the following is from a draft-manuscript. It worked in the past, but a recent update of Rsubread seems to cause problems (see my question on bioconductor). Well - if you use the right version of R/Bioconductor, it should work though. And I hope that the current problem will be fixed in future.
Download the Cygwin-installer and start the setup. Go through the dialog until you can select the packages you would like to install. Select the following packages in addition to what is per default selected (for the libraries ending on "-devel", double check if the version without "-devel" is selected as well).
- libbz2-devel: BZip file de/compressor
- gcc-core: GNU Compiler Collection (C, OpenMP)
- gcc-g++: GNU Compiler Collection (C++)
- gcc-fortran: GNU Compiler Collection (Fortran)
- make: The GNU version of the 'make' utility
- libcurl-devel: Multi-protocol file transfer library (development)
- libiconv-devel: Unicode iconv() implementation
- libicu-devel: IBM Internationalization Component for Unicode
- libintl-devel: GNU Internationalization runtime library
- liblzma-devel: LZMA de/compressor library (development)
- libpcre-devel: Perl Compatible Regular Expressions library development
- libtirpc-devel: A port of Sun's Transport-Independent RPC library
- libxml2-devel: GNOME XML library (development)
- zlib-devel: Gzip de/compression library (development)
- R: R Statistical computing language
After completing the Cygwin installation, start Cygwin, type "R" and press enter to start an R console. At least for the alignment of the short reads (i.e. usage of Rsubread), you need to use this console. Note that packages installed in the Cygwin R console are not available to any other native R installation (i.e. R installed with the installer available on cran.r-project.org).
And well - this should be clear, to install Rsubread in the Cygwin-R:
source("THE BIOCONDUCTOR LINK - yes, I'm not allowed to post more than 2 links")
With the steps above, this packages will work as well:
biocLite(c("SRAdb", "Rsamtools", "biomaRt", "DESeq2", "edgeR", "limma"))