Dear Simon,
I installed the ncdf package in the way you suggested but still i got the
same error i got before. I haves pasted below the installation log and
errors.
> *install.packages('ncdf')*
Warning in install.packages("ncdf") :
argument 'lib' is missing: using '/usr/lib/R/library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL '
http://rm.mirror.garr.it/mirrors/CRAN/src/contrib/ncdf_1.6.tar.gz'
Content type 'application/x-gzip' length 72533 bytes (70 Kb)
opened URL
==================================================
downloaded 70 Kb
* Installing *source* package 'ncdf' ...
checking for gcc... gcc -m32 -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 -m32 -std=gnu99 accepts -g... yes
checking for gcc -m32 -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -m32 -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 -m32 -std=gnu99 -I/usr/include/R -I. -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -c ncdf2.c -o ncdf2.o
gcc -m32 -std=gnu99 -I/usr/include/R -I. -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -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
ncdf3.c:249: warning: rv_data may be used uninitialized in this function
gcc -m32 -std=gnu99 -I/usr/include/R -I. -I/usr/local/include -fpic -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
-fasynchronous-unwind-tables -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 -m32 -std=gnu99 -shared -L/usr/local/lib -o ncdf.so ncdf2.o ncdf3.o
ncdf.o -L. -lnetcdf -L/usr/lib/R/lib -lR
** 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 file 'att.get.ncdf.Rd' 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 file 'version.ncdf.Rd' on or after line 6
Note: removing empty section \arguments in file 'version.ncdf.Rd'
version.ncdf text html latex
** building package indices ...
** DONE (ncdf)*
The downloaded packages are in
/tmp/RtmpKrf8Vc/downloaded_packages
Updating HTML index of packages in '.Library'
> *library(ncdf)*
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so':
/usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after
reloc: Permission denied
Error in library(ncdf) : .First.lib failed for 'ncdf'
What should i do now ?
Bala
On Tue, Apr 21, 2009 at 10:48 AM, Simon Pickett <simon.pick...@bto.org>wrote:
> Hi,
>
> Check out the FAQ on the home page about installing packages.
>
> You need to
> 1. Install the package from a local mirror, you can do this from the drop
> down menu ("Install packages")
> 2. then call the package using "library(name of the package)"
>
> It helps to know where your R library directory is on your computer.
>
> HTH Simon.
>
>
> ----- Original Message ----- From: "Bala subramanian" <
> bala.biophys...@gmail.com>
> To: <r-help@r-project.org>
> Sent: Tuesday, April 21, 2009 9:34 AM
> Subject: [R] joined R-today
>
>
> Friends,
>>
>> I am a newbie to R. Just installed and started with R. I installed netcdf
>> library (netcdf-4.0.tar.gz) and then ncdf package of R from CRAN with the
>> following command.
>>
>> R CMD INSTALL
>> --configure-args="-with-netcdf_incdir=/usr/local/netcdf/include
>> -with-netcdf_libdir=/usr/local/netcdf/lib" ncdf_1.6.tar.gz
>>
>> The installation was successful. But when i try to use ncdf inside R, i
>> get
>> the following error. Kindly help me how to resolve the problem.
>>
>> trjfile<-system.file('test.netcdf',package='bio3d')
>>> trj<-read.ncdf(trjfile)
>>>
>> Loading required package: ncdf
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared library '/usr/lib/R/library/ncdf/libs/ncdf.so':
>> /usr/lib/R/library/ncdf/libs/ncdf.so: cannot restore segment prot after
>> reloc: Permission denied
>> Error in read.ncdf(trjfile) : Please install the ncdf package from CRAN
>>
>> Thanks in advance,
>> Bala
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> 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.
>>
>>
>
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
