> 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@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 <massimodisa...@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@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@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) dpie...@ucsd.edu ______________________________________________ R-help@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.
