* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘adegenet’ ...
** package ‘adegenet’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpk6cXCi/R.INSTALL2f109b59f48d71/adegenet/src'
gcc-13 -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 GLfunctions.c -o GLfunctions.o
gcc-13 -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 adesub.c -o adesub.o
gcc-13 -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 init.c -o init.o
gcc-13 -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 monmonier-utils.c -o monmonier-utils.o
gcc-13 -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 sharedAll.c -o sharedAll.o
gcc-13 -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 snpbin.c -o snpbin.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o adegenet.so GLfunctions.o adesub.o init.o monmonier-utils.o sharedAll.o snpbin.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpk6cXCi/R.INSTALL2f109b59f48d71/adegenet/src'
make[1]: Entering directory '/tmp/Rtmpk6cXCi/R.INSTALL2f109b59f48d71/adegenet/src'
make[1]: Leaving directory '/tmp/Rtmpk6cXCi/R.INSTALL2f109b59f48d71/adegenet/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adegenet/00new/adegenet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘adegenet’
    finding HTML links ... done
    AIC.snapclust                           html  
    AICc                                    html  
    BIC.snapclust                           html  
    H3N2                                    html  
    HWE                                     html  
    Hs                                      html  
    Hs.test                                 html  
    KIC                                     html  
    SNPbin                                  html  
    accessors                               html  
    adegenet.package                        html  
    as-methods                              html  
    as.SNPbin                               html  
    as.genlight                             html  
    ascore                                  html  
    auxil                                   html  
    chooseCN                                html  
    colorplot                               html  
    compoplot                               html  
    coords.monmonier                        html  
    dapc                                    html  
    dapcGraphics                            html  
    dapcIllus                               html  
    df2genind                               html  
    finding level-2 HTML links ... done

    dist.genpop                             html  
    doc_C_routines                          html  
    eHGDP                                   html  
    export_to_mvmapper                      html  
    fasta2DNAbin                            html  
    fasta2genlight                          html  
    find.clusters                           html  
    gengraph                                html  
    genind                                  html  
    genind2df                               html  
    genind2genpop                           html  
    genlight                                html  
    genpop                                  html  
    glAux                                   html  
    glPca                                   html  
    glPlot                                  html  
    glSim                                   html  
    haploGen                                html  
    hierarchy-methods                       html  
    hybridize                               html  
    hybridtoy                               html  
    import2genind                           html  
    inbreeding                              html  
    isPoly                                  html  
    loadingplot                             html  
    makefreq                                html  
    microbov                                html  
    minorAllele                             html  
    monmonier                               html  
    mutations                               html  
    nancycats                               html  
    new.genind                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adegenet/00new/adegenet/help/genind.html
    new.genpop                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-adegenet/00new/adegenet/help/genpop.html
    old2new                                 html  
    pairDist                                html  
    population-methods                      html  
    propShared                              html  
    propTyped                               html  
    read.PLINK                              html  
    read.fstat                              html  
    read.genepop                            html  
    read.genetix                            html  
    read.snp                                html  
    read.structure                          html  
    repool                                  html  
    rupica                                  html  
    scaleGen                                html  
    selpopsize                              html  
    seploc                                  html  
    seppop                                  html  
    seqTrack                                html  
    sequences                               html  
    servers                                 html  
    showmekittens                           html  
    sim2pop                                 html  
    snapclust                               html  
    snapclust.choose.k                      html  
    snpposi                                 html  
    snpzip                                  html  
    spca                                    html  
    spca.rtests                             html  
    spcaIllus                               html  
    spca_randtest                           html  
    strata-methods                          html  
    swallowtails                            html  
    tab                                     html  
    truenames                               html  
    virClasses                              html  
    web                                     html  
    xvalDapc                                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
* creating tarball
packaged installation of ‘adegenet’ as ‘adegenet_2.1.10_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (adegenet)