* installing *source* package ‘RNetCDF’ ...
** this is package ‘RNetCDF’ version ‘2.11-1’
** package ‘RNetCDF’ successfully unpacked and MD5 sums checked
** using staged installation
configure: Find compiler/linker variables from environment:
checking CFLAGS... -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes
checking CPPFLAGS... -I/usr/local/include
checking LDFLAGS... -L/usr/local/lib64
checking LIBS... 
configure: Select C compiler:
checking C compiler from --with-cc... 
checking C compiler from R... gcc
configure: Find compiler/linker variables from R:
checking R_CFLAGS... -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes
checking R_CPPFLAGS... -I/usr/local/include
checking R_LDFLAGS... -L/usr/local/lib64
checking for gcc... gcc
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for gcc options needed to detect all undeclared functions... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking whether _WIN32 is declared... no
checking whether __APPLE__ is declared... no
configure: Operating system is Unix-alike
checking for nc-config... yes
configure: Checking compiler/linker variables from nc-config
configure: To skip nc-config, use --without-nc-config
checking nc-config --cflags... -I/usr/include -I/usr/include/hdf
checking nc-config --libs... -L/usr/lib64 -lnetcdf
checking build with nc-config... yes
configure: Proceeding with settings from nc-config
configure: Skipping pkg-config
configure: Check compiler type sizes and language features
checking size of int... 4
checking size of long long... 8
checking size of size_t... 8
checking for C/C++ restrict keyword... __restrict__
configure: Check NetCDF features:
checking for netcdf.h... yes
checking for library containing nc_open... none required
checking for nc_rename_grp... yes
checking for nc_get_var_chunk_cache... yes
checking for nc_inq_var_szip... yes
checking for nc_inq_var_endian... yes
checking for nc_def_var_filter... yes
checking for nc_inq_var_filter_ids... yes
checking for nc_inq_var_filter_info... yes
checking for nc_reclaim_data... yes
checking for netcdf_filter.h... yes
checking whether NC_64BIT_DATA is declared... yes
checking whether NC_FORMAT_64BIT_DATA is declared... yes
checking whether NC_DISKLESS is declared... yes
checking whether NC_PERSIST is declared... yes
configure: Check for parallel NetCDF features:
checking for mpi.h... no
checking for MPI_Init... no
checking whether MPI_INFO_NULL is declared... no
checking whether MPI_Info_c2f is declared... no
configure: WARNING: MPI not found - RNetCDF parallel I/O support is not enabled.
configure: If NetCDF was built with an MPI compiler, try the compiler via --with-cc
configure: Check for udunits2 features:
checking for library containing XML_ErrorString... -lexpat
checking for library containing ut_read_xml... -ludunits2
checking for ut_offset_by_time... yes
checking for ut_decode_time... yes
checking for ut_encode_time... yes
checking for udunits2.h... no
checking for udunits2/udunits2.h... yes
configure: Final compiler and linker variables for make:
CC=gcc
PKG_CFLAGS=-I/usr/include -I/usr/include/hdf
PKG_CPPFLAGS=
PKG_LDFLAGS=
LIBS=-ludunits2 -lexpat -L/usr/lib64 -lnetcdf
configure: creating ./config.status
config.status: creating src/Makefile.common
config.status: creating R/config.R
config.status: creating src/config.h
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/RNetCDF/src'
WINDOWS="FALSE" \
        MAKE="make" \
        R_HOME="/data/gannet/ripley/R/R-devel" \
        R_ARCH="" \
        /bin/sh ../tools/make-recursive.sh
make -f /data/gannet/ripley/R/R-devel/etc//Makeconf -f /data/gannet/ripley/R/R-devel/share/make/shlib.mk -f Makefile.common OBJECTS= attribute.o common.o convert.o dataset.o dimension.o group.o init.o type.o udunits.o variable.o SHLIB=RNetCDF$(SHLIB_EXT) RNetCDF_all
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/RNetCDF/src'
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c attribute.c -o attribute.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c common.c -o common.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c convert.c -o convert.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c dataset.c -o dataset.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c dimension.c -o dimension.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c group.c -o group.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c init.c -o init.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c type.c -o type.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c udunits.c -o udunits.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG   -I/usr/local/include   -I/usr/include -I/usr/include/hdf -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c variable.c -o variable.o
gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/lib64 -o RNetCDF.so attribute.o common.o convert.o dataset.o dimension.o group.o init.o type.o udunits.o variable.o -ludunits2 -lexpat -L/usr/lib64 -lnetcdf
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/RNetCDF/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/RNetCDF/src'
installing to /data/gannet/ripley/R/packages/tests-devel/RNetCDF.Rcheck/00LOCK-RNetCDF/00new/RNetCDF/libs
** R
** demo
** 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 (RNetCDF)