Install log for 'statgenGWAS'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘statgenGWAS’ ...
** package ‘statgenGWAS’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++-13 -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking for macOS... not found as on Linux
checking for OpenMP... found
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++11
make[1]: Entering directory '/tmp/Rtmp2kGVWB/R.INSTALL114ea31949e1f/statgenGWAS/src'
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c EMMA.cpp -o EMMA.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c codeCharMarkers.cpp -o codeCharMarkers.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fastGLS.cpp -o fastGLS.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c getThr.cpp -o getThr.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c kinship.cpp -o kinship.o
g++-13 -std=gnu++11 -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/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -fopenmp -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c utils.cpp -o utils.o
g++-13 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o statgenGWAS.so EMMA.o RcppExports.o codeCharMarkers.o fastGLS.o getThr.o kinship.o utils.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp2kGVWB/R.INSTALL114ea31949e1f/statgenGWAS/src'
make[1]: Entering directory '/tmp/Rtmp2kGVWB/R.INSTALL114ea31949e1f/statgenGWAS/src'
make[1]: Leaving directory '/tmp/Rtmp2kGVWB/R.INSTALL114ea31949e1f/statgenGWAS/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-statgenGWAS/00new/statgenGWAS/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 ‘statgenGWAS’
    finding HTML links ... done
    codeMarkers                             html  
    dropsData                               html  
    gData                                   html  
    kinship                                 html  
    plot.GWAS                               html  
    plot.gData                              html  
    readPLINK                               html  
    runSingleTraitGwas                      html  
    finding level-2 HTML links ... done

    statgenGWAS-package                     html  
    summary.GWAS                            html  
    summary.gData                           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 (statgenGWAS)