=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Installing for R-nloptr-1.2.2.2
=> Generating pre-install file lists
=> Creating installation directories
* installing *source* package 'nloptr' ...
file 'configure' has the wrong MD5 checksum
** 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 we are using the GNU C++ compiler... yes
checking whether c++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... c++ -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether c++ -std=gnu++14 accepts -g... (cached) yes
checking for pkg-config... yes
configure: Now testing for NLopt header file.
checking for grep that handles long lines and -e... /usr/pkgsrc/math/R-nloptr/work/.tools/bin/grep
checking for egrep... /usr/pkgsrc/math/R-nloptr/work/.tools/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking nlopt.h usability... yes
checking nlopt.h presence... yes
checking for nlopt.h... yes
configure: Now testing for NLopt version 2.4.0 or greater.
configure: Suitable NLopt library found.
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/PkgFlags.R
** libs
c++ -std=gnu++14 -I"/usr/pkg/lib/R/include" -DNDEBUG   -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/X11R7/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5  -fpic  -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/X11R7/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5  -c dummy.cpp -o dummy.o
gcc -I"/usr/pkg/lib/R/include" -DNDEBUG   -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/X11R7/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5 -I/usr/pkg/include -fPIC  -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/X11R7/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5  -c init_nloptr.c -o init_nloptr.o
gcc -I"/usr/pkg/lib/R/include" -DNDEBUG   -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/X11R7/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5 -I/usr/pkg/include -fPIC  -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/X11R7/include -I/usr/X11R7/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5  -c nloptr.c -o nloptr.o
c++ -std=gnu++14 -shared -Wl,-R/usr/pkg/lib/R/lib -L/usr/pkg/lib/R/lib -Wl,-zrelro -L/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -Wl,-R/usr/pkg/lib -pthread -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -latomic -o nloptr.so dummy.o init_nloptr.o nloptr.o -L/usr/pkg/lib -lnlopt -Wl,-R/usr/pkg/lib/R/lib -L/usr/pkg/lib/R/lib -lR
ld: cannot find -latomic
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/math/R-nloptr/work/nloptr/src
ERROR: compilation failed for package 'nloptr'
* removing '/usr/pkgsrc/math/R-nloptr/work/.destdir/usr/pkg/lib/R/library/nloptr'
*** Error code 1

Stop.
make[1]: stopped in /usr/pkgsrc/math/R-nloptr
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/math/R-nloptr