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Question: Problem while installing Rsubread
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gravatar for jackeikee
21 months ago by
jackeikee0
jackeikee0 wrote:

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.

ADD COMMENTlink modified 21 months ago by James W. MacDonald45k • written 21 months ago by jackeikee0
2
gravatar for Aaron Lun
21 months ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

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 COMMENTlink modified 21 months ago • written 21 months ago by Aaron Lun17k

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 REPLYlink written 21 months ago by Martin Morgan ♦♦ 20k

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

ADD REPLYlink written 21 months ago by jackeikee0
1
gravatar for James W. MacDonald
21 months ago by
United States
James W. MacDonald45k wrote:

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.

ADD COMMENTlink written 21 months ago by James W. MacDonald45k

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

ADD REPLYlink written 21 months ago by jackeikee0
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