* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘RPANDA’ ...
** package ‘RPANDA’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUKary9/R.INSTALL2b7fb1606b5604/RPANDA/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c C_panda-covar-ou.c -o C_panda-covar-ou.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c RPANDA_init.c -o RPANDA_init.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c diversif_lognormal.c -o diversif_lognormal.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c fitness.c -o fitness.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c permute.c -o permute.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o RPANDA.so C_panda-covar-ou.o RPANDA_init.o diversif_lognormal.o fitness.o permute.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUKary9/R.INSTALL2b7fb1606b5604/RPANDA/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUKary9/R.INSTALL2b7fb1606b5604/RPANDA/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpUKary9/R.INSTALL2b7fb1606b5604/RPANDA/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-RPANDA/00new/RPANDA/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘RPANDA’
    finding HTML links ... done
    Anolis.data                             html  
    BGB.examples                            html  
    BICompare                               html  
    Balaenopteridae                         html  
    Calomys                                 html  
    Caprimulgidae                           html  
    Caprimulgidae_ClaDS2                    html  
    Cetacea                                 html  
    Cetacea_clades                          html  
    ClaDS0_example                          html  
    CreateClassObject                       html  
    finding level-2 HTML links ... done

    CreateGeoObject                         html  
    CreateGeoObject_BioGeoBEARS             html  
    CreateGeobyClassObject                  html  
    GIC                                     html  
    InfTemp                                 html  
    JSDt_cluster                            html  
    JSDtree                                 html  
    JSDtree_cluster                         html  
    MPhiFFT                                 html  
    PhenotypicACDC-class                    html  
    PhenotypicADiag-class                   html  
    PhenotypicBM-class                      html  
    PhenotypicDD-class                      html  
    PhenotypicGMM-class                     html  
    PhenotypicModel-class                   html  
    PhenotypicOU-class                      html  
    PhenotypicPM-class                      html  
    Phocoenidae                             html  
    Phyllostomidae                          html  
    Phyllostomidae_genera                   html  
    Posdef                                  html  
    RPANDA-package                          html  
    add.gts                                 html  
    ancestral                               html  
    apply_prob_dtt                          html  
    build_network.BipartiteEvol             html  
    co2                                     html  
    co2_res                                 html  
    coccolithophore                         html  
    createModel                             html  
    createModelCoevolution                  html  
    d13c                                    html  
    define_species.BipartiteEvol            html  
    delineate_phylotypes                    html  
    div.models                              html  
    div.rates                               html  
    fitTipData-methods                      html  
    fitTipData                              html  
    fit_ClaDS                               html  
    fit_ClaDS0                              html  
    fit_bd                                  html  
    fit_bd_backbone                         html  
    fit_bd_backbone_c                       html  
    fit_coal_cst                            html  
    fit_coal_var                            html  
    fit_env                                 html  
    fit_sgd                                 html  
    fit_t_comp                              html  
    fit_t_comp_subgroup                     html  
    fit_t_env                               html  
    fit_t_env_ou                            html  
    fit_t_pl                                html  
    fit_t_standard                          html  
    foraminifera                            html  
    get.comb.shift                          html  
    get.sampling.fractions                  html  
    getDataLikelihood-methods               html  
    getDataLikelihood                       html  
    getMAPS_ClaDS                           html  
    getMAPS_ClaDS0                          html  
    getTipDistribution-methods              html  
    getTipDistribution                      html  
    gic_criterion                           html  
    greenalgae                              html  
    landplant                               html  
    likelihood_bd                           html  
    likelihood_bd_backbone                  html  
    likelihood_coal_cst                     html  
    likelihood_coal_var                     html  
    likelihood_sgd                          html  
    likelihood_subgroup_model               html  
    likelihood_t_DD                         html  
    likelihood_t_DD_geog                    html  
    likelihood_t_MC                         html  
    likelihood_t_MC_geog                    html  
    likelihood_t_env                        html  
    lines.fit_t.env                         html  
    lines.fit_t_env.ou                      html  
    make_gen.BipartiteEvol                  html  
    mantel_test                             html  
    mantel_test_nbpartners                  html  
    modelSelection-methods                  html  
    modelSelection                          html  
    mycorrhizal_network                     html  
    ostracoda                               html  
    paleodiv                                html  
    phyl.pca_pl                             html  
    phylosignal_network                     html  
    phylosignal_sub_network                 html  
    pi_estimator                            html  
    plot.fit_t.env                          html  
    plot.fit_t_env.ou                       html  
    plot_BICompare                          html  
    plot_ClaDS0_chains                      html  
    plot_ClaDS_chains                       html  
    plot_ClaDS_phylo                        html  
    plot_div.BipartiteEvol                  html  
    plot_dtt                                html  
    plot_fit_bd                             html  
    plot_fit_env                            html  
    plot_net.BipartiteEvol                  html  
    plot_phylo_comb                         html  
    plot_phylosignal_sub_network            html  
    plot_prob_dtt                           html  
    plot_spectR                             html  
    prob_dtt                                html  
    radiolaria                              html  
    redalgae                                html  
    remove.model                            html  
    sealevel                                html  
    shift.estimates                         html  
    shifts_cetacea                          html  
    silica                                  html  
    sim.BipartiteEvol                       html  
    sim.convergence.geo                     html  
    sim.divergence.geo                      html  
    sim_ClaDS                               html  
    sim_MCBD                                html  
    sim_env_bd                              html  
    sim_sgd                                 html  
    sim_t_comp                              html  
    sim_t_env                               html  
    sim_t_env_ou                            html  
    sim_t_tworegime                         html  
    simul.comb.shift                        html  
    simulateTipData-methods                 html  
    simulateTipData                         html  
    spectR                                  html  
    spectR_t                                html  
    taxo_cetacea                            html  
    theta_estimator                         html  
** building package indices
** 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
* DONE (RPANDA)