install cnv-seq.tar.gz in R

Question

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.

@jbaums forget to mention that. my bad. You can access the file from http://tiger.dbs.nus.edu.sg/cnv-seq/ — ads27, Oct 29 '14 at 00:19

score 1 · Answer 1 · edited Oct 29 '14 at 00:32

1

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.

edited Oct 29 '14 at 00:32

jbaums

27,115
5
79
119

answered Oct 29 '14 at 00:30

R3CKL3SS

11
4

Yep, this works fine (and yes, 7zip can extract the archive). – jbaums Oct 29 '14 at 00:33
@jbaums i don't have trouble extract the files but import the package into R. :( – ads27 Oct 29 '14 at 02:04
@jbaums just fix the problem. Thanks! :D – ads27 Oct 29 '14 at 02:12

jbaums · Accepted Answer · 2014-10-29T07:40:31.513

1

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)

edited Oct 29 '14 at 07:40

answered Oct 29 '14 at 00:31

jbaums

27,115
5
79
119

install cnv-seq.tar.gz in R

2 Answers2