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Muhammad Rahiz <muhammad.rahiz@ouce.ox.ac.uk> wrote:
Dear all,
I'm having issues with the installation of the ncdf package. It returns a
non-zero exit status. Can anyone suggest what I should do next? FYI, I do
not have problems installing other packages.
Thanks.
Muhammad
* installing *source* package ‘ncdf’ ...
checking for nc-config... /usr/local/bin/nc-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -c ncdf.c -o ncdf.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -c ncdf2.c -o ncdf2.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -c ncdf3.c -o ncdf3.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ncdf.so ncdf.o ncdf2.o
ncdf3.o -L/usr/local/lib -lnetcdf -L/usr/lib64/R/lib -lR
/usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32
against `.rodata' 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
ERROR: compilation failed for package ‘ncdf’
* removing ‘/home/rahiz/R/x86_64-redhat-linux-gnu-library/2.13/ncdf’
The downloaded packages are in
‘/tmp/Rtmp5khIxy/downloaded_packages’
Warning message:
In install.packages("ncdf") :
installation of package 'ncdf' had non-zero exit
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Dear all,
I'm having issues with the installation of the ncdf package. It returns a
non-zero exit status. Can anyone suggest what I should do next? FYI, I do
not have problems installing other packages.
Thanks.
Muhammad
* installing *source* package ?ncdf? ...
checking for nc-config... /usr/local/bin/nc-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -c ncdf.c -o ncdf.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -c ncdf2.c -o ncdf2.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -c ncdf3.c -o ncdf3.o
gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ncdf.so ncdf.o ncdf2.o
ncdf3.o -L/usr/local/lib -lnetcdf -L/usr/lib64/R/lib -lR
/usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32
against `.rodata' 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
ERROR: compilation failed for package ?ncdf?
* removing ?/home/rahiz/R/x86_64-redhat-linux-gnu-library/2.13/ncdf?
The downloaded packages are in
?/tmp/Rtmp5khIxy/downloaded_packages?
Warning message:
In install.packages("ncdf") :
installation of package 'ncdf' had non-zero exit status
2011/9/24 Muhammad Rahiz <muhammad.rahiz at ouce.ox.ac.uk>:> Dear all, > > I'm having issues with the installation of the ncdf package. It returns a > non-zero exit status. Can anyone suggest what I should do next? FYI, I do > not have problems installing other packages. >[...] > /usr/bin/ld: /usr/local/lib/libnetcdf.a(attr.o): relocation R_X86_64_32 > against `.rodata' 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 > ERROR: compilation failed for package ?ncdf? > * removing ?/home/rahiz/R/x86_64-redhat-linux-gnu-library/2.13/ncdf?See that part where it said /usr/local/lib/libnetcdf.a needed to be recompiled with -fPIC? It means that the netcdf library on your machine, which is located in /usr/local/lib, needs to be recompiled with the -fPIC flag specified. :) I suggest consulting the netcdf library documentation for how to do this, or talk to your system administrator, or ask one of your local computer experts. Regards, --Dave -- David W. Pierce Division of Climate, Atmospheric Science, and Physical Oceanography Scripps Institution of Oceanography (858) 534-8276 (voice) ?/ ?(858) 534-8561 (fax) ? ?dpierce at ucsd.edu