a problem of install

[PanfengZhang]

When I was installing packages on the Ubuntu system, I encountered some issues. Below are the error messages.

• installing source package ‘RNetCDF’ ... package ‘RNetCDF’ successfully unpacked and MD5 sums checked using staged installation configure: Find compiler/linker variables from environment: checking CFLAGS... -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 checking CPPFLAGS... -I/sw/include checking LDFLAGS... -L/sw/lib checking LIBS... configure: Select C compiler: checking C compiler from --with-mpicc... checking C compiler from R... gcc configure: Find compiler/linker variables from R: checking R_CFLAGS... -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 checking R_CPPFLAGS... checking R_LDFLAGS... -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro 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: Check compiler/linker variables from nc-config: checking NC_CC... x86_64-conda-linux-gnu-cc checking NC_CC matches selected C compiler... no ... specify --with-mpicc if needed checking nc-config --cflags... -I/home/zhang/miniconda3/include checking nc-config --libs ... -L/home/zhang/miniconda3/lib -lnetcdf 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 configure: WARNING: MPI not available. Specify --with-mpicc if needed. configure: WARNING: NetCDF parallel I/O requires MPI 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... yes configure: Final compiler and linker variables for make: CC=gcc PKG_CFLAGS=-I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 PKG_CPPFLAGS=-I/sw/include PKG_LDFLAGS=-L/sw/lib LIBS=-ludunits2 -lexpat -L/home/zhang/miniconda3/lib -lnetcdf configure: creating ./config.status config.status: creating src/Makefile.common config.status: creating R/config.R ** libs WINDOWS="FALSE" \ MAKE="make" \ R_HOME="/usr/lib/R" \ R_ARCH="" \ /bin/bash ../tools/make-recursive.sh make -f /usr/lib/R/etc//Makeconf -f /usr/share/R/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[1]: Entering directory '/home/zhang/RNetCDF.Rcheck/00_pkg_src/RNetCDF/src' gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVEDECLAPPLE=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c attribute.c -o attribute.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVEDECLAPPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c common.c -o common.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c convert.c -o convert.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dataset.c -o dataset.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dimension.c -o dimension.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c group.c -o group.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c type.c -o type.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c udunits.c -o udunits.o gcc -I"/usr/share/R/include" -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"2.9-2\" -DPACKAGE_STRING=\"RNetCDF\ 2.9-2\" -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 -DHAVE_DECLWIN32=0 -DHAVE_DECL_APPLE__=0 -DSIZEOF_INT=4 -DSIZEOF_LONG_LONG=8 -DSIZEOF_SIZE_T=8 -Drestrict=restrict__ -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_RECLAIM_DATA=1 -DHAVE_NETCDF_FILTER_H=1 -DHAVE_DECL_NC_64BIT_DATA=1 -DHAVE_DECL_NC_FORMAT_64BIT_DATA=1 -DHAVE_DECL_NC_DISKLESS=1 -DHAVE_DECL_NC_PERSIST=1 -DHAVE_UDUNITS2_H=1 -DHAVE_LIBUDUNITS2=1 -I/sw/include -I/home/zhang/miniconda3/include -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -ffile-prefix-map=/build/r-base-2y82rL/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c variable.c -o variable.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RNetCDF.so attribute.o common.o convert.o dataset.o dimension.o group.o init.o type.o udunits.o variable.o -L/sw/lib -ludunits2 -lexpat -L/home/zhang/miniconda3/lib -lnetcdf -L/usr/lib/R/lib -lR make[1]: Leaving directory '/home/zhang/RNetCDF.Rcheck/00_pkg_src/RNetCDF/src' installing to /home/zhang/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 Error: package or namespace load failed for ‘RNetCDF’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/zhang/RNetCDF.Rcheck/00LOCK-RNetCDF/00new/RNetCDF/libs/RNetCDF.so': /home/zhang/RNetCDF.Rcheck/00LOCK-RNetCDF/00new/RNetCDF/libs/RNetCDF.so: undefined symbol: nc_reclaim_data Error: loading failed Execution halted ERROR: loading failed
• removing ‘/home/zhang/RNetCDF.Rcheck/RNetCDF’

[mjwoods]

Hi @PanfengZhang ,

I think the problem is that the netcdf library is being detected in your miniconda installation, but that is not in the normal library path.

RNetCDF uses the command nc-config to determine details of the netcdf installation, and nc-config is being found in the miniconda directory. If you have the Ubuntu version of netcdf installed, you could use it by removing miniconda from your PATH environment variable (temporarily) before installing RNetCDF.

Otherwise it may be possible to use the miniconda netcdf by installing RNetCDF from the R command prompt with a command like this:

install.packages("RNetCDF", configure.args="LDFLAGS='-L/home/zhang/miniconda3/lib -Wl,-rpath=/home/zhang/miniconda3/lib'")

The -rpath option ensures that R can find the miniconda netcdf library when loading RNetCDF.

As a last resort, another option is to set the library path as follows, but it could have unwanted side-effects for other software:

export LD_LIBRARY_PATH=/home/zhang/miniconda3/lib