Hi All,
i'm on a debian linux 64bit,
i'm tying to install the netcdf intraface, i tried both ncdf and ncdf4
but trying to build i received the error :
(i have necdf installed on my machine and it is able to fiund it .. no missed .h)
epy at epinux:~$ sudo R CMD INSTALL --configure-args="-with-netcdf_incdir=/usr/include -with-netcdf_libdir=/usr/lib" ncdf4_1.8.tar.gz
* installing to library ?/usr/local/lib/R/site-library?
* installing *source* package ?ncdf4? ...
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:
This netCDF 4.2.1.1 has been built with the following features:
--cc -> gcc
--cflags -> -I/usr/local/include -I/usr/local/include
--libs -> -L/usr/local/lib -lnetcdf
--has-c++ -> no
--cxx ->
--has-c++4 -> no
--cxx4 ->
--fc ->
--fflags ->
--flibs ->
--has-f90 -> no
--has-dap -> yes
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-pnetcdf-> no
--has-szlib ->
--prefix -> /usr/local
--includedir-> /usr/local/include
--version -> netCDF 4.2.1.1
---
netcdf.m4: about to set rpath, here is source string: >-L/usr/local/lib -lnetcdf<
netcdf.m4: final rpath: -Wl,-rpath,/usr/local/lib
Netcdf library version: netCDF 4.2.1.1
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: gcc
configure: creating ./config.status
config.status: creating R/load.R
config.status: creating src/Makevars
********************** Results of ncdf4 package configure *******************
netCDF v4 CPP flags = -I/usr/local/include -I/usr/local/include
netCDF v4 LD flags = -Wl,-rpath,/usr/local/lib -L/usr/local/lib -lnetcdf
netCDF v4 runtime path = -Wl,-rpath,/usr/local/lib
******************************************************************************
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/local/include -I/usr/local/include -fpic -O2 -pipe -g -c ncdf.c -o ncdf.o
ncdf.c: In function ?R_nc4_nctype_to_Rtypecode?:
ncdf.c:40:18: error: ?NC_INT? undeclared (first use in this function)
ncdf.c:40:18: note: each undeclared identifier is reported only once for each function it appears in
ncdf.c:49:18: error: ?NC_UBYTE? undeclared (first use in this function)
ncdf.c:51:18: error: ?NC_USHORT? undeclared (first use in this function)
ncdf.c:53:18: error: ?NC_UINT? undeclared (first use in this function)
ncdf.c:55:18: error: ?NC_INT64? undeclared (first use in this function)
ncdf.c:57:18: error: ?NC_UINT64? undeclared (first use in this function)
ncdf.c: In function ?R_nc4_varsize?:
ncdf.c:69:28: error: ?NC_MAX_DIMS? undeclared (first use in this function)
ncdf.c:75:2: warning: implicit declaration of function ?nc_inq_varndims? [-Wimplicit-function-declaration]
ncdf.c:78:4: warning: implicit declaration of function ?nc_strerror? [-Wimplicit-function-declaration]
ncdf.c:84:2: warning: implicit declaration of function ?nc_inq_vardimid? [-Wimplicit-function-declaration]
ncdf.c:94:3: warning: implicit declaration of function ?nc_inq_dimlen? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_varunlim?:
ncdf.c:112:2: warning: implicit declaration of function ?nc_inq_unlimdim? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_var?:
ncdf.c:152:2: warning: implicit declaration of function ?nc_inq_var? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_vartype?:
ncdf.c:168:2: warning: implicit declaration of function ?nc_inq_vartype? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_varname?:
ncdf.c:181:2: warning: implicit declaration of function ?nc_inq_varname? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_get_vara_double?:
ncdf.c:214:2: warning: implicit declaration of function ?nc_get_vara_double? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_get_vara_int?:
ncdf.c:257:2: warning: implicit declaration of function ?nc_get_vara_int? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_get_vara_text?:
ncdf.c:313:2: warning: implicit declaration of function ?nc_get_vara_text? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_dimid?:
ncdf.c:345:2: warning: implicit declaration of function ?nc_inq_dimid? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_varid?:
ncdf.c:355:2: warning: implicit declaration of function ?nc_inq_varid? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_dimids?:
ncdf.c:377:9: warning: implicit declaration of function ?nc_inq_dimids? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_dim?:
ncdf.c:387:12: error: ?NC_MAX_NAME? undeclared (first use in this function)
ncdf.c:391:2: warning: implicit declaration of function ?nc_inq_dim? [-Wimplicit-function-declaration]
ncdf.c:408:2: warning: implicit declaration of function ?nc_inq_unlimdims? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq?:
ncdf.c:451:2: warning: implicit declaration of function ?nc_inq? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_open?:
ncdf.c:475:2: warning: implicit declaration of function ?nc_open? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_create?:
ncdf.c:499:15: error: ?NC_SHARE? undeclared (first use in this function)
ncdf.c:501:15: error: ?NC_64BIT_OFFSET? undeclared (first use in this function)
ncdf.c:503:15: error: ?NC_NETCDF4? undeclared (first use in this function)
ncdf.c:505:2: warning: implicit declaration of function ?nc_create? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_ttc_to_nctype?:
ncdf.c:518:11: error: ?NC_INT? undeclared (first use in this function)
ncdf.c: In function ?R_nc4_put_att_logical?:
ncdf.c:554:4: warning: implicit declaration of function ?nc_put_att_float? [-Wimplicit-function-declaration]
ncdf.c:564:4: warning: implicit declaration of function ?nc_put_att_double? [-Wimplicit-function-declaration]
ncdf.c:579:3: warning: implicit declaration of function ?nc_put_att_int? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_put_att_text?:
ncdf.c:633:2: warning: implicit declaration of function ?nc_put_att_text? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_get_att_int?:
ncdf.c:645:2: warning: implicit declaration of function ?nc_get_att_int? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_get_att_double?:
ncdf.c:653:2: warning: implicit declaration of function ?nc_get_att_double? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_att?:
ncdf.c:669:2: warning: implicit declaration of function ?nc_inq_att? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_get_att_text?:
ncdf.c:698:2: warning: implicit declaration of function ?nc_get_att_text? [-Wimplicit-function-declaration]
ncdf.c:705:2: warning: implicit declaration of function ?nc_inq_attlen? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_put_vara_double?:
ncdf.c:753:2: warning: implicit declaration of function ?nc_put_vara_double? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_put_vara_int?:
ncdf.c:780:2: warning: implicit declaration of function ?nc_put_vara_int? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_put_var_int?:
ncdf.c:789:2: warning: implicit declaration of function ?nc_put_var_int? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_put_var_double?:
ncdf.c:798:2: warning: implicit declaration of function ?nc_put_var_double? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_put_vara_text?:
ncdf.c:835:3: warning: implicit declaration of function ?nc_put_vara_text? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_def_var_byte?:
ncdf.c:947:2: warning: implicit declaration of function ?nc_def_var? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_def_var_int?:
ncdf.c:964:3: error: ?NC_INT? undeclared (first use in this function)
ncdf.c: In function ?R_nc4_def_dim?:
ncdf.c:1043:2: warning: implicit declaration of function ?nc_def_dim? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_redef?:
ncdf.c:1054:2: warning: implicit declaration of function ?nc_redef? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_rename_var?:
ncdf.c:1063:2: warning: implicit declaration of function ?nc_rename_var? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_attname?:
ncdf.c:1072:2: warning: implicit declaration of function ?nc_inq_attname? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_def_var_chunking?:
ncdf.c:1102:16: error: ?NC_CONTIGUOUS? undeclared (first use in this function)
ncdf.c:1104:16: error: ?NC_CHUNKED? undeclared (first use in this function)
ncdf.c:1116:2: warning: implicit declaration of function ?nc_def_var_chunking? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_var_chunking?:
ncdf.c:1139:2: warning: implicit declaration of function ?nc_inq_var_chunking? [-Wimplicit-function-declaration]
ncdf.c:1145:20: error: ?NC_CONTIGUOUS? undeclared (first use in this function)
ncdf.c:1147:25: error: ?NC_CHUNKED? undeclared (first use in this function)
ncdf.c: In function ?R_nc4_inq_var_deflate?:
ncdf.c:1173:2: warning: implicit declaration of function ?nc_inq_var_deflate? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_def_var_deflate?:
ncdf.c:1212:2: warning: implicit declaration of function ?nc_def_var_deflate? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_ngroups?:
ncdf.c:1227:2: warning: implicit declaration of function ?nc_inq_grps? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_grpname?:
ncdf.c:1307:2: warning: implicit declaration of function ?nc_inq_grpname_len? [-Wimplicit-function-declaration]
ncdf.c:1317:2: warning: implicit declaration of function ?nc_inq_grpname? [-Wimplicit-function-declaration]
ncdf.c: In function ?R_nc4_inq_format?:
ncdf.c:1364:2: warning: implicit declaration of function ?nc_inq_format? [-Wimplicit-function-declaration]
ncdf.c:1374:8: error: ?NC_FORMAT_CLASSIC? undeclared (first use in this function)
ncdf.c:1378:8: error: ?NC_FORMAT_64BIT? undeclared (first use in this function)
ncdf.c:1382:8: error: ?NC_FORMAT_NETCDF4? undeclared (first use in this function)
ncdf.c:1386:8: error: ?NC_FORMAT_NETCDF4_CLASSIC? undeclared (first use in this function)
make: *** [ncdf.o] Error 1
ERROR: compilation failed for package ?ncdf4?
* removing ?/usr/local/lib/R/site-library/ncdf4?
Thanks for any help!
Massimo.