/usr/bin/tar: sommer/DESCRIPTION: time stamp 2025-02-03 19:36:10 is 5707.405696905 s in the future downloading reverse dependencies ... downloading gpcp_0.1.0.tar.gz ... ok downloading IPLGP_2.0.5.tar.gz ... ok downloading lmDiallel_1.0.1.tar.gz ... ok downloading mlmm.gwas_1.0.6.tar.gz ... ok downloading pcgen_0.2.0.tar.gz ... ok downloading statgenGWAS_1.0.10.tar.gz ... ok downloading statgenQTLxT_1.0.2.tar.gz ... ok downloading lucid_1.8.tar.gz ... ok downloading MoBPS_1.6.64.tar.gz ... ok installing dependencies ‘AGHmatrix’, ‘alstructure’, ‘BGLR’, ‘cPCG’, ‘doMPI’, ‘EMMREML’, ‘NAM’, ‘optiSel’, ‘phylogram’, ‘sommer’, ‘statgenGWAS’, ‘VariantAnnotation’ Warning: package ‘alstructure’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘HaploSim’, ‘cccp’, ‘nadiv’, ‘pedigree’, ‘optiSolve’ begin installing package ‘HaploSim’ begin installing package ‘nadiv’ begin installing package ‘cccp’ begin installing package ‘VariantAnnotation’ begin installing package ‘AGHmatrix’ begin installing package ‘EMMREML’ begin installing package ‘BGLR’ begin installing package ‘phylogram’ begin installing package ‘NAM’ begin installing package ‘doMPI’ begin installing package ‘cPCG’ begin installing package ‘sommer’ * installing *source* package ‘phylogram’ ... ** this is package ‘phylogram’ version ‘2.1.0’ ** package ‘phylogram’ 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 (phylogram) * installing *source* package ‘HaploSim’ ... ** this is package ‘HaploSim’ version ‘1.8.4.2’ ** package ‘HaploSim’ 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 (HaploSim) begin installing package ‘pedigree’ * installing *source* package ‘doMPI’ ... ** this is package ‘doMPI’ version ‘0.2.2’ ** package ‘doMPI’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** demo ** 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 (doMPI) * installing *source* package ‘EMMREML’ ... ** this is package ‘EMMREML’ version ‘3.1’ ** package ‘EMMREML’ 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 (EMMREML) * installing *source* package ‘AGHmatrix’ ... ** this is package ‘AGHmatrix’ version ‘2.1.4’ ** package ‘AGHmatrix’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (AGHmatrix) * installing *source* package ‘BGLR’ ... ** this is package ‘BGLR’ version ‘1.1.3’ ** package ‘BGLR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8prvzZ/R.INSTALL1c22dd4ce44909/BGLR/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util_sample.c -o util_sample.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util_plink.c -o util_plink.o util_plink.c: In function ‘read_string’: util_plink.c:39:25: warning: pointer ‘buffer’ may be used after ‘realloc’ [-Wuse-after-free] 39 | free(buffer); | ^~~~~~~~~~~~ util_plink.c:36:43: note: call to ‘realloc’ here 36 | char *tmp = (char *) realloc(buffer, buf_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~ util_plink.c: In function ‘read_ped_’: util_plink.c:190:23: warning: ‘Line_copy’ may be used uninitialized [-Wmaybe-uninitialized] 190 | token=strtok(Line_copy,"\t "); | ^~~~~~~~~~~~~~~~~~~~~~~ util_plink.c:105:15: note: ‘Line_copy’ was declared here 105 | char *Line_copy; | ^~~~~~~~~ util_plink.c:263:17: warning: ‘Line’ may be used uninitialized [-Wmaybe-uninitialized] 263 | free(Line); | ^~~~~~~~~~ util_plink.c:104:15: note: ‘Line’ was declared here 104 | char *Line; | ^~~~ util_plink.c:229:51: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 229 | if(tmp=='0' && token[0]=='0') | ^ util_plink.c:114:14: note: ‘tmp’ was declared here 114 | char tmp; | ^~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util_sample_cross.c -o util_sample_cross.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler_multitrait.c -o sampler_multitrait.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o BGLR.so util_sample.o util_plink.o util_sample_cross.o sampler_multitrait.o init.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8prvzZ/R.INSTALL1c22dd4ce44909/BGLR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BGLR/00new/BGLR/libs ** R ** data ** demo ** 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 (BGLR) * installing *source* package ‘pedigree’ ... ** this is package ‘pedigree’ version ‘1.4.2’ ** package ‘pedigree’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpajBQmd/R.INSTALL1c249a247017b4/pedigree/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Pedigree.cpp -o Pedigree.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pedigree_init.c -o pedigree_init.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o pedigree.so Pedigree.o pedigree_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpajBQmd/R.INSTALL1c249a247017b4/pedigree/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigree/00new/pedigree/libs ** 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 ** 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 (pedigree) * installing *source* package ‘cPCG’ ... ** this is package ‘cPCG’ version ‘1.0’ ** package ‘cPCG’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTK1mnV/R.INSTALL1c22e4d2da0c5/cPCG/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -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 g++-14 -std=gnu++11 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpparma_cPCG.cpp -o rcpparma_cPCG.o g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o cPCG.so RcppExports.o init.o rcpparma_cPCG.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTK1mnV/R.INSTALL1c22e4d2da0c5/cPCG/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cPCG/00new/cPCG/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 (cPCG) * installing *source* package ‘nadiv’ ... ** this is package ‘nadiv’ version ‘2.18.0’ ** package ‘nadiv’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpfysc8i/R.INSTALL1c22cf659b4bc2/nadiv/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Trow.cc -o Trow.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c ainv.cc -o ainv.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_cumsum.c -o cs_cumsum.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_malloc.c -o cs_malloc.o cs_malloc.c: In function ‘cs_realloc’: cs_malloc.c:34:26: warning: pointer ‘p’ may be used after ‘realloc’ [-Wuse-after-free] 34 | return ((*ok) ? pnew : p) ; /* return original p if failure */ | ~~~~~~~~~~~~~~^~~~ cs_malloc.c:32:12: note: call to ‘realloc’ here 32 | pnew = realloc (p, CS_MAX (n,1) * size) ; /* realloc the block */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_multiply.c -o cs_multiply.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_norm.c -o cs_norm.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_scatter.c -o cs_scatter.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_transpose.c -o cs_transpose.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cs_util.c -o cs_util.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dfc.cc -o dfc.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c diif.cc -o diif.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dij.cc -o dij.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dsim.cc -o dsim.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c ga.cc -o ga.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genedrop.cc -o genedrop.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/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 g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c minv.cc -o minv.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c reT.cc -o reT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c sdsim.cc -o sdsim.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c sinv.cc -o sinv.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o nadiv.so Trow.o ainv.o cs_cumsum.o cs_malloc.o cs_multiply.o cs_norm.o cs_scatter.o cs_transpose.o cs_util.o dfc.o diif.o dij.o dsim.o ga.o genedrop.o init.o minv.o reT.o sdsim.o sinv.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpfysc8i/R.INSTALL1c22cf659b4bc2/nadiv/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-nadiv/00new/nadiv/libs ** R ** data *** moving datasets to lazyload DB ** 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 (nadiv) * installing *source* package ‘NAM’ ... ** this is package ‘NAM’ version ‘1.7.3’ ** package ‘NAM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpnzRwbA/R.INSTALL1c22e144725129/NAM/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c Functions.cpp -o Functions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c c.c -o c.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o NAM.so Functions.o RcppExports.o c.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpnzRwbA/R.INSTALL1c22e144725129/NAM/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-NAM/00new/NAM/libs ** R ** data ** demo ** 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 (NAM) * installing *source* package ‘sommer’ ... ** this is package ‘sommer’ version ‘4.3.7’ ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1CuUNT/R.INSTALL1c22e5280a3b34/sommer/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c MNR.cpp -o MNR.o MNR.cpp: In function ‘arma::mat dmat(const arma::mat&, const bool&, double)’: MNR.cpp:306:7: warning: unused variable ‘p’ [-Wunused-variable] 306 | int p = X.n_cols; | ^ MNR.cpp: In function ‘arma::cube scorecalc(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, int, double)’: MNR.cpp:457:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 457 | for (int i = 0; i < b.n_rows; ++i) { | ~~^~~~~~~~~~ MNR.cpp: In function ‘Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’: MNR.cpp:642:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 642 | for(int h=0; h < provX.n_cols ; h++){ // for each random effect unlist | ~~^~~~~~~~~~~~~~ MNR.cpp: In function ‘Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)’: MNR.cpp:1306:12: warning: unused variable ‘ok’ [-Wunused-variable] 1306 | bool ok = log_det(val, sign, arma::mat(Ai[i])); // calculate the logDet of the covariance matrix | ^~ MNR.cpp:1529:14: warning: unused variable ‘ok’ [-Wunused-variable] 1529 | bool ok = log_det(val, sign, theta(i)); // form 2 | ^~ MNR.cpp:1577:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1577 | for(int iRow = 0; iRow < partitionsP.n_rows; ++iRow){ // for each partition row | ~~~~~^~~~~~~~~~~~~~~~~~~~ MNR.cpp:1595:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1595 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1596:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1596 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1621:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 1621 | for(int iS = 0; iS < S.size(); ++iS){ | ~~~^~~~~~~~~~ MNR.cpp:1702:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1702 | for(int iRow = 0; iRow < lambdaProv.n_rows; ++iRow){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1703:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1703 | for(int iCol = 0; iCol < lambdaProv.n_cols; ++iCol){ | ~~~~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1729:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 1729 | for(int iS = 0; iS < S.size(); ++iS){ // Rij <- S[[iS]]%*%Ri | ~~~^~~~~~~~~~ MNR.cpp:1787:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare] 1787 | for(int i = 0; i < thetaCUnlisted.size() ; ++i){ | ~~^~~~~~~~~~~~~~~~~~~~~~~ MNR.cpp:1794:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 1794 | for(int j = 0; j < toBoundary.n_cols ; ++j){ | ~~^~~~~~~~~~~~~~~~~~~ MNR.cpp:1535:10: warning: unused variable ‘ok’ [-Wunused-variable] 1535 | bool ok = log_det(val, sign, theta(nRRe-1)); // form 2 | ^~ MNR.cpp: In function ‘arma::vec varCols(const arma::mat&)’: MNR.cpp:148:19: warning: ‘n’ may be used uninitialized [-Wmaybe-uninitialized] 148 | out(j) = M2/(n-1); | ~~^~~ MNR.cpp:138:9: note: ‘n’ was declared here 138 | int n; | ^ MNR.cpp: In function ‘Rcpp::List MNR(const arma::mat&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const bool&, int, double, double, const bool&, const bool&, const bool&, const bool&, const arma::vec&, const arma::vec&)’: MNR.cpp:1115:36: warning: ‘cycle2’ may be used uninitialized [-Wmaybe-uninitialized] 1115 | arma::mat monitor2 = monitor.cols(0, cycle2); | ~~~~~~~~~~~~^~~~~~~~~~~ MNR.cpp:726:14: note: ‘cycle2’ was declared here 726 | int cycle, cycle2, ikk; | ^~~~~~ MNR.cpp:1106:20: warning: ‘llik’ may be used uninitialized [-Wmaybe-uninitialized] 1106 | double AIC = (-2 * llik) + (2 * Xm.n_cols); | ~~~~^~~~~~~ MNR.cpp:727:16: note: ‘llik’ was declared here 727 | double ldet, llik, llik0, delta_llik, checkP, seconds; // to store likelihoods and determinants | ^~~~ MNR.cpp: In function ‘Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)’: MNR.cpp:1293:37: warning: ‘nRe’ may be used uninitialized [-Wmaybe-uninitialized] 1293 | arma::field Ai(nReAl); // allocate size of Ai field | ^ MNR.cpp:1252:7: note: ‘nRe’ was declared here 1252 | int nRe; | ^~~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o sommer.so MNR.o RcppExports.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1CuUNT/R.INSTALL1c22e5280a3b34/sommer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-sommer/00new/sommer/libs ** R ** data ** 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 (sommer) begin installing package ‘statgenGWAS’ * installing *source* package ‘VariantAnnotation’ ... ** this is package ‘VariantAnnotation’ version ‘1.52.0’ ** package ‘VariantAnnotation’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpytPUvw/R.INSTALL1c22d864272db4/VariantAnnotation/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o In file included from vcftype.h:8, from writevcf.h:4, from R_init_VariantAnnotation.c:3: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dna_hash.c -o dna_hash.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rle.c -o rle.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c strhash.c -o strhash.o In file included from strhash.c:2: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ strhash.c:5:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 5 | khash_t(strhash) *_strhash_new() | ^~~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utilities.c -o utilities.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcffile.c -o vcffile.o In file included from vcftype.h:8, from vcffile.c:4: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ vcffile.c:22:27: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 22 | static khash_t(WARNINGS) *vcfwarn_new() | ^~~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcftype.c -o vcftype.o In file included from vcftype.h:8, from vcftype.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c writevcf.c -o writevcf.o In file included from vcftype.h:8, from writevcf.h:4, from writevcf.c:1: strhash.h:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] 8 | khash_t(strhash) *_strhash_new(); | ^~~~~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpytPUvw/R.INSTALL1c22d864272db4/VariantAnnotation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** 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 (VariantAnnotation) * installing *source* package ‘statgenGWAS’ ... ** this is package ‘statgenGWAS’ version ‘1.0.10’ ** package ‘statgenGWAS’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++-14 -std=gnu++17 accepts -g... yes checking for g++-14 -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++-14 -std=gnu++17 -E checking for macOS... not found as on Linux checking for OpenMP... found configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpocBfYI/R.INSTALL1c277e75627e48/statgenGWAS/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c EMMA.cpp -o EMMA.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c codeCharMarkers.cpp -o codeCharMarkers.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastGLS.cpp -o fastGLS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c getThr.cpp -o getThr.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c kinship.cpp -o kinship.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -I../inst/include -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c utils.cpp -o utils.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o statgenGWAS.so EMMA.o RcppExports.o codeCharMarkers.o fastGLS.o getThr.o kinship.o utils.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpocBfYI/R.INSTALL1c277e75627e48/statgenGWAS/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-statgenGWAS/00new/statgenGWAS/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 (statgenGWAS) * installing *source* package ‘cccp’ ... ** this is package ‘cccp’ version ‘0.3-1’ ** package ‘cccp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmRDVZs/R.INSTALL1c22da6d4c44f7/cccp/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CONEC.cpp -o CONEC.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c DCP.cpp -o DCP.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c DLP.cpp -o DLP.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c DNL.cpp -o DNL.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c DQP.cpp -o DQP.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c GPP.cpp -o GPP.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c Modules.cpp -o Modules.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RPP.cpp -o RPP.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I../inst/include/ -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c SOPS.cpp -o SOPS.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o cccp.so CONEC.o DCP.o DLP.o DNL.o DQP.o GPP.o Modules.o RPP.o RcppExports.o SOPS.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmRDVZs/R.INSTALL1c22da6d4c44f7/cccp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cccp/00new/cccp/libs ** R ** demo ** 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 (cccp) begin installing package ‘optiSolve’ * installing *source* package ‘optiSolve’ ... ** this is package ‘optiSolve’ version ‘1.0’ ** package ‘optiSolve’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (optiSolve) begin installing package ‘optiSel’ * installing *source* package ‘optiSel’ ... ** this is package ‘optiSel’ version ‘2.0.9’ ** package ‘optiSel’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-12) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxKitJu/R.INSTALL1c2c6357f22e48/optiSel/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_completeness.cpp -o rcpp_completeness.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_genecont.cpp -o rcpp_genecont.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_haplofreq.cpp -o rcpp_haplofreq.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_makeA.cpp -o rcpp_makeA.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_makeA_lowMem.cpp -o rcpp_makeA_lowMem.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_segBreedComp.cpp -o rcpp_segBreedComp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_segIBD.cpp -o rcpp_segIBD.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_segIBDandN.cpp -o rcpp_segIBDandN.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_segIBDandNVersion2.cpp -o rcpp_segIBDandNVersion2.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_segInbreeding.cpp -o rcpp_segInbreeding.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c rcpp_segN.cpp -o rcpp_segN.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o optiSel.so RcppExports.o rcpp_completeness.o rcpp_genecont.o rcpp_haplofreq.o rcpp_makeA.o rcpp_makeA_lowMem.o rcpp_segBreedComp.o rcpp_segIBD.o rcpp_segIBDandN.o rcpp_segIBDandNVersion2.o rcpp_segInbreeding.o rcpp_segN.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxKitJu/R.INSTALL1c2c6357f22e48/optiSel/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-optiSel/00new/optiSel/libs ** R ** data ** 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 (optiSel) checking sommer_4.3.7.tar.gz ... checking gpcp_0.1.0.tar.gz ... checking IPLGP_2.0.5.tar.gz ... checking lmDiallel_1.0.1.tar.gz ... checking mlmm.gwas_1.0.6.tar.gz ... checking pcgen_0.2.0.tar.gz ... checking statgenGWAS_1.0.10.tar.gz ... checking statgenQTLxT_1.0.2.tar.gz ... checking lucid_1.8.tar.gz ... checking MoBPS_1.6.64.tar.gz ... Depends: Package: sommer Depends: R (>= 3.5.0), Matrix (>= 1.1.1), methods, stats, MASS, crayon Imports: Rcpp (>= 0.12.19) LinkingTo: Rcpp, RcppArmadillo, RcppProgress Timings: user system elapsed sommer 140.224 7.811 150.67 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 3 6 Check results summary: sommer ... OK rdepends_gpcp ... OK rdepends_IPLGP ... OK rdepends_lmDiallel ... OK rdepends_lucid ... OK rdepends_mlmm.gwas ... OK rdepends_MoBPS ... NOTE * checking Rd files ... [1s/1s] NOTE rdepends_pcgen ... OK rdepends_statgenGWAS ... NOTE * checking top-level files ... NOTE rdepends_statgenQTLxT ... NOTE * checking Rd cross-references ... NOTE