* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘poolfstat’ ...
** package ‘poolfstat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’
make[1]: Entering directory '/tmp/Rtmpagzs4p/R.INSTALL3c726f24cf5308/poolfstat/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c extract_counts.cpp -o extract_counts.o
extract_counts.cpp: In function ‘Rcpp::IntegerMatrix scan_allele_info(Rcpp::StringVector)’:
extract_counts.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
36 | for(int j=0;j<istring.size();j++){
| ~^~~~~~~~~~~~~~~
extract_counts.cpp: In function ‘Rcpp::NumericMatrix extract_vscan_counts(Rcpp::StringMatrix, int, int)’:
extract_counts.cpp:93:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
93 | while(i < istring.size() && j!=max_idx){
| ~~^~~~~~~~~~~~~~~~
extract_counts.cpp: In function ‘Rcpp::NumericMatrix extract_nonvscan_counts(Rcpp::StringMatrix, Rcpp::IntegerVector, int, int)’:
extract_counts.cpp:165:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
165 | while(i < istring.size() && j!=ad_idx){
| ~~^~~~~~~~~~~~~~~~
extract_counts.cpp:180:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
180 | while(i < ad_string.size() && ad_string[i] != ','){i++;}
| ~~^~~~~~~~~~~~~~~~~~
extract_counts.cpp:190:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
190 | while(i < ad_string.size()){
| ~~^~~~~~~~~~~~~~~~~~
extract_counts.cpp: In function ‘Rcpp::StringMatrix extract_allele_names(Rcpp::StringVector, Rcpp::IntegerMatrix)’:
extract_counts.cpp:262:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
262 | while(k < istring.size()){
| ~~^~~~~~~~~~~~~~~~
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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppProgress/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fast_block_averages.cpp -o fast_block_averages.o
fast_block_averages.cpp: In function ‘Rcpp::NumericVector compute_F4fromF2(Rcpp::NumericVector, int)’:
fast_block_averages.cpp:565:28: warning: unused variable ‘b’ [-Wunused-variable]
565 | int cnt=0, i, j , k, l, b ;
| ^
fast_block_averages.cpp:566:11: warning: unused variable ‘dumval’ [-Wunused-variable]
566 | double dumval;
| ^~~~~~
fast_block_averages.cpp: In function ‘Rcpp::NumericMatrix compute_QmatfromF2samples(Rcpp::NumericMatrix, int, Rcpp::LogicalVector)’:
fast_block_averages.cpp:885:11: warning: unused variable ‘dumval’ [-Wunused-variable]
885 | double dumval ;
| ^~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o poolfstat.so RcppExports.o extract_counts.o fast_block_averages.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmpagzs4p/R.INSTALL3c726f24cf5308/poolfstat/src'
make[1]: Entering directory '/tmp/Rtmpagzs4p/R.INSTALL3c726f24cf5308/poolfstat/src'
make[1]: Leaving directory '/tmp/Rtmpagzs4p/R.INSTALL3c726f24cf5308/poolfstat/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-poolfstat/00new/poolfstat/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘heatmap’ from package ‘stats’ in package ‘poolfstat’
** help
*** installing help indices
converting help for package ‘poolfstat’
finding HTML links ... done
add.leaf html
bjack_cov html
compare.fitted.fstats html
compute.f4ratio html
compute.fstats html
compute.pairwiseFST html
computeFST html
compute_Ddenom html
compute_Ddenom_bjmeans html
compute_F2_bjmeans html
compute_F3fromF2 html
compute_F3fromF2samples html
compute_F4DfromF2samples html
compute_F4fromF2 html
compute_F4fromF2samples html
compute_H1 html
compute_Q2 html
compute_Q_bjmeans html
compute_QmatfromF2samples html
compute_blockDdenom html
countdata-class html
countdata.subset html
extract_allele_names html
extract_nonvscan_counts html
extract_vscan_counts html
find.tree.popset html
find_indelneighbor_idx html
fit.graph html
fitted.graph-class html
fstats-class html
generate.graph.params html
generate.jackknife.blocks html
generateF3names html
generateF4names html
genobaypass2countdata html
genobaypass2pooldata html
genoselestim2pooldata html
genotreemix2countdata html
graph.builder html
graph.params-class html
graph.params2qpGraphFiles html
graph.params2symbolic.fstats html
heatmap-pairwisefst-method html
is.countdata html
is.fitted.graph html
is.fstats html
is.graph.params html
is.pairwisefst html
is.pooldata html
make.example.files html
pairwisefst-class html
plot-fitted.graph-method html
plot-fstats-method html
plot-graph.params-method html
plot-pairwisefst-method html
plot_fstats html
pooldata-class html
pooldata.subset html
pooldata2diyabc html
pooldata2genobaypass html
pooldata2genoselestim html
poolfstat html
poppair_idx html
popsync2pooldata html
randomallele.pca html
rooted.njtree.builder html
scan_allele_info html
show-countdata-method html
show-fitted.graph-method html
show-fstats-method html
show-graph.params-method html
show-pairwisefst-method html
show-pooldata-method html
vcf2pooldata 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 (poolfstat)