Problem while installing Rsubread
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jackeikee • 0
@jackeikee-9646
Last seen 5.6 years ago

Hi ,I got a problem while i installing the Rsubread package. I am using Windows10 OS, I tried to install Rsubread through Rstudio.

I typed as :

source("https://bioconductor.org/biocLite.R")
biocLite("Rsubread")

then I got :

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘Rsubread’
These will not be installed
Old packages: 'nnet'
Update all/some/none? [a/s/n]:

Even I typed a or s, this information kept showing up. How can I correctly install 'Rsubread' in R?

installation rsubread • 4.7k views
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Entering edit mode
Aaron Lun ★ 27k
@alun
Last seen 5 hours ago
The city by the bay

I don't think Rsubread is available for Windows, unfortunately. You'll need a Mac or a Unix machine, or install a Unix-like environment on your Windows machine, e.g., cygwin.

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Entering edit mode

Yep, availability is listed on the package 'landing page', https://bioconductor.org/packages/Rsubread. It would be more fun to use a docker image than cygwin (R itself is not supported on cygwin, even if Rsubread can be compiled there -- this sounds like a pretty 'advanced' solution).

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Thanks, using cygwin like environment is too troublesome for me. Otherwise, I would not use R package for reads alignment.

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@james-w-macdonald-5106
Last seen 1 day ago
United States

The short answer is that you can't. There are facilities (the Rtools set) to allow you to compile source packages on Windows, but Rtools is missing, at the very least, the zlib headers. And fixing that would require way more effort than I imagine it's worth.

There are at least three alternatives. You could use an AMI instance, or a Docker container, or if your computer has sufficient resources, you could go all old school and set up a dual boot with Ubuntu. Probably one of the first two is the way to go though.

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Entering edit mode

Thanks, you are right. Too much time consuming is not a good option for me.