Pinto wrote: > > Dear R users > > I am attempting to add lncdf_1.6.tar.gz libraries within R, and have > failed. I have R version 2.8.1, and are running on fedora 10 Kernel Linux > 2.6.293.-60.fc10.x86_64. > I've run R CMD INSTALL ncdf_1.6.tar.gz > and I have the following > --------------- > * Installing to library '/usr/lib64/R/library' > * Installing *source* package 'ncdf' ... > checking for gcc... gcc -m64 -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 -m64 -std=gnu99 accepts -g... yes > checking for gcc -m64 -std=gnu99 option to accept ANSI C... none needed > checking how to run the C preprocessor... gcc -m64 -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 -m64 -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 -m64 -mtune=generic -c ncdf2.c -o ncdf2.o > gcc -m64 -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 -m64 -mtune=generic -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 -m64 -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 -m64 -mtune=generic -c ncdf.c -o ncdf.o > ncdf.c: In function ‘R_nc_get_vara_double’: > ncdf.c:196: warning: format ‘%u’ expects type ‘unsigned int’, but argument > 3 has type ‘size_t’ > ncdf.c:202: warning: format ‘%u’ expects type ‘unsigned int’, but argument > 3 has type ‘size_t’ > ncdf.c: In function ‘R_nc_get_vara_int’: > ncdf.c:239: warning: format ‘%u’ expects type ‘unsigned int’, but argument > 3 has type ‘size_t’ > ncdf.c:245: warning: format ‘%u’ expects type ‘unsigned int’, but argument > 3 has type ‘size_t’ > ncdf.c: In function ‘R_nc_get_vara_text’: > ncdf.c:296: warning: format ‘%u’ expects type ‘unsigned int’, but argument > 3 has type ‘size_t’ > ncdf.c:302: warning: format ‘%u’ expects type ‘unsigned int’, but argument > 3 has type ‘size_t’ > 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’ > ncdf.c: In function ‘R_nc_put_vara_double’: > ncdf.c:582: warning: format ‘%d’ expects type ‘int’, but argument 3 has > type ‘size_t’ > ncdf.c:585: warning: format ‘%d’ expects type ‘int’, but argument 3 has > type ‘size_t’ > gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o ncdf.so ncdf2.o ncdf3.o > ncdf.o -L. -lnetcdf -L/usr/lib64/R/lib -lR > /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 `/usr/lib64/R/library/ncdf/libs/*': No such file or > directory > ERROR: compilation failed for package 'ncdf' > ** Removing '/usr/lib64/R/library/ncdf' > --------------- > > Any help is strongly appreciated, > thank you in advance >
Based on the error: /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 I would guess that R is complaining about libnetcdf.a was not compiled to use position independent code, hence the request for -fPIC. However, my expertise in these areas is amateur at best-- someone else may be able to provide a more informed opinion. Also, you stated you are using R 2.8.1 which is out of date by two, soon to be three, major releases. It is highly recommended to keep your version of R as current as possible. A newer version of R may contain changes to package compilation that addresses the issues you are having- especially as you are compiling for a 64 bit platform. Good luck! -Charlie ----- Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://n4.nabble.com/install-ncdf-package-tp1680818p1684264.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.
