* installing *source* package ‘bio3d’ ...
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -DSTRICT_R_HEADERS=1  -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. -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 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c gzstream.cpp -o gzstream.o
gcc-14  -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -DSTRICT_R_HEADERS=1  -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. -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 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c read_cif.cpp -o read_cif.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c read_crd.cpp -o read_crd.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c read_pdb.cpp -o read_pdb.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -DSTRICT_R_HEADERS=1  -fpic  -g -O2 -Wall -pedantic -mtune=native  -DR_NO_REMAP -c read_prmtop.cpp -o read_prmtop.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I. -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 -DSTRICT_R_HEADERS=1  -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 bio3d.so RcppExports.o gzstream.o init.o read_cif.o read_crd.o read_pdb.o read_prmtop.o utils.o -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR
installing to /home/hornik/tmp/CRAN_recheck/bio3d.Rcheck/00LOCK-bio3d/00new/bio3d/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (bio3d)