[R-SIG-Mac] R, sudo, and install.packages()

Jan de Leeuw deleeuw at stat.ucla.edu
Mon Jun 16 23:17:31 MEST 2003 

1. gstat never worked for me either, because the R package assumes  
there are
several include files available from the regular gstat distribution

2. If you think sudo R is bothersome, just do sudo chown -R yourself  
/usr/local/lib/R
once.

On Monday, Jun 16, 2003, at 12:47 US/Pacific, Don MacQueen wrote:

> Following up in my recent message about a problem with library(gstat),  
> for which the error message is:
>
>>  library(gstat)
> Error: package gstat was built for  Win32
>
> I tried install.packages('gstat'). Note the failure.
>
> Naturally, since this version of R was installed in /usr/local with an  
> installer that required admin privileges, R files are owned by root,  
> and a user running R in "ordinary" mode can't write to /usr/local.  
> When I was installing from sources, I never had this problem, because  
> I installed R as myself, thus I owned RHOME, and so I could use  
> install.packages().
>
>>  install.packages('gstat')
> trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
> Content type `text/plain; charset=iso-8859-1' length 108772 bytes
> opened URL
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> ......
> downloaded 106Kb
>
> trying URL `http://cran.r-project.org/src/contrib/gstat_0.9-6.tar.gz'
> Content type `application/x-tar' length 367529 bytes
> opened URL
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> ........
> downloaded 358Kb
>
> ERROR: cannot write to or create directory '/usr/local/lib/R/library'
>
> Delete downloaded files (y/N)? y
>
> Warning message:
> Installation of package gstat had non-zero exit status in:  
> install.packages("gstat")
>>  ?install.packages
>>  q()
> Save workspace image? [y/n/c]: y
> Warning messages:
> 1: namespaces may not be available when loading
> 2: names in persistent strings are currently ignored
>
> --------------------------------------------------------------------
> The work-around is to start R with
>
>   sudo R
>
> in which case installation is possible. This is kind of a bother, but  
> at least it's possible.
>
> Specific to gstat, there is unfortunately still a problem, but at  
> least now it's something to do with how the package and maybe its  
> makefiles are coded.
>
>>  install.packages('gstat')
> trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
> Content type `text/plain; charset=iso-8859-1' length 108772 bytes
> opened URL
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> ......
> downloaded 106Kb
>
> trying URL `http://cran.r-project.org/src/contrib/gstat_0.9-6.tar.gz'
> Content type `application/x-tar' length 367529 bytes
> opened URL
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> .......... .......... .......... .......... ..........
> ........
> downloaded 358Kb
>
> * Installing *source* package 'gstat' ...
> creating cache ./config.cache
> checking for gcc... gcc
> checking whether the C compiler (gcc -I/sw/include -L/sw/lib) works...  
> yes
> checking whether the C compiler (gcc -I/sw/include -L/sw/lib) is a  
> cross-compiler... no
> checking whether we are using GNU C... yes
> checking whether gcc accepts -g... yes
> checking how to run the C preprocessor... gcc -E -traditional-cpp
> checking for AIX... no
> checking for minix/config.h... no
> checking for POSIXized ISC... no
> checking for ANSI C header files... yes
> checking for working const... yes
> checking whether time.h and sys/time.h may both be included... yes
> checking for 8-bit clean memcmp... yes
> checking for vprintf... yes
> checking for strstr... yes
> checking for strtod... yes
> checking for strtol... yes
> checking for popen... yes
> checking for drand48... yes
> checking for gettimeofday... yes
> checking for getopt... yes
> checking whether byte ordering is bigendian... yes
> checking for memory.h... yes
> checking for ANSI C header files... (cached) yes
> checking for gcc option to accept ANSI C...
> checking for function prototypes... yes
> checking for working const... (cached) yes
> checking for complex.h... no
> checking for malloc.h... no
> checking for varargs.h... yes
> checking for size_t... yes
> checking for working const... (cached) yes
> checking whether byte ordering is bigendian... (cached) yes
> checking for u_int
> computing machine epsilon(s)
> gcc -o macheps ./src/meschach/dmacheps.c
> gcc -o macheps ./src/meschach/fmacheps.c
> computing M_MAX_INT
> gcc -o maxint maxint.c
> checking char \\0 vs. float zeros
> checking for bcopy... yes
> checking for bzero... yes
> checking for function prototypes
> checking for function prototypes in structures
> updating cache ./config.cache
> creating ./config.status
> creating makefile
> creating src/makefile
> creating src/config.h
> creating src/machine.h
> ** libs
> Makefile:306: warning: overriding commands for target `.c.o'
> /usr/local/lib/R/etc/Makeconf:65: warning: ignoring old commands for  
> target `.c.o'
> gcc -c -g -Wall -I../include -I/sw/include  -DHAVE_CONFIG_H block.c
> gcc -c -g -Wall -I../include -I/sw/include  -DHAVE_CONFIG_H data.c
> gcc -c -g -Wall -I../include -I/sw/include  -DHAVE_CONFIG_H direct.c
> make: *** No rule to make target `palet.h', needed by `fig.o'.  Stop.
> ERROR: compilation failed for package 'gstat'
>
> Delete downloaded files (y/N)? y
>
> Warning message:
> Installation of package gstat had non-zero exit status in:  
> install.packages("gstat")
>>
>
>
> This is still R 1.7.0 installed using the gifi version.
>
> Thanks
> -Don
> --  
> --------------------------------------
> Don MacQueen
> Environmental Protection Department
> Lawrence Livermore National Laboratory
> Livermore, CA, USA
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
>
>
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical  
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw at stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
   
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           No matter where you go, there you are. --- Buckaroo Banzai
                    http://gifi.stat.ucla.edu/sounds/nomatter.au

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