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On 7/9/2013 6:12 AM, Enrico Ferrero wrote:
Hi, I have R installed through Cygwin ports, and I am trying to compile some external R packages (from Bioconductor). 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 =91IRanges=92As far as I understand, this is an issue related to paths/links on Cygwin, as math.h is indeed installed by the mingw-runtime package, but R apparently can't find it. If you want to reproduce the issue just install R through the Cygwin ports, open an R session and write:source("http://bioconductor.org/biocLite.R") biocLite()which will perform a standard Bioconductor installation. Can anybody please help me to find a fix or workaround for this? Any help is really appreciated.
If you are using the R from Cygwin Ports, it must be an old package since R is no longer offered there. I suggest you install the R package from the Cygwin distribution instead and retry. Since this list supports the Cygwin distribution only, this would put your issue firmly on-topic for this list if you can still reproduce it. For Cygwin Ports packages, they are supported through the Ports site: <http://sourceware.org/cygwinports/> If you have a package from that site and have questions, problems, or comments, it's best to consult the mailing list there. -- Larry _____________________________________________________________________ A: Yes. > Q: Are you sure? >> A: Because it reverses the logical flow of conversation. >>> Q: Why is top posting annoying in email? -- Problem reports: http://cygwin.com/problems.html FAQ: http://cygwin.com/faq/ Documentation: http://cygwin.com/docs.html Unsubscribe info: http://cygwin.com/ml/#unsubscribe-simple
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