* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘PAC’ ...
** package ‘PAC’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
using C++11
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4L7gsg/R.INSTALL352b4914411ba/PAC/src'
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bsp.cc -o bsp.o
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pac-wrapper.cc -o pac-wrapper.o
pac-wrapper.cc: In function ‘Rcpp::NumericMatrix BSPLeaveCenterCpp(Rcpp::NumericMatrix, SEXP, SEXP)’:
pac-wrapper.cc:69:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
69 | for(int j = 0; j < T.leafctr[0].size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~
gcc-14 -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 -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c util.cc -o util.o
g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o PAC.so RcppExports.o bsp.o pac-wrapper.o registerDynamicSymbol.o util.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4L7gsg/R.INSTALL352b4914411ba/PAC/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4L7gsg/R.INSTALL352b4914411ba/PAC/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4L7gsg/R.INSTALL352b4914411ba/PAC/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-PAC/00new/PAC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘PAC’
finding HTML links ... done
BSPLeaveCenter html
JaccardSM html
MAN html
MINetworkPlot_topEdges html
MINetwork_matrix_topEdges html
MINetwork_simplified_topEdges html
PAC html
aggregateData html
annotateClades html
annotationMatrix_withSubpopProp html
constellationPlot html
fmeasure html
getAverageSpreadOf2SubpopClades html
getExtraneousCladeSubpopulations html
getRepresentativeNetworks html
heatmapInput html
outputNetworks_topEdges_matrix html
outputRepresentativeNetworks_topEdges html
recordWithinClusterSpread html
refineSubpopulationLabels html
renamePrunedSubpopulations html
runElbowPointAnalysis html
samplePass 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 (PAC)