[BioC] Bioconductor on Cygwin: mingw/math.h not found

[Enrico Ferrero [guest]]

Hi,

I have R installed on Cygwin, and I am trying to install Bioconductor on top of it.

When doing so, I get the following error while building the IRanges Bioconductor package:

> In file included from IntervalTree.c:3:0:
> common.h:59:24: fatal error: mingw/math.h: No such file or directory
> compilation terminated.
> /usr/lib/R/etc/Makeconf:121: recipe for target `IntervalTree.o' failed
> make: *** [IntervalTree.o] Error 1
> ERROR: compilation failed for package ‘IRanges’

As far as I understand, this is an issue related to paths/links between Cygwin and R/Bioconductor, as math.h is indeed installed by the mingw-runtime package, but R apparently can't find it.

Can anybody please help me to find a fix or workaround for this?
Any help is really appreciated.

Thank you.
Best,

Enrico Ferrero

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i686-pc-cygwin (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.8.3

loaded via a namespace (and not attached):
[1] tools_2.15.1


--
Sent via the guest posting facility at bioconductor.org.