[BioC] Error installing development version of DESeq2

Steve Lianoglou lianoglou.steve at gene.com
Sat Jan 18 00:58:43 CET 2014

Hi Katrina,

Sounds like we're almost there ... comments inline:

On Fri, Jan 17, 2014 at 3:12 PM, Kristina M Fontanez <fontanez at mit.edu> wrote:
> Hi Steve-
> Thanks for the help. I deleted the development and corrupted release versions of R from my computer. Then, I downloaded the release version. Next, I renamed the release version in my Applications folder to R_3.0.

Nice one! Good move on your part to have done that and sorry that I
neglected to point that out earlier -- I don't use R.app, so it
slipped my mind.

> Then I downloaded the installer package from att.com<http://att.com> for the development version. I opened up a terminal and in my / directory I typed in sudo pkgutil —forget org.r-project.R.x86_64.fw.pkg.
> parsons-three-sixty:/ fontanez$ sudo pkgutil --forget org.r-project.R.x86_64.fw.pkg
> Forgot package 'org.r-project.R.x86_64.fw.pkg' on '/'.
> Then, I proceeded to install the development version from the R development installer package. It installed correctly and I was able to download the development version of DESeq and my other packages. However, this is where I ran into a problem.
> I shut down R and opened up the R_3.0 app from my Applications. It opened, which was good but it drops a ton of warnings. Anytime I try to type something (as I’m typing) that “anyNA” is not a builtin function error pops up. It looks like my R 3.0 is still corrupted. I didn’t change anything in /Library/Frameworks - should I have done that as well, like Dan suggested?

No, do not change anything in /Library/Frameworks/* manually --
RSwitch handles those "delicate" details for you. So, you now have to
download RSwitch and use that to change the version of R that is
currently "live".

So, if you want to use R 3.0.x, you would:

(i) first quit the current R process you are running
(ii) open up RSwitch and select "R 3.0". This does some magic inside
the /LibraryFrameworks/R.framwork/* for you.
(iii) After selecting that, you can then launch your R_3.0.app

If you want to run R-devel you would
(i) Quit current version of R
(ii) Open up RSwitch and select R 3.1
(iii) open up the R.app that the R-devel package installed for you.

That should do the trick -- if not, please post back with an update as
I'm *pretty* sure you don't have to do anything much more involved
than that.


Steve Lianoglou
Computational Biologist

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