On Tue, Nov 26, 2013 at 12:09 PM, Horne, Nigel (NIH/NLM/NCBI) [C] <
nigel.horne@nih.gov> wrote:

> I am a system admin who has been asked by a user to install GenomicRanges,
> however it is failing.  I know absolutely nothing about R, so I'd like some
> (gentle!) help on how to install it.
>
> This is on CentOS6, with gcc 4.4.7, R2.15.1.  The error I get is:
>
> bash-4.1$ /usr/local/R/2.15.1/lib64/R/bin/Rcmd INSTALL
> GenomicRanges_1.14.3.tar.gz
>

Hi, Nigel.

It turns out that the Bioconductor packages (of which GenomicRanges is one)
are matched to the version of R.  You are trying to install on a fairly old
version of R and the GenomicRanges version does not match.  While R does
not change too quickly, Bioconductor does continue to add features, so my
suggestion is to first install the most recent version of R (3.0.2, I
believe) so that your users have the most updated release.   Then install
using the instructions here:

http://www.bioconductor.org/packages/2.13/bioc/html/GenomicRanges.html

Let us know how it goes.

Sean




> * installing to library '/usr/local/R/2.15.1/lib64/R/library'
> * installing *source* package 'GenomicRanges' ...
> ** libs
> gcc -std=gnu99 -I/usr/local/R/2.15.1/lib64/R/include -DNDEBUG
>  -I/usr/local/include
> -I"/usr/local/R/2.15.1/lib64/R/library/IRanges/include"
> -I"/usr/local/R/2.15.1/lib64/R/library/XVector/include"   -fpic  -g -O2  -c
> IRanges_stubs.c -o IRanges_stubs.o
> In file included from /usr/local/R/2.15.1/lib64/R/include/Rdefines.h:25,
>                  from
> /usr/local/R/2.15.1/lib64/R/library/IRanges/include/IRanges_defines.h:18,
>                  from
> /usr/local/R/2.15.1/lib64/R/library/IRanges/include/IRanges_interface.h:12,
>                  from
> /usr/local/R/2.15.1/lib64/R/library/IRanges/include/_IRanges_stubs.c:1,
>                  from IRanges_stubs.c:1:
> /usr/local/R/2.15.1/lib64/R/include/R_ext/Memory.h:27:38: error: stddef.h:
> No such file or directory
>
> Stddef.h does exist and is installed, this simple C program compiles
> correctly.
>
> [hornenj@c6build64 tmp]$ cat std.c
> #include <stddef.h>
>
> main()
> {
> }
>
> Thanks,
>
> -Nigel
>
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