CODEWITHSUNDEEP
r
ads27
ads27

Reputation: 71

install cnv-seq.tar.gz in R

I'm trying to install this cnv-seq package on my R library to help copying number variation analysis. However, when I type in 

install.packages("cnv-seq")

in R command, an error code pops out saying it is not available for 3.1.1 version. So I tried the old versions as well. All says not available. And I double check with the menu, Packages-> Install packages->. No cnv-seq

Ok. Then I tried to install it from a local source which is the "cnv-seq.tar.gz"

when i type in 

install.packages("C:/cnv-seq.tar.gz", repos=NULL, type="source")

it still returns an error that says cannot extract package from this file. Installation of package had non-zero exit status.

Anything went wrong or is there another I can install this package manually to my PC? After take a look at a similar question here couple years ago,

How do I install an R package from source?

I still could not fix this problem.

Upvotes: 0

Views: 432

Answers (2)

jbaums
jbaums

Reputation: 27388

This is a case of RTFM ;)

You can do the whole process from within R. Below, we download the archive to the temporary directory, then extract it and finally install it.

download.file('http://tiger.dbs.nus.edu.sg/cnv-seq/cnv-seq.tar.gz', 
              f <- tempfile())
untar(f, exdir=tempdir())
install.packages(file.path(tempdir(), 'cnv-seq', 'cnv'), type='source', repos=NULL)

Upvotes: 1

R3CKL3SS
R3CKL3SS

Reputation: 11

I believe you first must untar the file. I believe 7zip has this capability if you do not have access to a linux machine. The linux command would be:

tar -xvf  /path/to/file/cnv-seq.tar.gz

After you do this you should be able to import the package into R.

Upvotes: 1

Related Questions