* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘hsphase’ ...
** this is package ‘hsphase’ version ‘3.0.0’
** package ‘hsphase’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-12) 14.3.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpEBAI1M/R.INSTALL25dbc92d176fdc/hsphase/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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c FastDist.cpp -o FastDist.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c FillGap.cpp -o FillGap.o
FillGap.cpp: In function ‘int fillGapFunction(int*, int*, int*)’:
FillGap.cpp:24:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
24 | for (size_t j = 0; j < *length; j++)
| ~~^~~~~~~~~
FillGap.cpp:33:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
33 | for (size_t j = 0; j < gapLength; j++)
| ~~^~~~~~~~~~~
FillGap.cpp:51:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
51 | for (size_t j = *length - 1; j > (*length-gapLength - 1); j--)
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~
FillGap.cpp:72:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
72 | for (size_t j = i; j < (*length - 1); j++)
| ~~^~~~~~~~~~~~~~~
FillGap.cpp:81:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
81 | for (size_t j = i; j < i + (gapLength / 2); j++)
| ~~^~~~~~~~~~~~~~~~~~~~~
FillGap.cpp:87:64: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
87 | for (size_t j = i + (gapLength / 2); j < i + gapLength; j++)
| ~~^~~~~~~~~~~~~~~
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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c FixBothStrand.cpp -o FixBothStrand.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c MAF.cpp -o MAF.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Ohd.cpp -o Ohd.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c SwitchAdd.cpp -o SwitchAdd.o
SwitchAdd.cpp: In function ‘SEXPREC* switchAdd(SEXP, SEXP, SEXP)’:
SwitchAdd.cpp:29:9: warning: unused variable ‘minLength’ [-Wunused-variable]
29 | int minLength = as<int>(minlength);
| ^~~~~~~~~
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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c SwitchDetector.cpp -o SwitchDetector.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c TypeConversion.cpp -o TypeConversion.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c block.cpp -o block.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c block4Phase.cpp -o block4Phase.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c co.cpp -o co.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c diag.cpp -o diag.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c fixRotation.cpp -o fixRotation.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c hsp.cpp -o hsp.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ibdcluster.cpp -o ibdcluster.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c main.cpp -o main.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c memory.cpp -o memory.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mhMat.cpp -o mhMat.o
mhMat.cpp: In member function ‘void mhMat::keep2MostFrequent()’:
mhMat.cpp:102:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
102 | for (int j = 0; j < groupResult.size(); ++j)
| ~~^~~~~~~~~~~~~~~~~~~~
mhMat.cpp:146:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
146 | if (*it != itr->second && *it != itr2->second)
| ~~~~^~~~~~~~~~~~~~
mhMat.cpp:146:63: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
146 | if (*it != itr->second && *it != itr2->second)
| ~~~~^~~~~~~~~~~~~~~
mhMat.cpp:150:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
150 | else if (*it == itr->second)
| ~~~~^~~~~~~~~~~~~~
mhMat.cpp:154:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
154 | else if (*it == itr2->second)
| ~~~~^~~~~~~~~~~~~~~
mhMat.cpp:161:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
161 | if (*it != itr->second)
| ~~~~^~~~~~~~~~~~~~
mhMat.cpp:165:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
165 | else if (*it == itr->second)
| ~~~~^~~~~~~~~~~~~~
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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c oh.cpp -o oh.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ohg.cpp -o ohg.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ohp.cpp -o ohp.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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c swDetect.cpp -o swDetect.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o hsphase.so FastDist.o FillGap.o FixBothStrand.o MAF.o Ohd.o SwitchAdd.o SwitchDetector.o TypeConversion.o block.o block4Phase.o co.o diag.o fixRotation.o hsp.o ibdcluster.o main.o memory.o mhMat.o oh.o ohg.o ohp.o swDetect.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpEBAI1M/R.INSTALL25dbc92d176fdc/hsphase/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpEBAI1M/R.INSTALL25dbc92d176fdc/hsphase/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpEBAI1M/R.INSTALL25dbc92d176fdc/hsphase/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-hsphase/00new/hsphase/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘hsphase’
finding HTML links ... done
addSwitch html
aio html
bmh html
co html
cs html
dot-fastdist html
dot-fillGap html
dot-fixBothStrand html
dot-fixRotation html
dot-hblock html
dot-ibdCluster html
dot-maf html
dot-o2tH html
dot-phfnoGenotype html
dot-prCalus html
dot-prManual html
dot-prSimple html
dot-ptr2por html
dot-rpohhsphase html
dot-simulateHalfsib html
fixSW html
genotypes html
groupMatSingle html
hbp html
hh html
hsphase-package html
hss html
imageplot html
impute html
map html
ohd html
ohg html
ohplot html
para html
pedigree html
pedigreeNaming html
phf html
pm html
pogc html
readGenotype html
recombinations html
rplot html
rpoh html
ssp html
switchDetector 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 (hsphase)