* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘SNPkit’ ...
** this is package ‘SNPkit’ version ‘0.1.0’
** package ‘SNPkit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbeVDeC/R.INSTALL37b62c3f4608ca/SNPkit/src'
g++-15 -std=gnu++20 -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++-15 -std=gnu++20 -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 fimpute_cpp.cpp -o fimpute_cpp.o
g++-15 -std=gnu++20 -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 read_fimpute.cpp -o read_fimpute.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o SNPkit.so RcppExports.o fimpute_cpp.o read_fimpute.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbeVDeC/R.INSTALL37b62c3f4608ca/SNPkit/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbeVDeC/R.INSTALL37b62c3f4608ca/SNPkit/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbeVDeC/R.INSTALL37b62c3f4608ca/SNPkit/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-SNPkit/00new/SNPkit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘SNPkit’
    finding HTML links ... done
    FImputeExport-class                     html  
    FImputeRunner-class                     html  
    FImputeRunner                           html  
    SNPFileConfig-class                     html  
    SNPImportList-class                     html  
    SNPkit                                  html  
    Subset                                  html  
    as_snpmatrix                            html  
    cbind_SnpMatrix                         html  
    check.call.rate                         html  
    check.ibs                               html  
    check.identical.samples                 html  
    check.identical.samples.by.block        html  
    check.mendelian.inconsistencies         html  
    check.mendelian.inconsistencies.pair    html  
    check.sample.call.rate                  html  
    check.sample.heterozygosity             html  
    check.snp.chromo                        html  
    check.snp.hwe                           html  
    check.snp.hwe.chi2                      html  
    check.snp.maf                           html  
    check.snp.mgf                           html  
    check.snp.monomorf                      html  
    check.snp.no.position                   html  
    check.snp.same.position                 html  
    combineSNPData                          html  
    doPCA                                   html  
    exploratory.plots                       html  
    genoToDF                                html  
    get.correl.fc                           html  
    get.gender                              html  
    get.hwe.chi2                            html  
    getGeno                                 html  
    ibs.pair                                html  
    importAllGenos                          html  
    importFImputeResults                    html  
    import_geno_list                        html  
    pairs2sets                              html  
    plotPCAgroups                           html  
    print.summary.SNPDataLong               html  
    qcSNPs                                  html  
    qcSamples                               html  
    qc_header                               html  
    rbindSnpFlexible                        html  
    rbind_SnpMatrix                         html  
    read.fimpute                            html  
    runAnticlusteringPCA                    html  
    runFImpute                              html  
    run_admixture                           html  
    saveFImpute                             html  
    saveFImputeRaw                          html  
    savePlink                               html  
    summary-SNPDataLong-method              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
* DONE (SNPkit)