Question

Problem while installing Rsubread

0

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jackeikee • 0

@jackeikee-9646

Last seen 8.3 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).
Installing package(s) ‘Rsubread’
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?

Please help.

installation rsubread • 5.7k views

ADD COMMENT • link updated 8.3 years ago by James W. MacDonald 65k • written 8.3 years ago by jackeikee • 0

score 2 · Answer 1 · 2016-02-02

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Aaron Lun ★ 28k

@alun

Last seen 12 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.

ADD COMMENT • link 8.3 years ago Aaron Lun ★ 28k

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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).

ADD REPLY • link 8.3 years ago Martin Morgan 25k

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

ADD REPLY • link 8.3 years ago jackeikee • 0

score 1 · Answer 2 · 2016-02-02

1

Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 6 hours 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.