[BioC] Building GenomicRanges1.14.3 on Centos6

Horne, Nigel (NIH/NLM/NCBI) [C] nigel.horne at nih.gov
Tue Nov 26 18:09:00 CET 2013

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
* 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 at c6build64 tmp]$ cat std.c
#include <stddef.h>




More information about the Bioconductor mailing list