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

February 18, 2020 @Andrea Andrea Panizza

@Andrea wrote:

Hello, hello! :wave:

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,

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:

> 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?

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