these 2 derivations will be built: /nix/store/27hz58zx2csr8gh5axic6i5938j1ydpl-rate4site-3.0.0.orig.tar.gz.drv /nix/store/faky5wvvxb82ig95ssajqa3frwn8qn85-rate4site-3.0.0.drv building '/nix/store/y753azjz0ih11rz2d4if6j48g9va90yr-rate4site-3.0.0.orig.tar.gz.drv' rate4site-3.0.0.orig.tar.gz> structuredAttrs is enabled rate4site-3.0.0.orig.tar.gz> rate4site-3.0.0.orig.tar.gz> trying https://snapshot.debian.org/file/837fb82c4ac368ebc64a5d8697706be3b0679829 rate4site-3.0.0.orig.tar.gz> % Total % Received % Xferd Average Speed Time Time Time Current rate4site-3.0.0.orig.tar.gz> Dload Upload Total Spent Left Speed rate4site-3.0.0.orig.tar.gz> rate4site-3.0.0.orig.tar.gz> 0 0 0 0 0 0 0 0 0 rate4site-3.0.0.orig.tar.gz> 0 0 0 0 0 0 0 0 00:01 0 rate4site-3.0.0.orig.tar.gz> 100 296.3k 100 296.3k 0 0 238.1k 0 00:01 00:01 247.2k rate4site-3.0.0.orig.tar.gz> 100 296.3k 100 296.3k 0 0 238.0k 0 00:01 00:01 247.2k rate4site-3.0.0.orig.tar.gz> 100 296.3k 100 296.3k 0 0 238.0k 0 00:01 00:01 247.2k building '/nix/store/faky5wvvxb82ig95ssajqa3frwn8qn85-rate4site-3.0.0.drv' rate4site-3.0.0> Running phase: unpackPhase rate4site-3.0.0> unpacking source archive /nix/store/3l71fvys70y7fhpcqdzni4ridd686bpi-rate4site-3.0.0.orig.tar.gz rate4site-3.0.0> source root is rate4site-3.0.0 rate4site-3.0.0> setting SOURCE_DATE_EPOCH to timestamp 1380939582 of file "rate4site-3.0.0/src/rate4site/Makefile.in" rate4site-3.0.0> Running phase: patchPhase rate4site-3.0.0> Running phase: updateAutotoolsGnuConfigScriptsPhase rate4site-3.0.0> Running phase: configurePhase rate4site-3.0.0> patching script interpreter paths in ./configure rate4site-3.0.0> ./configure: interpreter directive changed from "#! /bin/sh" to "/nix/store/svx59425zxp552p2b8gm11qj5r09b56i-bash-5.3p15/bin/sh" rate4site-3.0.0> configure flags: --disable-dependency-tracking --prefix=/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0 rate4site-3.0.0> checking for a BSD-compatible install... /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/install -c rate4site-3.0.0> checking whether build environment is sane... yes rate4site-3.0.0> checking for a thread-safe mkdir -p... /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/mkdir -p rate4site-3.0.0> checking for gawk... gawk rate4site-3.0.0> checking whether make sets $(MAKE)... yes rate4site-3.0.0> checking for gcc... gcc rate4site-3.0.0> checking whether the C compiler works... yes rate4site-3.0.0> checking for C compiler default output file name... a.out rate4site-3.0.0> checking for suffix of executables... rate4site-3.0.0> checking whether we are cross compiling... no rate4site-3.0.0> checking for suffix of object files... o rate4site-3.0.0> checking whether we are using the GNU C compiler... yes rate4site-3.0.0> checking whether gcc accepts -g... yes rate4site-3.0.0> checking for gcc option to accept ISO C89... none needed rate4site-3.0.0> checking for style of include used by make... GNU rate4site-3.0.0> checking dependency style of gcc... none rate4site-3.0.0> ./configure: line 3620: test: syntax error: `-std=gnu++98' unexpected rate4site-3.0.0> checking whether we are using the GNU C++ compiler... yes rate4site-3.0.0> checking whether g++ accepts -g... yes rate4site-3.0.0> checking dependency style of g++... none rate4site-3.0.0> checking how to run the C++ preprocessor... g++ -E rate4site-3.0.0> checking for grep that handles long lines and -e... /nix/store/xmvbzzxm5snla5a2cyfhm7hjy9bifx7n-gnugrep-3.12/bin/grep rate4site-3.0.0> checking for egrep... /nix/store/xmvbzzxm5snla5a2cyfhm7hjy9bifx7n-gnugrep-3.12/bin/grep -E rate4site-3.0.0> checking for ANSI C header files... yes rate4site-3.0.0> checking for sys/types.h... yes rate4site-3.0.0> checking for sys/stat.h... yes rate4site-3.0.0> checking for stdlib.h... yes rate4site-3.0.0> checking for string.h... yes rate4site-3.0.0> checking for memory.h... yes rate4site-3.0.0> checking for strings.h... yes rate4site-3.0.0> checking for inttypes.h... yes rate4site-3.0.0> checking for stdint.h... yes rate4site-3.0.0> checking for unistd.h... yes rate4site-3.0.0> checking string usability... yes rate4site-3.0.0> checking string presence... yes rate4site-3.0.0> checking for string... yes rate4site-3.0.0> checking iostream usability... yes rate4site-3.0.0> checking iostream presence... yes rate4site-3.0.0> checking for iostream... yes rate4site-3.0.0> checking for size_t... yes rate4site-3.0.0> checking whether we are using the GNU C++ compiler... (cached) yes rate4site-3.0.0> checking whether g++ accepts -g... (cached) yes rate4site-3.0.0> checking dependency style of g++... (cached) none rate4site-3.0.0> checking whether we are using the GNU C++ compiler... (cached) yes rate4site-3.0.0> checking whether g++ accepts -g... (cached) yes rate4site-3.0.0> checking dependency style of g++... (cached) none rate4site-3.0.0> checking for ranlib... ranlib rate4site-3.0.0> checking whether ln -s works... yes rate4site-3.0.0> checking whether make sets $(MAKE)... (cached) yes rate4site-3.0.0> configure: creating ./config.status rate4site-3.0.0> config.status: creating Makefile rate4site-3.0.0> config.status: creating src/phylogeny/Makefile rate4site-3.0.0> config.status: creating src/rate4site/Makefile rate4site-3.0.0> config.status: creating config.h rate4site-3.0.0> config.status: executing depfiles commands rate4site-3.0.0> Running phase: buildPhase rate4site-3.0.0> build flags: -j48 SHELL=/nix/store/svx59425zxp552p2b8gm11qj5r09b56i-bash-5.3p15/bin/bash rate4site-3.0.0> make all-recursive rate4site-3.0.0> make[1]: Entering directory '/build/rate4site-3.0.0' rate4site-3.0.0> Making all in src/phylogeny rate4site-3.0.0> make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o alphabet.o alphabet.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o sequenceContainer.o sequenceContainer.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o sequence.o sequence.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o mulAlphabet.o mulAlphabet.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o someUtil.o someUtil.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o logFile.o logFile.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gainLossAlphabet.o gainLossAlphabet.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o pijAccelerator.o pijAccelerator.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o replacementModel.o replacementModel.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o distribution.o distribution.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o readTree.o readTree.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o errorMsg.o errorMsg.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nucleotide.o nucleotide.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o amino.o amino.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o geneticCodeHolder.o geneticCodeHolder.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o codon.o codon.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o doubleRep.o doubleRep.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o uniDistribution.o uniDistribution.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o generalGammaDistribution.o generalGammaDistribution.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o readDatMatrix.o readDatMatrix.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o datMatrixHolder.o datMatrixHolder.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nucJC.o nucJC.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o aaJC.o aaJC.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gtrModel.o gtrModel.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromQtoPt.o fromQtoPt.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o distanceTable.o distanceTable.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nj.o nj.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o njConstrain.o njConstrain.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o numRec.o numRec.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o uniformDistribution.o uniformDistribution.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePijComponent.o computePijComponent.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o stochasticProcess.o stochasticProcess.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o suffStatComponent.o suffStatComponent.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o unObservableData.o unObservableData.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likeDist.o likeDist.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o countTableComponent.o countTableComponent.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fastStartTree.o fastStartTree.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestAlpha.o bestAlpha.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gammaDistribution.o gammaDistribution.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o siteSpecificRate.o siteSpecificRate.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputation.o likelihoodComputation.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o recognizeFormat.o recognizeFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblEM.o bblEM.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o hky.o hky.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestGtrModelParams.o bestGtrModelParams.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o tamura92.o tamura92.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestHKYparam.o bestHKYparam.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bestTamura92param.o bestTamura92param.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o talRandom.o talRandom.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeCounts.o computeCounts.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeDownAlg.o computeDownAlg.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeUpAlg.o computeUpAlg.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o gammaUtilities.o gammaUtilities.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o treeUtil.o treeUtil.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o matrixUtils.o matrixUtils.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp rate4site-3.0.0> 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 rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateJumps.o simulateJumps.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o treeIt.o treeIt.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o tree.o tree.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o likeDistPropEB.o likeDistPropEB.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o phylipFormat.o phylipFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o maseFormat.o maseFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o clustalFormat.o clustalFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o fastaFormat.o fastaFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o molphyFormat.o molphyFormat.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o getRandomWeights.o getRandomWeights.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -O3 -Wno-deprecated -I../../src -O2 -std=gnu++98 -fpermissive -w -c -o nexusFormat.o nexusFormat.cpp rate4site-3.0.0> rm -f libphylo.a rate4site-3.0.0> 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 rate4site-3.0.0> ar: `u' modifier ignored since `D' is the default (see `U') rate4site-3.0.0> ranlib libphylo.a rate4site-3.0.0> make[2]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny' rate4site-3.0.0> Making all in src/rate4site rate4site-3.0.0> make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site' rate4site-3.0.0> 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 rate4site-3.0.0> 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 rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4siteOptions.o rate4siteOptions.cpp rate4site-3.0.0> g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -c -o rate4site.o rate4site.cpp rate4site-3.0.0> sed -e 's|__pkgdatadir__|/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/share/rate4site|g;s|__examplesdir__||g;s|__sysconfdir__|/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/etc|g;s|__bindir__|/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/bin|g;s|__PACKAGE_VERSION__|3.0.0|g' "rate4site.cpp" | \ rate4site-3.0.0> pod2man --utf8 -c 'User Commands' -r "3.0.0" -name RATE4SITE > "rate4site.1" rate4site-3.0.0> g++ -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -o rate4site_doublerep rate4siteOptions.o rate4site.o ../../src/phylogeny/libphylo.a rate4site-3.0.0> g++ -I../../src/phylogeny/ -O2 -std=gnu++98 -fpermissive -w -o rate4site rate4site-rate4siteOptions.o rate4site-rate4site.o ../../src/phylogeny/libphylo.a rate4site-3.0.0> make[2]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' rate4site-3.0.0> make[2]: Entering directory '/build/rate4site-3.0.0' rate4site-3.0.0> make[2]: Leaving directory '/build/rate4site-3.0.0' rate4site-3.0.0> make[1]: Leaving directory '/build/rate4site-3.0.0' rate4site-3.0.0> Running phase: installPhase rate4site-3.0.0> install flags: -j48 SHELL=/nix/store/svx59425zxp552p2b8gm11qj5r09b56i-bash-5.3p15/bin/bash install rate4site-3.0.0> Making install in src/phylogeny rate4site-3.0.0> make[1]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' rate4site-3.0.0> make[2]: Entering directory '/build/rate4site-3.0.0/src/phylogeny' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/mkdir -p '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/lib' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/install -c -m 644 libphylo.a '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/lib' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/mkdir -p '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/include/libphylo' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-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/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/include/libphylo' rate4site-3.0.0> ( cd '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/lib' && ranlib libphylo.a ) rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-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/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/include/libphylo' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-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/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/include/libphylo' rate4site-3.0.0> make[2]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny' rate4site-3.0.0> make[1]: Leaving directory '/build/rate4site-3.0.0/src/phylogeny' rate4site-3.0.0> Making install in src/rate4site rate4site-3.0.0> make[1]: Entering directory '/build/rate4site-3.0.0/src/rate4site' rate4site-3.0.0> make[2]: Entering directory '/build/rate4site-3.0.0/src/rate4site' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/mkdir -p '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/bin' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/mkdir -p '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/share/man/man1' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/install -c rate4site rate4site_doublerep '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/bin' rate4site-3.0.0> /nix/store/xjl7p8dvyk2j53kqf7f43kdj4ypbxz7g-coreutils-9.11/bin/install -c -m 644 rate4site.1 '/nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/share/man/man1' rate4site-3.0.0> make[2]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' rate4site-3.0.0> make[1]: Leaving directory '/build/rate4site-3.0.0/src/rate4site' rate4site-3.0.0> make[1]: Entering directory '/build/rate4site-3.0.0' rate4site-3.0.0> make[2]: Entering directory '/build/rate4site-3.0.0' rate4site-3.0.0> make[2]: Nothing to be done for 'install-exec-am'. rate4site-3.0.0> make[2]: Nothing to be done for 'install-data-am'. rate4site-3.0.0> make[2]: Leaving directory '/build/rate4site-3.0.0' rate4site-3.0.0> make[1]: Leaving directory '/build/rate4site-3.0.0' rate4site-3.0.0> Running phase: fixupPhase rate4site-3.0.0> shrinking RPATHs of ELF executables and libraries in /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0 rate4site-3.0.0> shrinking /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/bin/rate4site rate4site-3.0.0> shrinking /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/bin/rate4site_doublerep rate4site-3.0.0> checking for references to /build/ in /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0... rate4site-3.0.0> gzipping man pages under /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/share/man/ rate4site-3.0.0> patching script interpreter paths in /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0 rate4site-3.0.0> stripping (with command strip and flags -S -p) in /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/lib /nix/store/5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0/bin post-build step Route build to niks3: ok Pushing SBEE-Lab/bioinformatics-toolkits to https://niks3.sjanglab.org time=2026-09-21T21:16:48.205+09:00 level=INFO msg="Uploading 1 paths to niks3.sjanglab.org (6 already cached)" time=2026-09-21T21:16:48.205+09:00 level=INFO msg="Uploading 5gjx3ca2ivdsc4p25dv4dkz34sivadjb-rate4site-3.0.0 (5.2MB)" time=2026-09-21T21:16:49.588+09:00 level=INFO msg="Uploading 1 narinfos" time=2026-09-21T21:16:50.171+09:00 level=INFO msg="Upload complete. (2.056s)"