* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Mega2R’ ...
** package ‘Mega2R’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgJfR2c/R.INSTALL28b3d168bc4a2c/Mega2R/src'
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c getgenotypes.cpp -o getgenotypes.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Mega2R.so RcppExports.o getgenotypes.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgJfR2c/R.INSTALL28b3d168bc4a2c/Mega2R/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgJfR2c/R.INSTALL28b3d168bc4a2c/Mega2R/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgJfR2c/R.INSTALL28b3d168bc4a2c/Mega2R/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Mega2R/00new/Mega2R/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘Mega2R’
    finding HTML links ... done
    DOSKAT                                  html  
    DOfamSKATRC                             html  
    DOpedgene                               html  
    Mega2ENVGenABEL                         html  
    Mega2GenABEL                            html  
    Mega2GenABELClean                       html  
    Mega2GenABELtst                         html  
    Mega2R-TBLS                             html  
    Mega2R-TBLSFilter                       html  
    Mega2R-package                          html  
    Mega2RVersion                           html  
    Mega2SKAT                               html  
    Mega2VCF                                html  
    Mega2famSKATRC                          html  
    Mega2gdsfmt                             html  
    finding level-2 HTML links ... done

    Mega2pedgene                            html  
    applyFnToGenes                          html  
    applyFnToMarkers                        html  
    applyFnToRanges                         html  
    clean_mega2rtutorial_data               html  
    computeDosage                           html  
    dbmega2_import                          html  
    dmpPed                                  html  
    dump_mega2rtutorial_data                html  
    getAlleles                              html  
    getgenotype_person                      html  
    getgenotypes                            html  
    getgenotypes_R                          html  
    getgenotypesdos                         html  
    getgenotypesgenabel                     html  
    getgenotypesraw                         html  
    init_SKAT                               html  
    init_famSKATRC                          html  
    init_pedgene                            html  
    mkAlleles                               html  
    mkGenABELcoding                         html  
    mkGenABELgenotype                       html  
    mkGenABELphenotype                      html  
    mkGenABELtfam                           html  
    mkGenABELtped                           html  
    mkMarkers                               html  
    mkVCFfam                                html  
    mkVCFfreq                               html  
    mkVCFhdr                                html  
    mkVCFmap                                html  
    mkVCFpen                                html  
    mkVCFphe                                html  
    mk_markers_with_skip                    html  
    mk_unified_genotype_table               html  
    mkfam                                   html  
    mkphenotype                             html  
    read.Mega2DB                            html  
    resetMega2ENV                           html  
    setAnnotations                          html  
    setRanges                               html  
    setfam                                  html  
    showMapNames                            html  
    showMega2ENV                            html  
    showPhenoNames                          html  
    uniqueFamMember                         html  
    where_mega2rtutorial_data               html  
** 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
* DONE (Mega2R)