'172make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny'173 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/mkdir -p '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/lib'174 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/mkdir -p '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/include/libphylo'175 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/install -c -m 644 libphylo.a '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/lib'176 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-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/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/include/libphylo'177 ( cd '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/lib' && ranlib libphylo.a )178 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-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/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/include/libphylo'179 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-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/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/include/libphylo'180make[2]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny'181make[1]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny'182Making install in src/rate4site183make[1]: Entering directory '/build/rate4site-3.0.0/src/rate4site'184make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site'185 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/mkdir -p '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/bin'186 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/mkdir -p '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/share/man/man1'187 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/install -c rate4site rate4site_doublerep '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/bin'188 /nix/store/2gfxiwls9hbgwdwcy43mprchwsq36mg6-coreutils-9.11/bin/install -c -m 644 rate4site.1 '/nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/share/man/man1'189make[2]: Leaving directory '/build/rate4site-3.0.0/src/rate4site'190make[1]: Leaving directory '/build/rate4site-3.0.0/src/rate4site'191make[1]: Entering directory '/build/rate4site-3.0.0'192make[2]: Entering directory '/build/rate4site-3.0.0'193make[2]: Nothing to be done for 'install-exec-am'.194make[2]: Nothing to be done for 'install-data-am'.195make[2]: Leaving directory '/build/rate4site-3.0.0'196make[1]: Leaving directory '/build/rate4site-3.0.0'fixupPhase
197shrinking RPATHs of ELF executables and libraries in /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0198shrinking /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/bin/rate4site199shrinking /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/bin/rate4site_doublerep200checking for references to /build/ in /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0...201gzipping man pages under /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/share/man/202patching script interpreter paths in /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0203stripping (with command strip and flags -S -p) in /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/lib /nix/store/30ybf1n0yi83wg47ck15niinlay883kb-rate4site-3.0.0/bin