I am running 64-bit Ubuntu 7.10 and unfortunately remember seeing that
error message but not how I got it to go away.
I would first try compiling netcdf-3.6.2 from source, without changing the
default directories for installation.
Looking at the error message it seems like the 3 shared libraries get made
but then linking them gives the error - that step seems to be where it
says to compile with "-fPIC".
My output of install.packages("ncdf") is below with that of
sessionInfo()
- I still see a lot of warnings.
* Installing *source* package 'ncdf' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
Found netcdf.h in: .
checking for nc_open in -lnetcdf... yes
Found netcdf library file libnetcdf.a in directory .
configure: creating ./config.status
config.status: creating R/load.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include
-I. -I/usr/local/include -fpic -g -O2 -c ncdf2.c -o ncdf2.o
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include
-I. -I/usr/local/include -fpic -g -O2 -c ncdf3.c -o ncdf3.o
ncdf3.c: In function R_nc_get_vara_charvarid:
ncdf3.c:221: warning: assignment discards qualifiers from pointer target
type
ncdf3.c: In function R_nc_get_vara_numvarid:
ncdf3.c:267: warning: assignment discards qualifiers from pointer target
type
gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include
-I. -I/usr/local/include -fpic -g -O2 -c ncdf.c -o ncdf.o
ncdf.c: In function R_nc_ttc_to_nctype:
ncdf.c:424: warning: implicit declaration of function exit
ncdf.c:424: warning: incompatible implicit declaration of built-in
function exit
gcc -std=gnu99 -shared -L/usr/local/lib64 -o ncdf.so ncdf2.o ncdf3.o
ncdf.o -L. -lnetcdf
** R
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'ncdf'
Formats: text html latex example
ancdf text html latex
aput.var.ncdf text html latex example
Note: unmatched right brace in 'att.get.ncdf' on or after line 6
att.get.ncdf text html latex example
att.put.ncdf text html latex example
close.ncdf text html latex example
create.ncdf text html latex example
dim.def.ncdf text html latex example
enddef.ncdf text html latex example
get.var.ncdf text html latex example
ncdf-internal text html latex
open.ncdf text html latex example
print.ncdf text html latex example
redef.ncdf text html latex example
set.missval.ncdf text html latex example
sync.ncdf text html latex example
var.add.ncdf text html latex example
var.def.ncdf text html latex example
Note: unmatched right brace in 'version.ncdf' on or after line 6
version.ncdf text html latex
** building package indices ...
* DONE (ncdf)
The downloaded packages are in
/tmp/RtmpcJ0Af9/downloaded_packages
Updating HTML index of packages in '.Library'>
> sessionInfo()
R version 2.6.1 (2007-11-26)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] splines grid tcltk stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] ncdf_1.6 xtable_1.5-2 TIMP_1.5 minpack.lm_1.0-5
[5] quadprog_1.4-11 nnls_1.2 gclus_1.2 gplots_2.3.2
[9] gdata_2.3.1 gtools_2.4.0 fields_3.5 vcd_1.0-6
[13] colorspace_0.95 MASS_7.2-38
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.1
On Tue, 22 Jan 2008, Linda Smith wrote:
> Dear All,
> I recently got a 64bit machine and had netcdf-3.6.2 installed. Then I tried
> to install ncdf package but got the following error message when using
> netcdflib:
>
> gcc -std=gnu99 -I/home/ljin/share/R-2.6.1/include
> -I/home/ljin/share/R-2.6.1/include
> -I. -I/usr/local/include -fpic -g -O2 -c ncdf2.c -o ncdf2.o
> gcc -std=gnu99 -I/home/ljin/share/R-2.6.1/include
> -I/home/ljin/share/R-2.6.1/include
> -I. -I/usr/local/include -fpic -g -O2 -c ncdf3.c -o ncdf3.o
> ncdf3.c: In function 'R_nc_get_vara_charvarid':
> ncdf3.c:221: warning: assignment discards qualifiers from pointer target
> type
> ncdf3.c: In function 'R_nc_get_vara_numvarid':
> ncdf3.c:267: warning: assignment discards qualifiers from pointer target
> type
> gcc -std=gnu99 -I/home/ljin/share/R-2.6.1/include
> -I/home/ljin/share/R-2.6.1/include
> -I. -I/usr/local/include -fpic -g -O2 -c ncdf.c -o ncdf.o
> ncdf.c: In function 'R_nc_ttc_to_nctype':
> ncdf.c:424: warning: implicit declaration of function 'exit'
> ncdf.c:424: warning: incompatible implicit declaration of built-in function
> 'exit'
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o ncdf.so ncdf2.o ncdf3.o
> ncdf.o-L. -lnetcdf
> /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32
> against `a local symbol' can not be used when making a shared object;
> recompile with -fPIC
> /usr/local/lib/libnetcdf.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make: *** [ncdf.so] Error 1
> chmod: cannot access `/home/ljin/share/R-2.6.1/library/ncdf/libs/*': No
such
> file or directory
> ERROR: compilation failed for package 'ncdf'
> ** Removing '/home/ljin/share/R-2.6.1/library/ncdf'
>
> =======> I had no problem when I install the ncdf package on my 32bit
linux machine.
> Could anyone help me with the installation on 64bit machine?
>
> Thanks!
>
> Linda
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> 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.
>