=> 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-ncdf4-1.17nb3
=> Generating pre-install file lists
=> Creating installation directories
* installing *source* package 'ncdf4' ...
file 'configure' has the wrong MD5 checksum
** using staged installation
configure.ac: starting
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:

This netCDF 4.6.1 has been built with the following features: 

  --cc        -> gcc
  --cflags    -> -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -I/usr/include/krb5
  --libs      -> -L/usr/pkg/lib -lnetcdf

  --has-c++   -> no
  --cxx       -> 

  --has-c++4  -> no
  --cxx4      -> 

  --has-fortran-> no
  --has-dap   -> yes
  --has-dap4  -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-logging-> no
  --has-pnetcdf-> no
  --has-szlib -> yes
  --has-parallel -> no
  --has-cdf5 -> no

  --prefix    -> /usr/pkg
  --includedir-> /usr/pkg/include
  --libdir    -> /usr/pkg/lib
  --version   -> netCDF 4.6.1

---
netcdf.m4: about to set rpath, here is source string: >-L/usr/pkg/lib -lnetcdf<
netcdf.m4: final rpath:   -Wl,-rpath,/usr/pkg/lib
Netcdf library version: netCDF 4.6.1
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: gcc
configure: creating ./config.status
config.status: creating src/Makevars
 
**********************  Results of ncdf4 package configure *******************
 
netCDF v4 CPP flags      = -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -I/usr/include/krb5
netCDF v4 LD flags       =   -Wl,-rpath,/usr/pkg/lib -L/usr/pkg/lib -lnetcdf -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib
netCDF v4 runtime path   =   -Wl,-rpath,/usr/pkg/lib
 
netCDF C compiler used   = gcc
R      C compiler used   = gcc -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
 
******************************************************************************
 
** libs
gcc -I"/usr/pkg/lib/R/include" -DNDEBUG -I/usr/pkg/include -I/usr/include -I/usr/pkg/include -I/usr/include/krb5  -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 ncdf.c -o ncdf.o
gcc -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 ncdf4.so ncdf.o -Wl,-rpath,/usr/pkg/lib -L/usr/pkg/lib -lnetcdf -Wl,-zrelro -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -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-ncdf4/work/ncdf4/src
ERROR: compilation failed for package 'ncdf4'
* removing '/usr/pkgsrc/math/R-ncdf4/work/.destdir/usr/pkg/lib/R/library/ncdf4'
*** Error code 1

Stop.
make[1]: stopped in /usr/pkgsrc/math/R-ncdf4
*** Error code 1

Stop.
make: stopped in /usr/pkgsrc/math/R-ncdf4