* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘bio3d’ ...
** package ‘bio3d’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 18.1.8 (1+b1)’
using C++ compiler: ‘Debian clang version 18.1.8 (1+b1)’
using C++11
make[1]: Entering directory '/tmp/RtmpmBowHy/R.INSTALL8f2d569bdd709/bio3d/src'
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c RcppExports.cpp -o RcppExports.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c gzstream.cpp -o gzstream.o
clang-18 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c read_cif.cpp -o read_cif.o
read_cif.cpp:18:7: warning: variable 'natoms' set but not used [-Wunused-but-set-variable]
   18 |   int natoms = 0;
      |       ^
1 warning generated.
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c read_crd.cpp -o read_crd.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c read_pdb.cpp -o read_pdb.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c read_prmtop.cpp -o read_prmtop.o
clang++-18 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion  -c utils.cpp -o utils.o
clang++-18 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/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.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpmBowHy/R.INSTALL8f2d569bdd709/bio3d/src'
make[1]: Entering directory '/tmp/RtmpmBowHy/R.INSTALL8f2d569bdd709/bio3d/src'
make[1]: Leaving directory '/tmp/RtmpmBowHy/R.INSTALL8f2d569bdd709/bio3d/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)