downloading reverse dependencies ‘RcppPlanc’, ‘smer’ trying URL 'file:///data/Repositories/CRAN/src/contrib/RcppPlanc_2.0.13.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/smer_0.0.2.tar.gz' installing dependencies ‘genio’, ‘hdf5r.Extra’, ‘HighFive’, ‘mvMAPIT’ also installing the dependencies ‘FMStable’, ‘easy.utils’, ‘harmonicmeanp’, ‘RcppSpdlog’ begin installing package ‘FMStable’ begin installing package ‘easy.utils’ begin installing package ‘RcppSpdlog’ begin installing package ‘HighFive’ begin installing package ‘genio’ * installing *source* package ‘HighFive’ ... ** this is package ‘HighFive’ version ‘3.3.0’ ** using staged installation ** inst ** help *** installing help indices ** building package indices ** 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 (HighFive) * installing *source* package ‘FMStable’ ... ** this is package ‘FMStable’ version ‘0.1-4’ ** package ‘FMStable’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpgq7oPs/R.INSTALLbbebab713c18/FMStable/src' gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c FMStable.c -o FMStable.o gcc-15 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o FMStable.so FMStable.o init.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpgq7oPs/R.INSTALLbbebab713c18/FMStable/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-FMStable/00new/FMStable/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (FMStable) begin installing package ‘harmonicmeanp’ * installing *source* package ‘easy.utils’ ... ** this is package ‘easy.utils’ version ‘0.1.0’ ** package ‘easy.utils’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (easy.utils) begin installing package ‘hdf5r.Extra’ * installing *source* package ‘harmonicmeanp’ ... ** this is package ‘harmonicmeanp’ version ‘3.0.1’ ** package ‘harmonicmeanp’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (harmonicmeanp) * installing *source* package ‘hdf5r.Extra’ ... ** this is package ‘hdf5r.Extra’ version ‘0.1.0’ ** package ‘hdf5r.Extra’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (hdf5r.Extra) * installing *source* package ‘genio’ ... ** this is package ‘genio’ version ‘1.1.2’ ** package ‘genio’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpShwYgm/R.INSTALLbbebe4605eed2/genio/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c count_lines_cpp.cpp -o count_lines_cpp.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_bed_cpp.cpp -o read_bed_cpp.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c write_bed_cpp.cpp -o write_bed_cpp.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o genio.so RcppExports.o count_lines_cpp.o read_bed_cpp.o write_bed_cpp.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpShwYgm/R.INSTALLbbebe4605eed2/genio/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-genio/00new/genio/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (genio) * installing *source* package ‘RcppSpdlog’ ... ** this is package ‘RcppSpdlog’ version ‘0.0.23’ ** package ‘RcppSpdlog’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNAQG77/R.INSTALLbbec03d80d0f8/RcppSpdlog/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c exampleRsink.cpp -o exampleRsink.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:30, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Rcpp:21, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Light:25, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Lighter:25, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Lightest:26, from ../inst/include/RcppSpdlog_types.h:4, from ../inst/include/RcppSpdlog:21, from exampleRsink.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’ 27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c formatter.cpp -o formatter.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:30, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Rcpp:21, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Light:25, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Lighter:25, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Lightest:26, from ../inst/include/RcppSpdlog_types.h:4, from ../inst/include/RcppSpdlog:21, from formatter.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’ 27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interface.cpp -o interface.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:30, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Rcpp:21, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Light:25, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Lighter:25, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/Lightest:26, from ../inst/include/RcppSpdlog_types.h:4, from ../inst/include/RcppSpdlog:21, from interface.cpp:7: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’ 27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o RcppSpdlog.so RcppExports.o exampleRsink.o formatter.o interface.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNAQG77/R.INSTALLbbec03d80d0f8/RcppSpdlog/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RcppSpdlog/00new/RcppSpdlog/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (RcppSpdlog) begin installing package ‘mvMAPIT’ * installing *source* package ‘mvMAPIT’ ... ** this is package ‘mvMAPIT’ version ‘2.0.3’ ** package ‘mvMAPIT’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpITb3hy/R.INSTALLbc07d45d8498c/mvMAPIT/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c MAPIT.cpp -o MAPIT.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c gsm/gsm.cpp -o gsm/gsm.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c logging/log.cpp -o logging/log.o logging/log.cpp: In function ‘std::string phenotype_vector_to_string(const std::vector >&)’: logging/log.cpp:6:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6 | for (int i = 1; i < v.size(); i++) { | ~~^~~~~~~~~~ logging/log.cpp: In function ‘std::string vector_to_string(const arma::vec&)’: logging/log.cpp:15:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 15 | for (int i = 1; i < v.n_elem; i++) { | ~~^~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mapit/davies.cpp -o mapit/davies.o mapit/davies.cpp: In function ‘arma::mat davies_routine(const arma::mat&, const arma::mat&, const arma::mat&, const std::vector >&)’: mapit/davies.cpp:16:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 16 | for (int i = 0; i < q.n_cols; i++) { | ~~^~~~~~~~~~ mapit/davies.cpp: In function ‘arma::vec davies_routine_vec(const arma::mat&, const arma::mat&, const arma::vec&, const std::vector >&)’: mapit/davies.cpp:36:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 36 | for (int i = 0; i < q_sub.n_elem; i++) { | ~~^~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mapit/normal.cpp -o mapit/normal.o mapit/normal.cpp: In function ‘arma::mat normal_pvalues(const arma::mat&, const arma::mat&)’: mapit/normal.cpp:23:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 23 | for (int j = 0; j < variance_estimate.n_cols; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ mapit/normal.cpp:24:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 24 | for (int i = 0; i < variance_estimate.n_rows; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mapit/projection.cpp -o mapit/projection.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mapit/pve.cpp -o mapit/pve.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mapit/util.cpp -o mapit/util.o mapit/util.cpp: In function ‘arma::vec remove_first_element(const arma::vec&)’: mapit/util.cpp:17:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare] 17 | for (int i = 1; i < vector.size(); i++) { | ~~^~~~~~~~~~~~~~~ mapit/util.cpp: In function ‘std::vector > matrix_to_vector_of_rows(const arma::mat&)’: mapit/util.cpp:37:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 37 | for (int i = 0; i < matrix.n_rows; ++i) { | ~~^~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mqs/mqs.cpp -o mqs/mqs.o mqs/mqs.cpp: In function ‘arma::mat compute_h_matrix(const arma::mat&, const std::vector >&)’: mqs/mqs.cpp:113:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 113 | for (int i = 0; i < matrices.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mqs/mqs.cpp: In function ‘arma::mat compute_v_matrix(const arma::vec&, const std::vector >&)’: mqs/mqs.cpp:129:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 129 | for (int i = 0; i < matrices.size(); i++) { | ~~^~~~~~~~~~~~~~~~~ mqs/mqs.cpp: In function ‘arma::vec compute_variance_delta(const std::vector >&, const arma::mat&, const arma::mat&, const std::vector >&)’: mqs/mqs.cpp:171:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare] 171 | for (int k = 0; k < delta.n_cols; k++) { | ~~^~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-compare-to-original-mapit.cpp -o tests/test-compare-to-original-mapit.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-davies.cpp -o tests/test-davies.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-gsm.cpp -o tests/test-gsm.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-log.cpp -o tests/test-log.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-mqs.cpp -o tests/test-mqs.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-normal.cpp -o tests/test-normal.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-projection.cpp -o tests/test-projection.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-pve.cpp -o tests/test-pve.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-runner.cpp -o tests/test-runner.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I. -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppSpdlog/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/testthat/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tests/test-util.cpp -o tests/test-util.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o mvMAPIT.so MAPIT.o RcppExports.o gsm/gsm.o logging/log.o mapit/davies.o mapit/normal.o mapit/projection.o mapit/pve.o mapit/util.o mqs/mqs.o tests/test-compare-to-original-mapit.o tests/test-davies.o tests/test-gsm.o tests/test-log.o tests/test-mqs.o tests/test-normal.o tests/test-projection.o tests/test-pve.o tests/test-runner.o tests/test-util.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpITb3hy/R.INSTALLbc07d45d8498c/mvMAPIT/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mvMAPIT/00new/mvMAPIT/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mvMAPIT) checking HighFive_3.3.0.tar.gz ... checking smer_0.0.2.tar.gz ... checking RcppPlanc_2.0.13.tar.gz ... Depends: Timings: user system elapsed HighFive 10.514 2.205 14.128 Results: Check status summary: OK Source packages 1 Reverse depends 2 Check results summary: HighFive ... OK rdepends_RcppPlanc ... OK rdepends_smer ... OK