* 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++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFNsZff/R.INSTALL1ad3021fd90101/poolfstat/src' g++-14 -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++-14 -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++-14 -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++-14 -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 '/home/hornik/tmp/scratch/RtmpFNsZff/R.INSTALL1ad3021fd90101/poolfstat/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFNsZff/R.INSTALL1ad3021fd90101/poolfstat/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFNsZff/R.INSTALL1ad3021fd90101/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)