* 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-13 (Debian 13.2.0-13) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/RtmpZmvadd/R.INSTALL2fc459184415e7/linkcomm/src'
gcc-13 -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++-13 -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++-13 -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++-13 -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++-13 -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++-13 -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-13 -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++-13 -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++-13 -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++-13 -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++-13 -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 '/tmp/RtmpZmvadd/R.INSTALL2fc459184415e7/linkcomm/src'
make[1]: Entering directory '/tmp/RtmpZmvadd/R.INSTALL2fc459184415e7/linkcomm/src'
make[1]: Leaving directory '/tmp/RtmpZmvadd/R.INSTALL2fc459184415e7/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)