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Re: mingw/math.h not found while compiling R packages

Il 7/11/2013 10:51 PM, Enrico Ferrero ha scritto:

Thanks for your help, I'll try to make things clearer.

I have a full installation of Cygwin, including R version 2.15.1,
running on my Windows XP box at work.
Bioconductor [1] is a a collection of packages for computational
biologists that is installed by compiling its packages within the R
To install the base packages (and reproduce what I believe is a bug),
one just has to type at the R prompt:


as you are not using R-3.x the last should be


During the compilation of the IRanges package [2], I get the following error:

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 =91IRanges=92

So, apparently, R needs the math.h library to compile IRanges but
can't find it for some reason.

likely the package is broken and incorrectly identify cygwin for mingw.

As far as I understand, in Cygwin, math.h is provided by the
mingw-runtime package, part of the MinGW suite [3].
According to this page [4] on the Cygwin website, math.h is indeed
installed by the mingw-runtime package, so I'm trying to figure out
why R can't access it. Maybe it's a path or symbolic links-related
problem? Maybe it has to do with the recently mentioned issues
affecting MinGW packages in Cygwin [5]?

wrong, cygwin have its own math.h

$ cygcheck -f /usr/include/math.h

Any help is very appreciated, thank you.

I am building biocLite, it will take some time...



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