* installing *source* package 'poolfstat' ...
** package 'poolfstat' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp8M6bwb/R.INSTALL154d04e431ddc/poolfstat/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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 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 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 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 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 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 long unsigned int'} [-Wsign-compare]
262 | while(k < istring.size()){
| ~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fst_utils.cpp -o fst_utils.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fstats_utils.cpp -o fstats_utils.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I'D:/RCompile/CRANpkg/lib/4.4/RcppProgress/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulate.readcounts.utils.cpp -o simulate.readcounts.utils.o
simulate.readcounts.utils.cpp: In function 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)':
simulate.readcounts.utils.cpp:230:7: warning: unused variable 'cur_cov' [-Wunused-variable]
230 | int cur_cov,nsnp=0,dum ;
| ^~~~~~~
simulate.readcounts.utils.cpp:231:10: warning: unused variable 'ref_freq' [-Wunused-variable]
231 | double ref_freq,p_nbinom,r_nbinom,lambda_cov ;
| ^~~~~~~~
In file included from D:/RCompile/recent/R-4.4.2/include/R.h:69,
from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/r/headers.h:70,
from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/RcppCommon.h:30,
from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:27,
from simulate.readcounts.utils.cpp:1:
In function 'Rcpp::NumericVector Rcpp::rnbinom(int, double, double)',
inlined from 'Rcpp::IntegerMatrix simureads_poly(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::NumericVector, double, int, double, double, double)' at simulate.readcounts.utils.cpp:87:28:
D:/RCompile/recent/R-4.4.2/include/R_ext/Arith.h:84:33: warning: 'p_nbinom' may be used uninitialized [-Wmaybe-uninitialized]
84 | # define R_FINITE(x) R_finite(x)
| ~~~~~~~~^~~
D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/stats/random/random.h:244:27: note: in expansion of macro 'R_FINITE'
244 | if(!R_FINITE(siz) || !R_FINITE(prob) || siz <= 0 || prob <= 0 || prob > 1)
| ^~~~~~~~
simulate.readcounts.utils.cpp: In function 'Rcpp::IntegerMatrix simureads_poly(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::NumericVector, double, int, double, double, double)':
simulate.readcounts.utils.cpp:57:19: note: 'p_nbinom' was declared here
57 | double ref_freq,p_nbinom,rho ;
| ^~~~~~~~
In file included from D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp.h:83:
In function 'double R::dnbinom(double, double, double, int)',
inlined from 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)' at simulate.readcounts.utils.cpp:267:48:
D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/Rmath.h:129:102: warning: 'p_nbinom' may be used uninitialized [-Wmaybe-uninitialized]
129 | inline double dnbinom(double x, double sz, double pb, int lg) { return ::Rf_dnbinom(x, sz, pb, lg); }
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
simulate.readcounts.utils.cpp: In function 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)':
simulate.readcounts.utils.cpp:231:19: note: 'p_nbinom' was declared here
231 | double ref_freq,p_nbinom,r_nbinom,lambda_cov ;
| ^~~~~~~~
In function 'double R::dnbinom(double, double, double, int)',
inlined from 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)' at simulate.readcounts.utils.cpp:267:48:
D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/Rmath.h:129:102: warning: 'r_nbinom' may be used uninitialized [-Wmaybe-uninitialized]
129 | inline double dnbinom(double x, double sz, double pb, int lg) { return ::Rf_dnbinom(x, sz, pb, lg); }
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
simulate.readcounts.utils.cpp: In function 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)':
simulate.readcounts.utils.cpp:231:28: note: 'r_nbinom' was declared here
231 | double ref_freq,p_nbinom,r_nbinom,lambda_cov ;
| ^~~~~~~~
In function 'double R::qpois(double, double, int, int)',
inlined from 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)' at simulate.readcounts.utils.cpp:259:22:
D:/RCompile/CRANpkg/lib/4.4/Rcpp/include/Rcpp/Rmath.h:144:84: warning: 'lambda_cov' may be used uninitialized [-Wmaybe-uninitialized]
144 | inline double qpois(double p, double lb, int lt, int lg) { return ::Rf_qpois(p, lb, lt, lg); }
| ~~~~~~~~~~^~~~~~~~~~~~~~~
simulate.readcounts.utils.cpp: In function 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)':
simulate.readcounts.utils.cpp:231:37: note: 'lambda_cov' was declared here
231 | double ref_freq,p_nbinom,r_nbinom,lambda_cov ;
| ^~~~~~~~~~
simulate.readcounts.utils.cpp:295:50: warning: 'tmp_readtot' may be used uninitialized [-Wmaybe-uninitialized]
295 | if(countalt>=min_rc && (double(countalt)/double(tmp_readtot))>min_maf){//only bi-allelic according to conditions on min_rc to retain alleles as ture alleles
| ^~~~~~~~~~~~~~~~~~~
simulate.readcounts.utils.cpp:278:23: note: 'tmp_readtot' was declared here
278 | int countalt,naltok,tmp_readtot;
| ^~~~~~~~~~~
g++ -std=gnu++17 -shared -s -static-libgcc -o poolfstat.dll tmp.def RcppExports.o extract_counts.o fst_utils.o fstats_utils.o simulate.readcounts.utils.o -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp8M6bwb/R.INSTALL154d04e431ddc/poolfstat/src'
make[1]: Entering directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp8M6bwb/R.INSTALL154d04e431ddc/poolfstat/src'
make[1]: Leaving directory '/d/temp/2024_12_21_01_50_00_6285/Rtmp8M6bwb/R.INSTALL154d04e431ddc/poolfstat/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-poolfstat/00new/poolfstat/libs/x64
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'poolfstat' as poolfstat_3.0.0.zip
* DONE (poolfstat)