R Update on Linux
1
0
Entering edit mode
6.2 years ago
oars ▴ 200

I'm trying to get my Linux environment updated with the latest R packages which is proving to be quite difficult. The R version on my Linux machine is 3.2.3 (Wooden Christmas-Tree), and despite 2-days of troubleshooting I still cannot get the update commands to execute. An updated version of R is required before the bioconductor suite can download (“A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install”).

Typically, two simple commands will update R in Linux:

sudo apt-get update

Followed by:

sudo apt-get install r-base

However, I cannot get the sudo apt-get update to work, I keep getting the following error message:

E: Could not get lock /var/lib/apt/lists/lock - open (11:Resource temporarily unavailable)
E: Unable to lock directory /var/lib/apt/lists/

From what I’ve read on the web, to fix the problem, you must remove the lock files using the commands below:

sudo rm /var/lib/apt/lists/lock
sudo rm /var/cache/apt/archives/lock
sudo rm /var/lib/dpkg/lock

After that, reconfigure the packages:

sudo dpkg --configure -a

But it doesn't work!?! Anyone else using Linux ever experience a similar error message?

R Bioconductor Linux • 4.7k views
ADD COMMENT
1
Entering edit mode

But it doesn't work!?

Since you have sudo privileges it is unclear why that is not working. Are you using both a GUI and a terminal window to try and update these packages?

ADD REPLY
1
Entering edit mode
sudo rm /var/lib/apt/lists/lock
sudo rm /var/cache/apt/archives/lock
sudo rm /var/lib/dpkg/lock
sudo dpkg --configure -a

But it doesn't work!?!

I suppose you mean that, even after trying the above solution, you get the same error:

E: Could not get lock /var/lib/apt/lists/lock - open (11:Resource temporarily unavailable)
E: Unable to lock directory /var/lib/apt/lists/

What is your operating system, and its version?

ADD REPLY
0
Entering edit mode

Alpha OS 1.0.0 Polaris, Built on "Ubuntu 16.04.3 LTS", Linux 4.13.0-45-generic.

ADD REPLY
1
Entering edit mode

I have found two Alpha OSes, one based on Arch Linux and another on Puppy Linux. I guess your Alpha OS is the Puppy Linux one, as Puppy is based on Ubuntu. Did you install it onto the hard-drive, or are you running from a pen-drive?

Anyway, my suggestion is to install one of the major Linux distributions, which have large user bases, both inside and outside the bioinformatics community.

ADD REPLY
1
Entering edit mode

see if aptitude, synaptic or update manager are running. Type ps aux| grep apt see if apt is running in the background.

ADD REPLY
0
Entering edit mode

I was able to update R using conda:

$ conda install -c r r=3.4.2

But when I launch a new R session, I keep seeing the older version...

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"

Do I need to restart my system? Something seems wrong.

ADD REPLY
1
Entering edit mode

Older version of R must be in your $PATH. You could either remove old R or append path to new R before your current path by doing export PATH=/path_to_new_R/$PATH.

ADD REPLY
1
Entering edit mode

You either need to add the newly installed R to your $PATH, or create a named conda environment and activate it:

conda create -n myrenv r=3.4.1
source activate myrenv
which R
ADD REPLY
0
Entering edit mode

This ^ was a winner! I'm now running 3.5.0 and was able to FINALLY install the Bioconductor suite. Thanks to all!

Seriously, thank you!

ADD REPLY
1
Entering edit mode

I moved @Ram's original comment (which has all the information needed) to an answer. You can accept that to provide closure to this thread.

ADD REPLY
4
Entering edit mode
6.2 years ago
Ram 44k

In my experience, it helps to use conda (as opposed to apt-get) to manage software where software version makes a significant difference. I use it for R and python. For example, I have environments with r=3.4.1 and r=3.3.x that I activate and use at will. You might benefit from using conda as well.

Conda: https://conda.io/docs/user-guide/install/index.html

Conda create environment: https://conda.io/docs/user-guide/tasks/manage-environments.html

Conda custom R environment: https://stackoverflow.com/a/44185194/1394178

ADD COMMENT

Login before adding your answer.

Traffic: 1943 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6