* 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 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpM1ZeMf/R.INSTALL3834c410d4e39c/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 fst_utils.cpp -o fst_utils.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 fstats_utils.cpp -o fstats_utils.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 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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include/RcppCommon.h:162,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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 /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o poolfstat.so RcppExports.o extract_counts.o fst_utils.o fstats_utils.o simulate.readcounts.utils.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpM1ZeMf/R.INSTALL3834c410d4e39c/poolfstat/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpM1ZeMf/R.INSTALL3834c410d4e39c/poolfstat/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpM1ZeMf/R.INSTALL3834c410d4e39c/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
block_sum html
block_sum2 html
compare.fitted.fstats html
compute.f4ratio html
compute.fstats html
compute.pairwiseFST html
computeFST html
compute_F3fromF2 html
compute_F3fromF2samples html
compute_F4DfromF2samples html
compute_F4fromF2 html
compute_F4fromF2samples html
compute_H1 html
compute_Q2 html
compute_QmatfromF2samples html
compute_blockDdenom html
compute_snpFstAov html
compute_snpHierFstAov html
compute_snpQ1 html
compute_snpQ1onepop html
compute_snpQ1rw html
compute_snpQ2 html
compute_snpQ2onepair html
compute_snpQ2w html
countdata-class html
countdata.subset html
countdata2genobaypass 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
sim.readcounts html
simureads_mono html
simureads_poly html
sliding.windows.fstat 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)