Install log for 'scellpam'

* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘scellpam’ ...
** package ‘scellpam’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpHt3ORp/R.INSTALL157065ff0ff6f/scellpam/src'
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c biodatatojmat.cpp -o biodatatojmat.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c buildresults.cpp -o buildresults.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c csvtojmat.cpp -o csvtojmat.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c debugpar.cpp -o debugpar.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c diftimehelper.cpp -o diftimehelper.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dissimmat.cpp -o dissimmat.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dissimmat_full.cpp -o dissimmat_full.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c dissimmat_sparse.cpp -o dissimmat_sparse.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fastpam.cpp -o fastpam.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c filternames.cpp -o filternames.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c filtersil.cpp -o filtersil.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c fullmatrix.cpp -o fullmatrix.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c jmatrix.cpp -o jmatrix.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c jmatrixaux.cpp -o jmatrixaux.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mainfastpam.cpp -o mainfastpam.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matgetcols.cpp -o matgetcols.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matgetdiag.cpp -o matgetdiag.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matgetrows.cpp -o matgetrows.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matinfo.cpp -o matinfo.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matmetadata.cpp -o matmetadata.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c matwrite.cpp -o matwrite.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c memhelper.cpp -o memhelper.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c silhouette.cpp -o silhouette.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sparsematrix.cpp -o sparsematrix.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c symmetricmatrix.cpp -o symmetricmatrix.o
g++-13 -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  -I../inst/include -fpic  -g -O2 -Wall -pedantic -mtune=native   -c threadhelper.cpp -o threadhelper.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o scellpam.so RcppExports.o biodatatojmat.o buildresults.o csvtojmat.o debugpar.o diftimehelper.o dissimmat.o dissimmat_full.o dissimmat_sparse.o fastpam.o filternames.o filtersil.o fullmatrix.o jmatrix.o jmatrixaux.o mainfastpam.o matgetcols.o matgetdiag.o matgetrows.o matinfo.o matmetadata.o matwrite.o memhelper.o silhouette.o sparsematrix.o symmetricmatrix.o threadhelper.o -lpthread -O2 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpHt3ORp/R.INSTALL157065ff0ff6f/scellpam/src'
make[1]: Entering directory '/tmp/RtmpHt3ORp/R.INSTALL157065ff0ff6f/scellpam/src'
make[1]: Leaving directory '/tmp/RtmpHt3ORp/R.INSTALL157065ff0ff6f/scellpam/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-scellpam/00new/scellpam/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘scellpam’
    finding HTML links ... done
    ApplyPAM                                html  
    BuildAbundanceMatrix                    html  
    CalcAndWriteDissimilarityMatrix         html  
    CalculateSilhouette                     html  
    ClassifAsDataFrame                      html  
    CsvToJMat                               html  
    FilterBySilhouetteQuantile              html  
    FilterBySilhouetteThreshold             html  
    FilterJMatByName                        html  
    GetJCol                                 html  
    GetJColByName                           html  
    GetJColNames                            html  
    GetJManyCols                            html  
    GetJManyColsByNames                     html  
    GetJManyRows                            html  
    GetJManyRowsByNames                     html  
    GetJNames                               html  
    GetJRow                                 html  
    GetJRowByName                           html  
    GetJRowNames                            html  
    GetSeuratGroups                         html  
    GetSubdiag                              html  
    GetTD                                   html  
    JMatInfo                                html  
    JMatToCsv                               html  
    JWriteBin                               html  
    NumSilToClusterSil                      html  
    SceToJMat                               html  
    ScellpamSetDebug                        html  
    dgCMatToJMat                            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 (scellpam)