> Hi All,
>
> i'm on a debian linux 64bit,
> i'm tying to install the netcdf intraface, i tried both ncdf and ncdf4
[error lines cut]
Hi Massimo,
things are getting confused because nc-config thinks that the netcdf
library is installed in one place, and you are telling R that it's
installed in a different place:
Your command line specifies /usr/lib and /usr/include:
> epy at epinux:~$ sudo R CMD INSTALL --configure-args="-with-
netcdf_incdir=/usr/include -with-netcdf_libdir=/usr/lib"
But nc-config thinks it's in /usr/local:
> --cflags -> -I/usr/local/include -I/usr/local/include
> --libs -> -L/usr/local/lib -lnetcdf
Is there a reason you specified the paths on the command line? I
suggest *not* specifying the paths in the command line and seeing if
it works automatically using the information in nc-config. However, if
the information in nc-config is outright wrong (for instance, if the
libraries were moved manually after the library was installed), I
suggest removing your current installation of the netcdf library and
re-installing it cleanly from scratch so that it has a correct and
working nc-config.
Regards,
--Dave
On Thu, Mar 7, 2013 at 3:45 PM, epi <massimodisasha at gmail.com>
wrote:> 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.
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography, La Jolla, California, USA
(858) 534-8276 (voice) / (858) 534-8561 (fax) dpierce at ucsd.edu