* installing *source* package ‘poolfstat’ ...
** package ‘poolfstat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/poolfstat/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -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"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c fst_utils.cpp -o fst_utils.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c fstats_utils.cpp -o fstats_utils.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -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 /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:162,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp.h:27,
from simulate.readcounts.utils.cpp:1:
In function 'TO Rcpp::internal::caster(FROM) [with FROM = double; TO = int]',
inlined from 'static Rcpp::internal::element_converter<RTYPE>::target Rcpp::internal::element_converter<RTYPE>::get(const T&) [with T = double; int RTYPE = 13]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/converter.h:34:27,
inlined from 'void Rcpp::Vector<RTYPE, StoragePolicy>::push_back(const T&) [with T = double; int RTYPE = 13; StoragePolicy = Rcpp::PreserveStorage]' at /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:452:45,
inlined from 'Rcpp::IntegerMatrix simureads_mono(int, int, Rcpp::NumericVector, double, int, double, double)' at simulate.readcounts.utils.cpp:252:25:
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/internal/caster.h:30:36: warning: 'lambda_cov' may be used uninitialized [-Wmaybe-uninitialized]
30 | return static_cast<TO>(from) ;
| ^
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++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o poolfstat.so RcppExports.o extract_counts.o fst_utils.o fstats_utils.o simulate.readcounts.utils.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/poolfstat/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/poolfstat/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/poolfstat/src'
installing to /data/gannet/ripley/R/packages/tests-devel/poolfstat.Rcheck/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
** 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)