* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘APackOfTheClones’ ...
** this is package ‘APackOfTheClones’ version ‘1.3.0’
** package ‘APackOfTheClones’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmptw6syr/R.INSTALL2c53d36a64d610/APackOfTheClones/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 APOTCPlotHelpers.cpp -o APOTCPlotHelpers.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 AdjustAPOTCHelpers.cpp -o AdjustAPOTCHelpers.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 CloneLinkHelpers.cpp -o CloneLinkHelpers.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 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 cpp_circle_layout.cpp -o cpp_circle_layout.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 exportedUtils.cpp -o exportedUtils.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 reduction_coords.cpp -o reduction_coords.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 repulsion.cpp -o repulsion.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o APackOfTheClones.so APOTCPlotHelpers.o AdjustAPOTCHelpers.o CloneLinkHelpers.o RcppExports.o cpp_circle_layout.o exportedUtils.o reduction_coords.o repulsion.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmptw6syr/R.INSTALL2c53d36a64d610/APackOfTheClones/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmptw6syr/R.INSTALL2c53d36a64d610/APackOfTheClones/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmptw6syr/R.INSTALL2c53d36a64d610/APackOfTheClones/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-APackOfTheClones/00new/APackOfTheClones/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘APackOfTheClones’
    finding HTML links ... done
    APOTCPlot                               html  
    APackOfTheClones-package                html  
    AdjustAPOTC                             html  
    RunAPOTC                                html  
    clonal_expansion_plot                   html  
    combined_pbmc                           html  
    containsApotcRun                        html  
    countCloneSizes                         html  
    count_clone_sizes                       html  
    deleteApotcData                         html  
    getApotcDataIds                         html  
    getLastApotcDataId                      html  
    getReductionCentroids                   html  
    getSharedClones                         html  
    integrate_tcr                           html  
    mergeCloneSizes                         html  
    overlayLegend                           html  
    removeLegend                            html  
    renameApotcRun                          html  
    showCloneHighlight                      html  
    updateApotc                             html  
    vizAPOTC                                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 (APackOfTheClones)