installing dependencies ‘fillpattern’, ‘ggdensity’, ‘mgcv’, ‘prettycode’, ‘tsne’ begin installing package ‘mgcv’ begin installing package ‘prettycode’ begin installing package ‘tsne’ * installing *source* package ‘tsne’ ... ** this is package ‘tsne’ version ‘0.1-3.1’ ** package ‘tsne’ 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 (tsne) * installing *source* package ‘prettycode’ ... ** this is package ‘prettycode’ version ‘1.1.0’ ** package ‘prettycode’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (prettycode) * installing *source* package ‘mgcv’ ... ** this is package ‘mgcv’ version ‘1.9-3’ ** package ‘mgcv’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Debian 20250322-1) 15.0.1 20250322 (experimental) [master r15-8663-g7a6bbab6ae5]’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp2wLaFn/R.INSTALL1c1852346373cb/mgcv/src' /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c coxph.c -o coxph.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c davies.c -o davies.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c discrete.c -o discrete.o In file included from discrete.c:29: discrete.c: In function 'ncvd': mgcv.h:62:14: warning: 'A' may be used uninitialized [-Wmaybe-uninitialized] 62 | #define FREE R_chk_free discrete.c:3448:29: note: in expansion of macro 'FREE' 3448 | FREE(B);FREE(cs);FREE(mk);FREE(A);FREE(Aaa);FREE(IAaa);FREE(IA);FREE(ba);FREE(rp); | ^~~~ discrete.c:2989:11: note: 'A' was declared here 2989 | double *A,*A2,**A1,*Aaa,*IAaa,*Ap,*Aaap,*IA,*IAp,*ba,*bp,*rp,one=1.0,zero=0.0,*dp0,*dp1,*dp2, | ^ mgcv.h:62:14: warning: 'A2' may be used uninitialized [-Wmaybe-uninitialized] 62 | #define FREE R_chk_free discrete.c:3449:53: note: in expansion of macro 'FREE' 3449 | FREE(beta2);FREE(L2);FREE(U2);FREE(mu2);FREE(wij);FREE(A2);FREE(ba2);FREE(ind);FREE(a1);FREE(a2);FREE(thlim); | ^~~~ discrete.c:2989:14: note: 'A2' was declared here 2989 | double *A,*A2,**A1,*Aaa,*IAaa,*Ap,*Aaap,*IA,*IAp,*ba,*bp,*rp,one=1.0,zero=0.0,*dp0,*dp1,*dp2, | ^~ /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gdi.c -o gdi.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c magic.c -o magic.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mat.c -o mat.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix.c -o matrix.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mgcv.c -o mgcv.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c misc.c -o misc.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mvn.c -o mvn.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ncv.c -o ncv.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qp.c -o qp.o qp.c: In function 'QPCLS': qp.c:429:10: warning: unused variable 'x' [-Wunused-variable] 429 | double x; | ^ /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c soap.c -o soap.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sparse-smooth.c -o sparse-smooth.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sparse.c -o sparse.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-snap/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tprs.c -o tprs.o /usr/lib/gcc-snapshot/bin/gcc -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-snap/lib -L/usr/lib/gcc-snapshot/lib -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -L/home/hornik/tmp/R-d-gcc-snap/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R-d-gcc-snap/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp2wLaFn/R.INSTALL1c1852346373cb/mgcv/src' installing to /home/hornik/tmp/CRAN_special_gcc15/Library/00LOCK-mgcv/00new/mgcv/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 (mgcv) begin installing package ‘fillpattern’ begin installing package ‘ggdensity’ * installing *source* package ‘fillpattern’ ... ** this is package ‘fillpattern’ version ‘1.0.2’ ** package ‘fillpattern’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (fillpattern) * installing *source* package ‘ggdensity’ ... ** this is package ‘ggdensity’ version ‘1.0.0’ ** package ‘ggdensity’ 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 (ggdensity) checking rbiom_2.2.0.tar.gz ... Depends: Package: rbiom Depends: R (>= 4.2.0) Imports: methods, mgcv, stats, utils, ape, dplyr, emmeans, fillpattern, ggbeeswarm, ggnewscale, ggplot2, ggrepel, ggtext, jsonlite, magrittr, parallelly, patchwork, pillar, plyr, readr, readxl, slam, vegan Timings: user system elapsed rbiom 138.22 9.172 150.419 Results: Check status summary: OK Source packages 1 Check results summary: rbiom ... OK