+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/local/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-RNetCDF-2.6.2nb2/work.log
+ su pbulk -c '"$@"' make /opt/local/bin/bmake stage-install BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/R-RNetCDF-2.6.2nb2/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Installing for R-RNetCDF-2.6.2nb2
=> Generating pre-install file lists
=> Creating installation directories
* installing *source* package 'RNetCDF' ...
file 'configure' has the wrong MD5 checksum
** using staged installation
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 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 size of int... 4
checking size of long long... 8
checking size of size_t... 8
checking for nc-config... yes
checking netcdf linker flags... -L/opt/local/lib -lnetcdf
checking netcdf preprocessor and compiler flags... -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED
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_create_par_fortran... yes
checking for nc_open_par_fortran... yes
checking for nc_var_par_access... yes
checking for netcdf_par.h... no
checking for netcdf_filter.h... yes
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... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c attribute.c -o attribute.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c common.c -o common.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c convert.c -o convert.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c dataset.c -o dataset.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c dimension.c -o dimension.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c group.c -o group.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c init.c -o init.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c type.c -o type.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c udunits.c -o udunits.o
gcc -I"/opt/local/lib/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.6-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.6-2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -DHAVE_NETCDF_H=1 -DHAVE_NC_RENAME_GRP=1 -DHAVE_NC_GET_VAR_CHUNK_CACHE=1 -DHAVE_NC_INQ_VAR_SZIP=1 -DHAVE_NC_INQ_VAR_ENDIAN=1 -DHAVE_NC_DEF_VAR_FILTER=1 -DHAVE_NC_INQ_VAR_FILTER_IDS=1 -DHAVE_NC_INQ_VAR_FILTER_INFO=1 -DHAVE_NC_CREATE_PAR_FORTRAN=1 -DHAVE_NC_OPEN_PAR_FORTRAN=1 -DHAVE_NC_VAR_PAR_ACCESS=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/opt/local/include -I/usr/include -I/opt/local/include -DLDAP_DEPRECATED -I/opt/local/include -I/usr/include -DLDAP_DEPRECATED -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -fPIC  -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/local/include -I/opt/local/include/glib-2.0 -I/opt/local/include/gio-unix-2.0 -I/opt/local/lib/glib-2.0/include -I/usr/include -I/opt/local/include/freetype2 -I/opt/local/include/harfbuzz -I/opt/local/include/ncurses -DLDAP_DEPRECATED  -c variable.c -o variable.o
gcc -shared -Wl,-R/opt/local/lib/R/lib -L/opt/local/lib/R/lib -L/opt/local/gcc13/lib/gcc/x86_64-sun-solaris2.11/13.2.0 -Wl,-R/opt/local/gcc13/lib/gcc/x86_64-sun-solaris2.11/13.2.0 -L/opt/local/lib -Wl,-R/opt/local/lib -liconv -lintl -pthread -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -o RNetCDF.so attribute.o common.o convert.o dataset.o dimension.o group.o init.o type.o udunits.o variable.o -L/opt/local/lib -lnetcdf -L/opt/local/gcc13/lib/gcc/x86_64-sun-solaris2.11/13.2.0 -Wl,-R/opt/local/gcc13/lib/gcc/x86_64-sun-solaris2.11/13.2.0 -L/opt/local/lib -Wl,-R/opt/local/lib -lintl -liconv -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -ludunits2 -lexpat -Wl,-R/opt/local/lib/R/lib -L/opt/local/lib/R/lib -lR
installing to /home/pbulk/build/math/R-RNetCDF/work/.destdir/opt/local/lib/R/library/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
elfedit: invalid option -- r
Usage: elfedit <option(s)> elffile(s)
 Update the ELF header of ELF files
 The options are:
  --input-mach [none|i386|iamcu|l1om|k1om|x86_64]
                              Set input machine type
  --output-mach [none|i386|iamcu|l1om|k1om|x86_64]
                              Set output machine type
  --input-type [none|rel|exec|dyn]
                              Set input file type
  --output-type [none|rel|exec|dyn]
                              Set output file type
  --input-osabi [none|HPUX|NetBSD|GNU|Linux|Solaris|AIX|Irix|FreeBSD|TRU64|Modesto|OpenBSD|OpenVMS|NSK|AROS|FenixOS]
                              Set input OSABI
  --output-osabi [none|HPUX|NetBSD|GNU|Linux|Solaris|AIX|Irix|FreeBSD|TRU64|Modesto|OpenBSD|OpenVMS|NSK|AROS|FenixOS]
                              Set output OSABI
  --input-abiversion [0-255]  Set input ABIVERSION
  --output-abiversion [0-255] Set output ABIVERSION
  --enable-x86-feature [ibt|shstk|lam_u48|lam_u57]
                              Enable x86 feature
  --disable-x86-feature [ibt|shstk|lam_u48|lam_u57]
                              Disable x86 feature
  -h --help                   Display this information
  -v --version                Display the version number of elfedit
elfedit: invalid option -- r
Usage: elfedit <option(s)> elffile(s)
 Update the ELF header of ELF files
 The options are:
  --input-mach [none|i386|iamcu|l1om|k1om|x86_64]
                              Set input machine type
  --output-mach [none|i386|iamcu|l1om|k1om|x86_64]
                              Set output machine type
  --input-type [none|rel|exec|dyn]
                              Set input file type
  --output-type [none|rel|exec|dyn]
                              Set output file type
  --input-osabi [none|HPUX|NetBSD|GNU|Linux|Solaris|AIX|Irix|FreeBSD|TRU64|Modesto|OpenBSD|OpenVMS|NSK|AROS|FenixOS]
                              Set input OSABI
  --output-osabi [none|HPUX|NetBSD|GNU|Linux|Solaris|AIX|Irix|FreeBSD|TRU64|Modesto|OpenBSD|OpenVMS|NSK|AROS|FenixOS]
                              Set output OSABI
  --input-abiversion [0-255]  Set input ABIVERSION
  --output-abiversion [0-255] Set output ABIVERSION
  --enable-x86-feature [ibt|shstk|lam_u48|lam_u57]
                              Enable x86 feature
  --disable-x86-feature [ibt|shstk|lam_u48|lam_u57]
                              Disable x86 feature
  -h --help                   Display this information
  -v --version                Display the version number of elfedit
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RNetCDF)
=> Generating CTF data
=> Automatic stripping of debug information
=> Automatic manual page handling
=> Generating post-install file lists
=> Checking file-check results for R-RNetCDF-2.6.2nb2
=> Checking for non-existent script interpreters in R-RNetCDF-2.6.2nb2
=> Checking file permissions in R-RNetCDF-2.6.2nb2
=> Checking for missing run-time search paths in R-RNetCDF-2.6.2nb2
ERROR: lib/R/library/RNetCDF/libs/RNetCDF.so: /opt/local/lib/libexpat.so.1: expat-2.5.0 is not a runtime dependency
*** Error code 1

Stop.
bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/R-RNetCDF
*** Error code 1

Stop.
bmake: stopped in /data/jenkins/workspace/pkgsrc-trunk-x86_64/math/R-RNetCDF