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### Running command:
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### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL miloR
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'miloR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function 'arma::mat initialiseG(Rcpp::List, arma::vec)':
computeMatrices.cpp:135:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
135 | for(unsigned long k=0; k < stot; k++){
| ~~^~~~~~
computeMatrices.cpp:143:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
143 | for(int l=0; l < q; l++){
| ~~^~~
computeMatrices.cpp: In function 'arma::mat invGmat(Rcpp::List, arma::vec)':
computeMatrices.cpp:327:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
327 | for(unsigned long k=0; k < stot; k++){
| ~~^~~~~~
computeMatrices.cpp:335:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
335 | for(int l=0; l < q; l++){
| ~~^~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp: In function 'Rcpp::List fitGeneticPLGlmm(const arma::mat&, const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitGeneticPLGlmm.cpp:197:10: warning: unused variable '_phi_est' [-Wunused-variable]
197 | bool _phi_est = true; // control if we re-estimate phi or not
| ^~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp: In function 'Rcpp::List fitPLGlmm(const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitPLGlmm.cpp:177:10: warning: unused variable '_phi_est' [-Wunused-variable]
177 | bool _phi_est = true; // control if we re-estimate phi or not
| ^~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inference.cpp -o inference.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c multiP.cpp -o multiP.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c paramEst.cpp -o paramEst.o
paramEst.cpp:46: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
46 | #pragma omp parallel for
|
paramEst.cpp:50: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
50 | #pragma omp parallel for
|
paramEst.cpp:257: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
257 | #pragma omp parallel for private(i, j, _ycovij)
|
paramEst.cpp:301: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
301 | #pragma omp parallel for private(i, j, _ycovij)
|
paramEst.cpp:380: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
380 | #pragma omp parallel for private(i, j, _ycovij)
|
paramEst.cpp:489: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
489 | #pragma omp parallel for private(i, j, _ycovij)
|
paramEst.cpp:714: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
714 | #pragma omp parallel for reduction(+:temp_value)
|
paramEst.cpp:729: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
729 | #pragma omp parallel for reduction(+:temp_value)
|
paramEst.cpp: In function 'arma::vec sigmaScoreREML_arma(const Rcpp::List&, const arma::vec&, const arma::mat&, const arma::vec&, const arma::mat&, const arma::mat&)':
paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
29 | double rhs = 0.5 * mid1[0, 0];
| ^
paramEst.cpp: In function 'arma::vec estHasemanElstonGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
258 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:259:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
259 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable]
252 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable]
252 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable]
253 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElston(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&)':
paramEst.cpp:302:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
302 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:303:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
303 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable]
294 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable]
294 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable]
295 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrained(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:381:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
381 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:382:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
382 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable]
373 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable]
373 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable]
374 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:490:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
490 | for (int i = 0; i < n; i++) {
| ~~^~~
paramEst.cpp:491:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
491 | for (int j = i; j < n; j++) {
| ~~^~~
paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable]
484 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable]
484 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable]
485 | double _ycovij; // Declare temp_value
| ^~~~~~~
paramEst.cpp: In function 'arma::vec nnlsSolve(const arma::mat&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:549:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
549 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:559:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
559 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:587:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
587 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:623:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
623 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable]
543 | unsigned int inner_count = 0;
| ^~~~~~~~~~~
paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable]
544 | unsigned int outer_count = 0;
| ^~~~~~~~~~~
paramEst.cpp: In function 'arma::mat vectoriseZ(const arma::mat&, const Rcpp::List&, const arma::mat&)':
paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable]
688 | int j, k, l, a;
| ^
paramEst.cpp: In function 'double phiLineSearch(double, double, double, const int&, const arma::vec&, const arma::mat&, double, const arma::vec&, const arma::vec&, const arma::vec&)':
paramEst.cpp:866:12: warning: unused variable 'half_logli' [-Wunused-variable]
866 | double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
| ^~~~~~~~~~
paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable]
871 | bool comp_vals = false;
| ^~~~~~~~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pseudovarPartial.cpp -o pseudovarPartial.o
pseudovarPartial.cpp:60: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
60 | #pragma omp parallel for reduction(+:temp_value)
|
pseudovarPartial.cpp: In function 'Rcpp::List pseudovarPartial_P(Rcpp::List, const arma::mat&)':
pseudovarPartial.cpp:58:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
58 | for (int j = 0; j < n; j++) {
| ~~^~~
pseudovarPartial.cpp:61:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
61 | for (int k = 0; k < n; k++) {
| ~~^~~
pseudovarPartial.cpp:64:32: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
64 | for(int a=0; a < n; a++){
| ~~^~~
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -std=c++11 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -s -static-libgcc -o miloR.dll tmp.def RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-miloR/00new/miloR/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'graph' in package 'miloR'
** 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
* DONE (miloR)