* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘TreeSearch’ ...
** package ‘TreeSearch’ 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++17
make[1]: Entering directory '/tmp/RtmpxmYEnI/R.INSTALL31898623657d03/TreeSearch/src'
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c RMorphy.c -o RMorphy.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c RMorphyUtils.c -o RMorphyUtils.o
g++-13 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c TreeSearch-init.c -o TreeSearch-init.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c fitch.c -o fitch.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c morphy.c -o morphy.o
g++-13 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c morphy_score.cpp -o morphy_score.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c mpl.c -o mpl.o
g++-13 -std=gnu++17 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c rearrange.cpp -o rearrange.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c statedata.c -o statedata.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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TreeTools/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c wagner.c -o wagner.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o TreeSearch.so RMorphy.o RMorphyUtils.o RcppExports.o TreeSearch-init.o fitch.o morphy.o morphy_score.o mpl.o rearrange.o statedata.o wagner.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpxmYEnI/R.INSTALL31898623657d03/TreeSearch/src'
make[1]: Entering directory '/tmp/RtmpxmYEnI/R.INSTALL31898623657d03/TreeSearch/src'
make[1]: Leaving directory '/tmp/RtmpxmYEnI/R.INSTALL31898623657d03/TreeSearch/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-TreeSearch/00new/TreeSearch/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘TreeSearch’
    finding HTML links ... done
    AdditionTree                            html  
    finding level-2 HTML links ... done

    AllSPR                                  html  
    Carter1                                 html  
    CharacterLength                         html  
    ClusterStrings                          html  
    ConcordantInformation                   html  
    Consistency                             html  
    DoubleNNI                               html  
    GapHandler                              html  
    JackLabels                              html  
    Jackknife                               html  
    LengthAdded                             html  
    MaximizeParsimony                       html  
    MinimumLength                           html  
    MorphyErrorCheck                        html  
    MorphyTreeLength                        html  
    MorphyWeights                           html  
    NNI                                     html  
    PhyDat2Morphy                           html  
    PlotCharacter                           html  
    PrepareDataProfile                      html  
    QuartetResolution                       html  
    RandomMorphyTree                        html  
    RandomTreeScore                         html  
    Ratchet                                 html  
    RearrangeEdges                          html  
    SPR                                     html  
    SingleCharMorphy                        html  
    SiteConcordance                         html  
    StepInformation                         html  
    StopUnlessBifurcating                   html  
    Suboptimality                           html  
    SuccessiveApproximations                html  
    TBR                                     html  
    TBRWarning                              html  
    TaxonInfluence                          html  
    TreeLength                              html  
    TreeSearch                              html  
    UnloadMorphy                            html  
    WhenFirstHit                            html  
    WithOneExtraStep                        html  
    cSPR                                    html  
    congreveLamsdellMatrices                html  
    dot-CombineResults                      html  
    dot-GapHandler                          html  
    dot-NonDuplicateRoot                    html  
    dot-UniqueExceptHits                    html  
    inapplicable.datasets                   html  
    is.morphyPtr                            html  
    mpl_apply_tipdata                       html  
    mpl_attach_rawdata                      html  
    mpl_attach_symbols                      html  
    mpl_delete_Morphy                       html  
    mpl_delete_rawdata                      html  
    mpl_first_down_recon                    html  
    mpl_first_up_recon                      html  
    mpl_get_charac_weight                   html  
    mpl_get_gaphandl                        html  
    mpl_get_num_charac                      html  
    mpl_get_num_internal_nodes              html  
    mpl_get_numtaxa                         html  
    mpl_get_symbols                         html  
    mpl_init_Morphy                         html  
    mpl_new_Morphy                          html  
    mpl_second_down_recon                   html  
    mpl_second_up_recon                     html  
    mpl_set_charac_weight                   html  
    mpl_set_num_internal_nodes              html  
    mpl_set_parsim_t                        html  
    mpl_translate_error                     html  
    mpl_update_lower_root                   html  
    mpl_update_tip                          html  
    profiles                                html  
    referenceTree                           html  
    summary.morphyPtr                       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 ‘TreeSearch’ as ‘TreeSearch_1.5.1_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (TreeSearch)