Cannot install RStudio in Ubuntu18.04 x86_64 (permission problem)

csarabia · November 27, 2018, 1:04am

Hi,

I am experiencing similar problems to user Aurele in Cannot install RStudio Desktop on my Linux machine (permission problem). My error message:

~/Downloads$ sudo dpkg -i rstudio-xenial-1.1.463-amd64.deb 
(Reading database ... 239410 files and directories currently installed.)
Preparing to unpack rstudio-xenial-1.1.463-amd64.deb ...
Unpacking rstudio (1.1.463) ...
dpkg: error processing archive rstudio-xenial-1.1.463-amd64.deb (--install):
 unable to open '/usr/lib/rstudio/www/rstudio/0E471A7ED100AFCB82EF81C71F4D11F4.cache.js.dpkg-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Errors were encountered while processing:
 rstudio-xenial-1.1.463-amd64.deb

I tried installing other older versions of rstudio (rstudio-1.0.153-amd64.deb, rstudio-0.99.903-i386.deb)

~/Downloads$ sudo gdebi rstudio-1.0.153-amd64.deb 
Reading package lists... Done
Building dependency tree        
Reading state information... Done
Reading state information... Done
RStudio
 RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.
Do you want to install the software package? [y/N]:y
(Reading database ... 239410 files and directories currently installed.)
Preparing to unpack rstudio-1.0.153-amd64.deb ...
Unpacking rstudio (1.0.153) ...
dpkg: error processing archive rstudio-1.0.153-amd64.deb (--install):
 unable to open '/usr/lib/rstudio/bin/r-ldpath.dpkg-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Errors were encountered while processing:
 rstudio-1.0.153-amd64.deb

~/Downloads$ sudo dpkg -i rstudio-0.99.903-i386.deb 
Selecting previously unselected package rstudio:i386.
(Reading database ... 239410 files and directories currently installed.)
Preparing to unpack rstudio-0.99.903-i386.deb ...
Unpacking rstudio:i386 (0.99.903) ...
dpkg: error processing archive rstudio-0.99.903-i386.deb (--install):
 unable to create new file '/var/lib/dpkg/info/rstudio.list-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Errors were encountered while processing:
 rstudio-0.99.903-i386.deb

As you can see, each error is in a different folder. I have tried 'sudo apt-get autoremove' and 'sudo apt-get autoremove rstudio', without success. rstudio appears as not having been installed at all.

sudo apt-get autoremove rstudio
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package 'rstudio' is not installed, so not removed
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

Aurele's topic was not solved in the end. Would anyone have an idea of what is happening? Thanks!

technocrat · November 25, 2018, 6:29pm

Aurele ended up moving from Mint to another Linux. I can tell you that I didn't have this problem with Ubuntu 10.18. Suggest you add your specific version of Linux to see if others on your platform have experienced the same isssue.

csarabia · March 21, 2021, 1:22am

My Linux version is Ubuntu 18.04, x86_64. I can see that the downloadable version of Rstudio is intended originally for Ubuntu 16 (xenial). I wonder if there is a problem of compatibility with Ubuntu 18?

csarabia · November 26, 2018, 5:42pm

I have tried to install it with gdebi and dpkg, and both of them gave me the same error.

technocrat · December 3, 2020, 5:50am

I can confirm that it works with 18.10 (this was a fresh install on a new box, and I skipped 18.04). I first install R base

sudo apt update
sudo apt -y install r-base

and then used the Ubuntu GUI software app to install RStudio

csarabia · November 24, 2020, 9:41pm

Thanks, technocrat. But I have tried it again and this is the result.

$ sudo apt -y install r-base
[sudo] password for carlos:
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-base is already the newest version (3.5.1-2bionic).
0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded.

The manual installation of rstudio-xenial-1.1.463-amd64.deb through the GUI hasn't worked, and neithwer have the two previous versions (rstudio-1.0.153-amd64.deb and rstudio-0.99.903-i386.deb), without throwing error messages. Upon installing with command line,

$ sudo gdebi rstudio-xenial-1.1.463-amd64.deb
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading state information... Done

RStudio
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, and workspace management.
Do you want to install the software package? [y/N]:y
(Reading database ... 239656 files and directories currently installed.)
Preparing to unpack rstudio-xenial-1.1.463-amd64.deb ...
Unpacking rstudio (1.1.463) ...
dpkg: error processing archive rstudio-xenial-1.1.463-amd64.deb (--install):
unable to open '/usr/lib/rstudio/www/rstudio/4778C355F136AB561E151D611D7BA769.cache.js.dpkg-new': Operation not permitted
Processing triggers for shared-mime-info (1.9-2) ...
Processing triggers for hicolor-icon-theme (0.17-2) ...
Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ...
Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ...
Processing triggers for mime-support (3.60ubuntu1) ...
Errors were encountered while processing:
rstudio-xenial-1.1.463-amd64.deb

Again the same error as before.

technocrat · November 24, 2020, 9:46pm

Progress! You've got R{base} and you need that for studio. I'm a CLI guy from way back, but rather than searching for the toolchain needed to install RStudio, as you're describing, I found the Ubuntu Software Application and searched there. As much as it pains me to admit that I point and click RStudio has worked with no glitches at all. Please try that? Let me know?

csarabia · November 27, 2018, 3:10am

Hi technocrat. I did as you recommended me last time, but with no results. It looks like it is never installed. I enclose a picture of the process (I could not upload more since I am a newcomer in this forum).

technocrat · November 27, 2018, 6:12am

Did you watch the whole time and it never reached the end? Or did you (as I would have done) go on to do other things? Try the 9-dot applications icon in the lowest left and if you don't see it, use the search bar. Is your internet connection solid? Or is there network congestion between your router and sites beyond the provider's network? (From the terminal traceroute to 4.4.4.4 (Google's nameserver) and if you see a lot of *****, it means that someone at your provider needs to reboot a router or there's been a wire cut somewhere.

csarabia · November 27, 2018, 1:15pm

Hi technocrat, thanks again for the support. I have manually installed it and waited to see the installation process. It starts going very fast from 0% to 100%, but then goes back to 0%, the bar does a little jump up to 16% installation and then it gets stuck. It never finishes the process.

I have my package downloaded from the website of Rstudio (https://www.rstudio.com/products/rstudio/download/) I have tried to install the three packages aforementioned plus a rstudio server version. No chance.

traceroute 4.4.4.4 shows 30 lines with * * *. I don't think what that could mean, but I have the impression that the internet connection is rather solid.

technocrat · November 27, 2018, 5:48pm

The traceroute shows the problem is network congestion somewhere between you and the Google nameserver, which could also be happening between you and the ubuntu app server. Whenever you see the *****, it mean that the packets are stuck. Usually, it's on your service providers network or the backbone they use.

If you have a connection through a campus or library try that. Otherwise, I'm afraid, you'll just have to be patient. You are doing every right.

csarabia · November 27, 2018, 6:39pm

Hi again. I contacted the informatics service at my university and they confirmed that they could download the .deb package and install it in a computer with Ubuntu 18.04. I took their package with a USB stick and tried to install it in mine, without success. I also created a new user and tried to install it from the same USB, but again it faced the exact same problem.

During the installation of my OS a couple of months ago, and since I work in an Asus K541U that had Windows 10 installed by default, we had to remove something called the nouveau driver of the Nvidia GeForce 920MX graphic card that was interfering with my Ubuntu.

R works fine when I open it and Rstudio doesn't. I wonder if the graphic card is an issue for rstudio to work?

BTW, My system:

$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 18.04.1 LTS Release: 18.04 Codename: bionic

kevinushey · November 27, 2018, 9:08pm

This signals to me that there is something funky going on with your filesystem. dpkg is attempting to write and update files on the filesystem, but is failing to do so.

It's very hard to say why this could be the case (I think we've seen things like this for users with networked filesystems before, but not local filesystems). You could try running fsck to see if there are any issues with the filesystem, or barring that, a clean reinstallation of Ubuntu (if that's possible).

technocrat · November 27, 2018, 11:40pm

Darn, I hoped it would be something simple enough I could help you with. Now that we are into possible hardware driver issues, I think I've reached the end of my usefulness. The best I can suggest is to find some experienced help and take a look at https://goo.gl/HzShgw for a recent suggested fix

system · December 18, 2018, 11:40pm

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

markvdloo · March 27, 2019, 12:43pm

Unfortunately this post is closed without solution due to inactivity (@rstudio, please keep such posts open longer!). We had the same issue and I would like to post our solution.

In our case f-secure was running which prevented installation, even though we were running as root.

We first stopped the f-secure services

sudo service fsaua stop
sudo service fsma stop

after that the command

sudo gdebi rstudio-server-pro-1.1.463-amd64.deb

ran as expected