* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘linkcomm’ ...
** package ‘linkcomm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-6) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeFioo3/R.INSTALL1ed73a30bf4a4e/linkcomm/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c OCG_algorithm.c -o OCG_algorithm.o
OCG_algorithm.c: In function ‘getOCGclusters’:
OCG_algorithm.c:568:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  568 |  for(j=0;j<CardMax;j++)
      |  ^~~
OCG_algorithm.c:571:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  571 |   k=0;
      |   ^
OCG_algorithm.c:445:52: warning: variable ‘flag3’ set but not used [-Wunused-but-set-variable]
  445 |   int   NbY, Nl, Long, NewLong, cli, flag1, flag2, flag3;
      |                                                    ^~~~~
OCG_algorithm.c:790:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  790 |     for (j=0; j<i; j++)
      |     ^~~
OCG_algorithm.c:794:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  794 |       for (k=0; k<N; k++) Clas[k]=0;
      |       ^~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c edge_duplicates.cpp -o edge_duplicates.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linkcomm_edgesims.cpp -o linkcomm_edgesims.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linkcomm_edgesims_all.cpp -o linkcomm_edgesims_all.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linkcomm_functions.cpp -o linkcomm_functions.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linkcomm_hclust.cpp -o linkcomm_hclust.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c linkcomm_init.c -o linkcomm_init.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linkcomm_linkdensities.cpp -o linkcomm_linkdensities.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c linkcommhclust_order.cpp -o linkcommhclust_order.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c read_OCG.cpp -o read_OCG.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o linkcomm.so OCG_algorithm.o edge_duplicates.o linkcomm_edgesims.o linkcomm_edgesims_all.o linkcomm_functions.o linkcomm_hclust.o linkcomm_init.o linkcomm_linkdensities.o linkcommhclust_order.o read_OCG.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeFioo3/R.INSTALL1ed73a30bf4a4e/linkcomm/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeFioo3/R.INSTALL1ed73a30bf4a4e/linkcomm/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeFioo3/R.INSTALL1ed73a30bf4a4e/linkcomm/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-linkcomm/00new/linkcomm/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘linkcomm’
    finding HTML links ... done
    LinkDensities                           html  
    corLinkcommCentrality                   html  
    cutDendrogramAt                         html  
    edge.duplicates                         html  
    get.community.overlaps                  html  
    get.shared.nodes                        html  
    getAllNestedComm                        html  
    getClusterRelatedness                   html  
    getCommunityCentrality                  html  
    getCommunityConnectedness               html  
    getCommunityMatrix                      html  
    getEdgesIn                              html  
    getLinkCommunities                      html  
    finding level-2 HTML links ... done

    getNestedHierarchies                    html  
    getNodesIn                              html  
    getOCG.clusters                         html  
    graph.feature                           html  
    human_pp                                html  
    integer.edgelist                        html  
    karate                                  html  
    layout.spencer.circle                   html  
    lesmiserables                           html  
    linkcomm-package                        html  
    linkcomm2clustnsee                      html  
    linkcomm2cytoscape                      html  
    meta.communities                        html  
    newLinkCommsAt                          html  
    numberEdgesIn                           html  
    orderCommunities                        html  
    plot.OCG                                html  
    plot.linkcomm                           html  
    plotLinkCommDend                        html  
    plotLinkCommGraph                       html  
    plotLinkCommMembers                     html  
    plotLinkCommSumm                        html  
    plotLinkCommSummComm                    html  
    plotOCGraph                             html  
    pp_rnapol                               html  
    print.OCG                               html  
    print.linkcomm                          html  
    read.OCG                                html  
    weighted                                html  
    which.communities                       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 (linkcomm)