* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘phangorn’ ...
** package ‘phangorn’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-25) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/Rtmp61QSI4/R.INSTALL5876f197b1ac3/phangorn/src'
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c dist.c -o dist.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dupAtomMat.cpp -o dupAtomMat.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fitch64.cpp -o fitch64.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c ml.c -o ml.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c phangorn.c -o phangorn.o
g++-13 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c phangorn_utils.cpp -o phangorn_utils.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sankoff.c -o sankoff.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c sprdist.c -o sprdist.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o phangorn.so RcppExports.o dist.o dupAtomMat.o fitch64.o ml.o phangorn.o phangorn_utils.o sankoff.o sprdist.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp61QSI4/R.INSTALL5876f197b1ac3/phangorn/src'
make[1]: Entering directory '/tmp/Rtmp61QSI4/R.INSTALL5876f197b1ac3/phangorn/src'
make[1]: Leaving directory '/tmp/Rtmp61QSI4/R.INSTALL5876f197b1ac3/phangorn/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-phangorn/00new/phangorn/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘phangorn’
    finding HTML links ... done
    Ancestors                               html  
    CI                                      html  
    Laurasiatherian                         html  
    NJ                                      html  
    SH.test                                 html  
    SOWH.test                               html  
    add.tips                                html  
    finding level-2 HTML links ... done

    addConfidences                          html  
    add_ci                                  html  
    add_edge_length                         html  
    allTrees                                html  
    ancestral.pml                           html  
    as.networx                              html  
    as.phyDat                               html  
    as.splits                               html  
    bab                                     html  
    baseFreq                                html  
    bootstrap.pml                           html  
    chloroplast                             html  
    cladePar                                html  
    coalSpeciesTree                         html  
    codonTest                               html  
    consensusNet                            html  
    cophenetic.networx                      html  
    delta.score                             html  
    densiTree                               html  
    designTree                              html  
    dfactorial                              html  
    discrete.gamma                          html  
    dist.hamming                            html  
    dist.p                                  html  
    distanceHadamard                        html  
    dna2codon                               html  
    getClans                                html  
    hadamard                                html  
    identify.networx                        html  
    image.phyDat                            html  
    lento                                   html  
    mast                                    html  
    maxCladeCred                            html  
    midpoint                                html  
    mites                                   html  
    modelTest                               html  
    neighborNet                             html  
    nni                                     html  
    parsimony                               html  
    phangorn-internal                       html  
    phangorn-package                        html  
    phyDat                                  html  
    plot.networx                            html  
    plotBS                                  html  
    pml                                     html  
    pml.control                             html  
    pml.fit                                 html  
    pmlCluster                              html  
    pmlMix                                  html  
    pmlPart                                 html  
    pml_bb                                  html  
    read.aa                                 html  
    read.nexus.splits                       html  
    read.phyDat                             html  
    reexports                               html  
    simSeq                                  html  
    splitsNetwork                           html  
    superTree                               html  
    transferBootstrap                       html  
    treedist                                html  
    upgma                                   html  
    writeDist                               html  
    yeast                                   html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
packaged installation of ‘phangorn’ as ‘phangorn_2.11.1_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (phangorn)