downloading reverse dependencies ... downloading ratematrix_1.2.4.tar.gz ... ok downloading RPANDA_2.3.tar.gz ... ok downloading mvSLOUCH_2.7.6.tar.gz ... ok downloading RRphylo_2.8.1.tar.gz ... ok installing dependencies ‘ddpcr’, ‘evolqg’, ‘geomorph’, ‘GUniFrac’, ‘inflection’, ‘mvMORPH’, ‘ouch’, ‘ParallelLogger’, ‘PCMBase’, ‘PCMBaseCpp’, ‘Rphylopars’, ‘smatr’, ‘TESS’, ‘vegan’ also installing the dependency ‘RRPP’ begin installing package ‘RRPP’ begin installing package ‘mvMORPH’ begin installing package ‘ParallelLogger’ begin installing package ‘TESS’ begin installing package ‘ouch’ begin installing package ‘PCMBase’ begin installing package ‘smatr’ begin installing package ‘ddpcr’ begin installing package ‘inflection’ begin installing package ‘Rphylopars’ begin installing package ‘vegan’ * installing *source* package ‘inflection’ ... ** package ‘inflection’ 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 (inflection) * installing *source* package ‘ParallelLogger’ ... ** package ‘ParallelLogger’ 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 (ParallelLogger) * installing *source* package ‘smatr’ ... ** package ‘smatr’ 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 ** 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 (smatr) * installing *source* package ‘ouch’ ... ** package ‘ouch’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpe3vI0c/R.INSTALL3698cf5b951f70/ouch/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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c covar-matrix.c -o covar-matrix.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 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 weight-matrix.c -o weight-matrix.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o ouch.so covar-matrix.o init.o weight-matrix.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpe3vI0c/R.INSTALL3698cf5b951f70/ouch/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ouch/00new/ouch/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 (ouch) * installing *source* package ‘ddpcr’ ... ** package ‘ddpcr’ 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 (ddpcr) * installing *source* package ‘TESS’ ... ** package ‘TESS’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpihpiOL/R.INSTALL3698d47294d7ac/TESS/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 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mass_extinction_equations.cpp -o mass_extinction_equations.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o TESS.so RcppExports.o mass_extinction_equations.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpihpiOL/R.INSTALL3698d47294d7ac/TESS/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TESS/00new/TESS/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 (TESS) * installing *source* package ‘RRPP’ ... ** package ‘RRPP’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (RRPP) begin installing package ‘geomorph’ * installing *source* package ‘PCMBase’ ... ** package ‘PCMBase’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (PCMBase) begin installing package ‘PCMBaseCpp’ * installing *source* package ‘mvMORPH’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQKKH4G/R.INSTALL3698d234d99540/mvMORPH/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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c chol_rpf_row.c -o chol_rpf_row.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 chol_rpf_univ.c -o chol_rpf_univ.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 covar-matrix-simmap.c -o covar-matrix-simmap.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 givens.c -o givens.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 kronecker.c -o kronecker.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 mvMORPH_init.c -o mvMORPH_init.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 mvmorph-covar-mat.c -o mvmorph-covar-mat.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 mvmorph-covar-ou-sparse.c -o mvmorph-covar-ou-sparse.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 mvmorph-covar-ou.c -o mvmorph-covar-ou.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 mvmorph_ou_mat_rpf.c -o mvmorph_ou_mat_rpf.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 pic_loglik_mvmorph.c -o pic_loglik_mvmorph.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 quadprod.c -o quadprod.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 root2tip.c -o root2tip.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 spherical.c -o spherical.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 sqrtMat.c -o sqrtMat.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 time_serie_expectation.c -o time_serie_expectation.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 utils.c -o utils.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 weight-matrix-mvmorph.c -o weight-matrix-mvmorph.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o mvMORPH.so chol_rpf_row.o chol_rpf_univ.o covar-matrix-simmap.o givens.o kronecker.o mvMORPH_init.o mvmorph-covar-mat.o mvmorph-covar-ou-sparse.o mvmorph-covar-ou.o mvmorph_ou_mat_rpf.o pic_loglik_mvmorph.o quadprod.o root2tip.o spherical.o sqrtMat.o time_serie_expectation.o utils.o weight-matrix-mvmorph.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/RtmpQKKH4G/R.INSTALL3698d234d99540/mvMORPH/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mvMORPH/00new/mvMORPH/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 (mvMORPH) * installing *source* package ‘vegan’ ... ** package ‘vegan’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-1) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmplhbqvX/R.INSTALL3698df6535b617/vegan/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 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c data2hill.c -o data2hill.o gfortran-14 -fpic -g -O2 -Wall -mtune=native -c decorana.f -o decorana.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 getF.c -o getF.o getF.c: In function ‘do_getF’: getF.c:436:13: warning: ‘wperm’ may be used uninitialized [-Wmaybe-uninitialized] 436 | wcentre(Xorig, qr, wperm, &nr, &nx); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ getF.c:347:13: note: ‘wperm’ was declared here 347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7; | ^~~~~ getF.c:436:13: warning: ‘Xorig’ may be used uninitialized [-Wmaybe-uninitialized] 436 | wcentre(Xorig, qr, wperm, &nr, &nx); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ getF.c:347:21: note: ‘Xorig’ was declared here 347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7; | ^~~~~ getF.c:347:29: warning: ‘Zorig’ may be used uninitialized [-Wmaybe-uninitialized] 347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7; | ^~~~~ getF.c:347:37: warning: ‘Zperm’ may be used uninitialized [-Wmaybe-uninitialized] 347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7; | ^~~~~ In file included from /home/hornik/tmp/R-d-gcc-14/include/R.h:78, from getF.c:11: getF.c:446:22: warning: ‘qrwork’ may be used uninitialized [-Wmaybe-uninitialized] 446 | F77_CALL(dqrdc2)(qr, &nr, &nr, &nx, &qrtol, &qrank, | ^ /home/hornik/tmp/R-d-gcc-14/include/R_ext/RS.h:80:25: note: in definition of macro ‘F77_CALL’ 80 | # define F77_CALL(x) x ## _ | ^ getF.c:347:45: note: ‘qrwork’ was declared here 347 | double *wperm, *Xorig, *Zorig, *Zperm, *qrwork, *zqrwork, qrtol=1e-7; | ^~~~~~ getF.c:472:22: warning: ‘resid’ may be used uninitialized [-Wmaybe-uninitialized] 472 | F77_CALL(dqrsl)(qr, &nr, &nr, &qrank, qraux, rY + i*nr, &dummy, | ^ /home/hornik/tmp/R-d-gcc-14/include/R_ext/RS.h:80:25: note: in definition of macro ‘F77_CALL’ 80 | # define F77_CALL(x) x ## _ | ^ getF.c:335:13: note: ‘resid’ was declared here 335 | double *resid; | ^~~~~ getF.c:370:13: warning: ‘transY’ may be used uninitialized [-Wmaybe-uninitialized] 370 | double *transY; | ^~~~~~ 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 goffactor.c -o goffactor.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 gfortran-14 -fpic -g -O2 -Wall -mtune=native -c monoMDS.f -o monoMDS.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 nestedness.c -o nestedness.o gfortran-14 -fpic -g -O2 -Wall -mtune=native -c ordering.f -o ordering.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 pnpoly.c -o pnpoly.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 stepacross.c -o stepacross.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 vegdist.c -o vegdist.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o vegan.so data2hill.o decorana.o getF.o goffactor.o init.o monoMDS.o nestedness.o ordering.o pnpoly.o stepacross.o vegdist.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmplhbqvX/R.INSTALL3698df6535b617/vegan/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-vegan/00new/vegan/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 (vegan) begin installing package ‘GUniFrac’ begin installing package ‘evolqg’ * installing *source* package ‘geomorph’ ... ** package ‘geomorph’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (geomorph) * installing *source* package ‘Rphylopars’ ... ** package ‘Rphylopars’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuGIvSa/R.INSTALL3698ddc063f59/Rphylopars/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 -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 -c phylopars_rcpp.cpp -o phylopars_rcpp.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o Rphylopars.so RcppExports.o phylopars_rcpp.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/RtmpuGIvSa/R.INSTALL3698ddc063f59/Rphylopars/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rphylopars/00new/Rphylopars/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 (Rphylopars) * installing *source* package ‘GUniFrac’ ... ** package ‘GUniFrac’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRIdek0/R.INSTALL369c4a3a09fd54/GUniFrac/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 -c PairwiseD.cpp -o PairwiseD.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 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gmpr.cpp -o gmpr.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o GUniFrac.so PairwiseD.o RcppExports.o gmpr.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRIdek0/R.INSTALL369c4a3a09fd54/GUniFrac/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GUniFrac/00new/GUniFrac/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 (GUniFrac) * installing *source* package ‘evolqg’ ... ** package ‘evolqg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpUnLjdV/R.INSTALL369c4c55d582c2/evolqg/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 -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 -c fast_RS.cpp -o fast_RS.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o evolqg.so RcppExports.o fast_RS.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/RtmpUnLjdV/R.INSTALL369c4c55d582c2/evolqg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-evolqg/00new/evolqg/libs ** R ** data ** 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 (evolqg) * installing *source* package ‘PCMBaseCpp’ ... ** package ‘PCMBaseCpp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzJizK8/R.INSTALL369b9567cff140/PCMBaseCpp/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 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -c Rcpp.cpp -o Rcpp.o In file included from QuadraticPoly.h:27, from QuadraticPolyWhite.h:28, from Rcpp.cpp:30: SPLITT.h:2053: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2053 | _PRAGMA_OMP_SIMD SPLITT.h:2071: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2071 | _PRAGMA_OMP_SIMD SPLITT.h:2084: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2084 | _PRAGMA_OMP_SIMD SPLITT.h:2096: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2096 | _PRAGMA_OMP_SIMD SPLITT.h:2106: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2106 | _PRAGMA_OMP_SIMD SPLITT.h:2132: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2132 | #pragma omp parallel SPLITT.h:2134: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2134 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2145: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 2145 | #pragma omp barrier SPLITT.h:2148: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2148 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2159: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 2159 | #pragma omp barrier SPLITT.h:2162: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2162 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2178: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2178 | #pragma omp parallel SPLITT.h:2187: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2187 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2197: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2197 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2223: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2223 | #pragma omp parallel SPLITT.h:2263: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2263 | #pragma omp parallel SPLITT.h:2265: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2265 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2276: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2276 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2290: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2290 | #pragma omp parallel SPLITT.h:2292: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2292 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2300: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2300 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2311: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2311 | #pragma omp parallel SPLITT.h:2320: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2320 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2331: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 2331 | #pragma omp barrier SPLITT.h:2334: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2334 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2343: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2343 | _PRAGMA_OMP_SIMD SPLITT.h:2357: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2357 | _PRAGMA_OMP_SIMD SPLITT.h:2375: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2375 | #pragma omp parallel SPLITT.h:2384: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2384 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2395: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 2395 | #pragma omp barrier SPLITT.h:2398: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2398 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2408: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2408 | _PRAGMA_OMP_SIMD SPLITT.h:2423: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2423 | #pragma omp parallel SPLITT.h:2432: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2432 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2442: warning: ignoring ‘#pragma omp barrier’ [-Wunknown-pragmas] 2442 | #pragma omp barrier SPLITT.h:2445: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2445 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2463: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2463 | _PRAGMA_OMP_SIMD SPLITT.h:2607: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2607 | _PRAGMA_OMP_SIMD SPLITT.h:2621: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2621 | _PRAGMA_OMP_SIMD SPLITT.h:2630: warning: ignoring ‘#pragma omp simd’ [-Wunknown-pragmas] 2630 | _PRAGMA_OMP_SIMD SPLITT.h:2638: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2638 | #pragma omp parallel SPLITT.h:2647: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2647 | _PRAGMA_OMP_FOR_SIMD SPLITT.h:2656: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 2656 | _PRAGMA_OMP_FOR_SIMD QuadraticPoly.h: In instantiation of ‘bool PCMBaseCpp::IsDiagonal(const MatType&) [with MatType = arma::Mat]’: QuadraticPoly.h:94:16: required from ‘void PCMBaseCpp::DecomposeH(MatEigvalType&, CubeEigvecType&, CubeEigvecType&, const CubeHType&, arma::uword, double) [with MatEigvalType = arma::Mat >; CubeEigvecType = arma::Cube >; CubeHType = arma::Cube; arma::uword = unsigned int]’ 94 | if(IsDiagonal(H.slice(r))) { | ~~~~~~~~~~^~~~~~~~~~~~ QuadraticPolyOU.h:152:17: required from ‘arma::uword PCMBaseCpp::CondGaussianOU::SetParameter(const std::vector&, arma::uword) [with TreeType = SPLITT::OrderedTree; DataType = PCMBaseCpp::NumericTraitData; arma::uword = unsigned int]’ 152 | DecomposeH(lambda, P, P_1, H, r, threshold_SV_); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyOU.h:203:28: required from here 203 | cond_dist_.SetParameter(par, 0); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ QuadraticPoly.h:47:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 47 | for(int i = 0; i < X.n_rows; ++i) { | ~~^~~~~~~~~~ QuadraticPoly.h:48:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare] 48 | for(int j = i + 1; j < X.n_cols; ++j) { | ~~^~~~~~~~~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::White]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::White; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::White; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::White; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:265:53: required from here 265 | .method( "TraverseTree", &QuadraticPolyWhite::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::BM]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::BM; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::BM; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::BM; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:335:48: required from here 335 | .method( "TraverseTree", &QuadraticPolyBM::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::BM1D]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::BM1D; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::BM1D; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::BM1D; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:407:52: required from here 407 | .method( "TraverseTree", &QuadraticPolyBM1D::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::OU]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::OU; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::OU; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::OU; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:477:48: required from here 477 | .method( "TraverseTree", &QuadraticPolyOU::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::OU1D]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::OU1D; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::OU1D; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::OU1D; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:546:52: required from here 546 | .method( "TraverseTree", &QuadraticPolyOU1D::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::JOU]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::JOU; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::JOU; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::JOU; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:620:49: required from here 620 | .method( "TraverseTree", &QuadraticPolyJOU::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::DOU]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::DOU; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::DOU; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::DOU; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:689:49: required from here 689 | .method( "TraverseTree", &QuadraticPolyDOU::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::MixedGaussian]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::MixedGaussian; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::MixedGaussian; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::MixedGaussian; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:762:61: required from here 762 | .method( "TraverseTree", &QuadraticPolyMixedGaussian::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ SPLITT.h: In instantiation of ‘void SPLITT::PostOrderTraversal::TraverseTreeMultiThreadLoopVisits() [with TraversalSpecification = PCMBaseCpp::MixedGaussian1D]’: SPLITT.h:1930:46: required from ‘void SPLITT::PostOrderTraversal::TraverseTree(ModeType) [with TraversalSpecification = PCMBaseCpp::MixedGaussian1D; ModeType = SPLITT::PostOrderMode]’ 1930 | case ModeType::MULTI_THREAD_LOOP_VISITS: TraverseTreeMultiThreadLoopVisits(); break; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SPLITT.h:623:28: required from ‘SPLITT::TraversalTask::StateType SPLITT::TraversalTask::TraverseTree(const ParameterType&, SPLITT::uint) [with TraversalSpecification = PCMBaseCpp::MixedGaussian1D; StateType = arma::Col; ParameterType = std::vector; SPLITT::uint = unsigned int]’ 623 | algorithm_.TraverseTree(static_cast(mode)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ QuadraticPolyCommon.h:128:31: required from ‘std::string PCMBaseCpp::TraversalTaskWrapper::TraverseTree(const ParameterType&, PCMBaseCpp::uint) [with TraversalSpec = PCMBaseCpp::MixedGaussian1D; std::string = std::__cxx11::basic_string; ParameterType = std::vector; PCMBaseCpp::uint = unsigned int]’ 128 | taskObject_.TraverseTree(par, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ Rcpp.cpp:834:63: required from here 834 | .method( "TraverseTree", &QuadraticPolyMixedGaussian1D::TraverseTree ) | ^~~~~~~~~~~~ SPLITT.h:2180:8: warning: variable ‘tid’ set but not used [-Wunused-but-set-variable] 2180 | uint tid; | ^~~ g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o PCMBaseCpp.so Rcpp.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/RtmpzJizK8/R.INSTALL369b9567cff140/PCMBaseCpp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-PCMBaseCpp/00new/PCMBaseCpp/libs ** R ** data *** moving datasets to lazyload DB ** 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 (PCMBaseCpp) checking mvMORPH_1.2.1.tar.gz ... checking ratematrix_1.2.4.tar.gz ... checking RPANDA_2.3.tar.gz ... checking mvSLOUCH_2.7.6.tar.gz ... checking RRphylo_2.8.1.tar.gz ... Depends: Package: mvMORPH Depends: R (>= 3.5.0), phytools, ape, corpcor, subplex Imports: stats, utils, spam, graphics, glassoFast, parallel, pbmcapply Timings: user system elapsed mvMORPH 104.349 8.048 113.884 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 3 1 Check results summary: mvMORPH ... NOTE * checking CRAN incoming feasibility ... [5s/6s] NOTE rdepends_mvSLOUCH ... NOTE * checking Rd cross-references ... NOTE rdepends_ratematrix ... NOTE * checking C++ specification ... NOTE rdepends_RPANDA ... NOTE * checking Rd cross-references ... NOTE rdepends_RRphylo ... OK Warning in normalizePath(dir) : path[1]="/home/hornik/tmp/CRAN": No such file or directory Calls: -> normalizePath Warning in normalizePath(dir) : path[1]="/home/hornik/tmp/CRAN": No such file or directory Calls: -> R_check_outdirs -> normalizePath