Cannot install packages in a container running the rocker/verse image of RStudio

[Andrea]

Hello, hello!

long time no see! I've been speaking another language for a bit and my R skills got a bit rusty, so I really need your help.

At work I got a big Linux server (512 Gb RAM, quite a few cores, etc.) and I'd like to run RStudio there, in order to analyze large datasets using the tidyverse. The easiest way to get a GUI there is (IMO) to use rocker/verse (for those who don't know it, it's a Docker image containing RStudio, Tex, the tidyverse & other packages). However, it's proving to be not that easy, actually. I need a few packages to run my analysis, on top of the tidyverse, but when I try to install something else I get:

> install.packages("pacman")
Warning in install.packages :
  unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Warning in install.packages :
  package ‘pacman’ is not available (for R version 3.6.2)

Well, not to worry: as mentioned by jcblum here,

Package ‘dplyr’ is not available (for R version 3.4.3)

If you are seeing exactly the same error message as above: Warning in install.packages : unable to access index for repository https://cloud.r-project.org/src/contrib: cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES' then the problem is also with your connection to the internet. As @cderv said, you need to check that you can access the internet from your computing environment and see if you are behind any proxies or firewalls that may be preventing R from accessing the CRAN repository URLs. If you are getting a different error message then you most likely have a different problem. In that case, please post a new topic including the exact code you ran and the exact …

let's first of all check Internet connectivity. From the RStudio terminal, this works smoothly:

rstudio@db1dce8100a8:~$ wget -p https://cran.rstudio.com/src/contrib/PACKAGES -O /dev/null
WARNING: combining -O with -r or -p will mean that all downloaded content
will be placed in the single file you specified.

--2020-02-18 10:56:39--  https://cran.rstudio.com/src/contrib/PACKAGES
Resolving **xxx** (**xxx**)... 3.198.224.34
Connecting to **xxx** (**xxx**)|3.198.224.34|:80... connected.
Proxy request sent, awaiting response... 200 OK
Length: 3299549 (3.1M)
Saving to: ‘/dev/null’

/dev/null                      100%[=================================================>]   3.15M  5.00MB/s    in 0.6s

2020-02-18 10:56:40 (5.00 MB/s) - ‘/dev/null’ saved [3299549/3299549]

FINISHED --2020-02-18 10:56:40--
Total wall clock time: 1.0s
Downloaded: 1 files, 3.1M in 0.6s (5.00 MB/s)

(note I doctored the lines containing my proxy address). Thus, from inside the Docker container, I can easily access the Internet. However, it looks like install.packages cannot, for some reasons. And it's not a repository issue, as suggested by andrie in the same thread as before:

Package ‘dplyr’ is not available (for R version 3.4.3)

There was a spelling mistake in the repos proposed by a previous answer (I've now fixed this). Try: install.packages('dplyr', repos = 'https://cloud.r-project.org') The root cause for your problem is that your CRAN mirror is incorrectly specified. You can try to fix this by adding the following line of code to the top of your script, or in your .Rprofile. options(repos = c(CRAN = 'https://cloud.r-project.org')) If you are using RStudio as your IDE, you can also fix this in the global options, under Tools > Global Options > Packages

> install.packages('pacman', repos = 'https://cloud.r-project.org')
Warning in install.packages :
  unable to access index for repository https://cran.rstudio.com/src/contrib:
  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository https://cloud.r-project.org/src/contrib:
  cannot open URL 'https://cloud.r-project.org/src/contrib/PACKAGES'
Warning in install.packages :
  package ‘pacman’ is not available (for R version 3.6.2)

Same as before. Can you help me? Should I ask on StackOverflow?