* installing *source* package ‘ncdf4’ ...
** package ‘ncdf4’ successfully unpacked and MD5 sums checked
** using staged installation
configure.ac: starting
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:

This netCDF 4.8.1 has been built with the following features: 

  --cc            -> gcc
  --cflags        -> -I/usr/include -I/usr/include/hdf -DH5_USE_110_API
  --libs          -> -L/usr/lib64 -lnetcdf
  --static        -> -ljpeg -lmfhdf -ldf -ljpeg -lhdf5_hl -lhdf5 -lm -lz -lcurl -ltirpc

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

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

  --has-fortran   -> yes
  --fc            -> gfortran
  --fflags        -> -I/usr/lib64/gfortran/modules
  --flibs         -> -lnetcdff
  --has-f90       -> 
  --has-f03       -> yes

  --has-dap       -> yes
  --has-dap2      -> yes
  --has-dap4      -> yes
  --has-nc2       -> yes
  --has-nc4       -> yes
  --has-hdf5      -> yes
  --has-hdf4      -> yes
  --has-logging   -> no
  --has-pnetcdf   -> no
  --has-szlib     -> yes
  --has-cdf5      -> yes
  --has-parallel4 -> no
  --has-parallel  -> no
  --has-nczarr    -> yes

  --prefix        -> /usr
  --includedir    -> /usr/include
  --libdir        -> /usr/lib64
  --version       -> netCDF 4.8.1

---
netcdf.m4: about to set rpath, here is source string: >-L/usr/lib64 -lnetcdf<
netcdf.m4: final rpath:   -Wl,-rpath,/usr/lib64
Netcdf library version: netCDF 4.8.1
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/include -I/usr/include/hdf -DH5_USE_110_API
netCDF v4 LD flags       =   -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lnetcdf -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64
netCDF v4 runtime path   =   -Wl,-rpath,/usr/lib64
 
netCDF C compiler used   = gcc
R      C compiler used   = /usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3
 
******************************************************************************
 
checking whether we are using the GNU C compiler... no
checking whether /usr/local/clang18/bin/clang accepts -g... no
checking for /usr/local/clang18/bin/clang option to accept ISO C89... unsupported
netcdf cc arg1: gcc  R cc arg1: /usr/local/clang18/bin/clang R_IS_GCC: 0 R_IS_CLANG: 1 NETCDF_IS_GCC: 1 NETCDF_IS_CLANG: 0  emit_warning: 0
** libs
using C compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ncdf4/src'
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include -I/usr/include/hdf -DH5_USE_110_API  -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c ncdf.c -o ncdf.o
/usr/local/clang18/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o ncdf4.so ncdf.o -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lnetcdf -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ncdf4/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ncdf4/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ncdf4/src'
installing to /data/gannet/ripley/R/packages/tests-clang/ncdf4.Rcheck/00LOCK-ncdf4/00new/ncdf4/libs
** 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
** 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 (ncdf4)