* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* 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 4.9.2 has been built with the following features: 

  --cc            -> /usr/bin/cc
  --cflags        -> -I/usr/include -I/usr/include/hdf5/serial
  --libs          -> -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf
  --static        -> -lhdf5_hl -lhdf5 -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -lzstd -lxml2


  --has-dap          -> yes
  --has-dap2         -> yes
  --has-dap4         -> yes
  --has-nc2          -> yes
  --has-nc4          -> yes
  --has-hdf5         -> yes
  --has-hdf4         -> no
  --has-logging      -> no
  --has-pnetcdf      -> no
  --has-szlib        -> no
  --has-cdf5         -> yes
  --has-parallel4    -> no
  --has-parallel     -> no
  --has-nczarr       -> yes
  --has-zstd         -> yes
  --has-benchmarks   -> no
  --has-multifilters -> no
  --has-stdfilters   -> deflate szip zstd bz2
  --has-quantize     -> no

  --prefix        -> /usr
  --includedir    -> /usr/include
  --libdir        -> /usr/lib/x86_64-linux-gnu
  --plugindir     -> 
  --version       -> netCDF 4.9.2

---
netcdf.m4: about to set rpath, here is source string: >-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf<
netcdf.m4: final rpath:   -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial
Netcdf library version: netCDF 4.9.2
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: /usr/bin/cc
configure: creating ./config.status
config.status: creating src/Makevars
 
**********************  Results of ncdf4 package configure *******************
 
netCDF v4 CPP flags      = -I/usr/include -I/usr/include/hdf5/serial
netCDF v4 LD flags       =   -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -Wl,-O1
netCDF v4 runtime path   =   -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial
 
netCDF C compiler used   = /usr/bin/cc
R      C compiler used   = clang-19 -g -O3 -Wall -pedantic
 
******************************************************************************
 
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 clang-19 accepts -g... yes
checking for clang-19 option to accept ISO C89... none needed
checking whether we are using the GNU C compiler... (cached) yes
checking whether clang-19 accepts -g... (cached) yes
checking for clang-19 option to accept ISO C89... (cached) none needed
netcdf cc arg1: /usr/bin/cc  R cc arg1: clang-19 R_IS_GCC: 1 R_IS_CLANG: 1 NETCDF_IS_GCC: 1 NETCDF_IS_CLANG: 0  emit_warning: 0
** libs
using C compiler: ‘Debian clang version 19.1.5 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppK8gnU/R.INSTALL262bcb41e44070/ncdf4/src'
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/include -I/usr/include/hdf5/serial  -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c ncdf.c -o ncdf.o
clang-19 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o ncdf4.so ncdf.o -Wl,-rpath,/usr/lib/x86_64-linux-gnu -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -Wl,-O1 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppK8gnU/R.INSTALL262bcb41e44070/ncdf4/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppK8gnU/R.INSTALL262bcb41e44070/ncdf4/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppK8gnU/R.INSTALL262bcb41e44070/ncdf4/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)