* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/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 = gcc-14 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native
******************************************************************************
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 gcc-14 accepts -g... yes
checking for gcc-14 option to accept ISO C89... none needed
netcdf cc arg1: /usr/bin/cc R cc arg1: gcc-14 R_IS_GCC: 1 R_IS_CLANG: 0 NETCDF_IS_GCC: 1 NETCDF_IS_CLANG: 0 emit_warning: 0
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLSDbYw/R.INSTALL17d42b78160aa/ncdf4/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ncdf.c -o ncdf.o
gcc-14 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/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-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLSDbYw/R.INSTALL17d42b78160aa/ncdf4/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLSDbYw/R.INSTALL17d42b78160aa/ncdf4/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLSDbYw/R.INSTALL17d42b78160aa/ncdf4/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ncdf4/00new/ncdf4/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘ncdf4’
finding HTML links ... done
ancvar_put html
nc_close html
nc_create html
nc_enddef html
nc_open html
nc_redef html
nc_sync html
nc_version html
ncatt_get html
ncatt_put html
ncdf4-internal html
ncdf4-package html
ncdim_def html
ncvar_add html
ncvar_change_missval html
ncvar_def html
ncvar_get html
ncvar_rename html
print.ncdf4 html
** 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)