[R] help compiling add-on package

[Timothy W. Hilton]

Hello r-help,

I am having trouble installing the add-on package gstat.  I suspect (but
I'm not sure) that the trouble may be that it runs all the checks for
gcc, then uses Intel's compiler to actually compile.  I have not been
able to successfully force it to use gcc to test that theory.  R CMD
INSTALL and R.version() output follow below; any help greatly
appreciated!

-Tim

--

Timothy W. Hilton
PhD Candidate, Department of Meteorology
The Pennsylvania State University
503 Walker Building, University Park, PA   16802
hilton at meteo.psu.edu


=======================================================================

$ R CMD INSTALL gstat_0.9-69.tar.gz -l ~/work/R/x86_64-unknown-linux-gnu-library/2.11
* installing *source* package ‘gstat’ ...
creating cache ./config.cache
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) 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
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 drand48... yes
checking for gettimeofday... yes
checking whether byte ordering is bigendian... no
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... yes
checking for malloc.h... yes
checking for varargs.h... no
checking for size_t... yes
checking for working const... (cached) yes
checking whether byte ordering is bigendian... (cached) no
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
./src/meschach/maxint.c: In function 'main':
./src/meschach/maxint.c:37: warning: incompatible implicit declaration of built-in function 'printf'
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/config.h
creating src/machine.h
** libs
icc -std=c99 -I/usr/global/R/2.11.1/lib64/R/include  -I/usr/local/include  -mp  -fpic  -i-dynamic -mieee-fp -prec-div -O2 -axSSE2,SSE3,SSEE3,SSE4.1,SSE4.2,AVX -c block.c -o block.o
icc: command line remark #10010: option '-mp' is deprecated and will be removed in a future release. See '-help deprecated'
block.c(66): (col. 70) remark: block_discr has been targeted for automatic cpu dispatch.
icc -std=c99 -I/usr/global/R/2.11.1/lib64/R/include  -I/usr/local/include  -mp  -fpic  -i-dynamic -mieee-fp -prec-div -O2 -axSSE2,SSE3,SSEE3,SSE4.1,SSE4.2,AVX -c chfactor.c -o chfactor.o
icc: command line remark #10010: option '-mp' is deprecated and will be removed in a future release. See '-help deprecated'
matrix.h(49): error: identifier "u_int" is undefined
                u_int   dim, max_dim;
                ^

matrix.h(55): error: identifier "u_int" is undefined
                u_int   m, n;
                ^
<snip>
lots of similar u_int errors in matrix.h and matrix2.h
</snip>

compilation aborted for chfactor.c (code 2)
make: *** [chfactor.o] Error 2
ERROR: compilation failed for package ‘gstat’

=======================================================================

> R.Version()
$platform
[1] "x86_64-unknown-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "2"

$minor
[1] "11.1"

$year
[1] "2010"

$month
[1] "05"

$day
[1] "31"

$`svn rev`
[1] "52157"

$language
[1] "R"

$version.string
[1] "R version 2.11.1 (2010-05-31)"