Comments (4)
Could it be that r-base did not pin its own base Debian image?
These are not pinned. If you want versioned Docker archives, look at rocker-versioned2.
R itself works off 'head', and always-rolling always-current repo (CRAN) expecting / working with the current verison of R. If you want to build a container off rocker/r-base, it is normal use 'latest'. That works (using just r-base
here):
edd@rob:~$ docker run --rm -ti r-base R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.4.2.1.tar.gz'
Content type 'application/x-gzip' length 152560 bytes (148 KB)
==================================================
downloaded 148 KB
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
The downloaded source packages are in
‘/tmp/RtmpSzr1KS/downloaded_packages’
>
>
edd@rob:~$
Moreover, calling just install.r remotes
is what we do in other contaienrs and easier, and the cloud CDN is already set.
edd@rob:~$ docker run --rm -ti r-base install.r remotes
trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.4.2.1.tar.gz'
Content type 'application/x-gzip' length 152560 bytes (148 KB)
==================================================
downloaded 148 KB
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
The downloaded source packages are in
‘/tmp/downloaded_packages’
edd@rob:~$
from rocker.
Argh, I just realized that I was installing sed
again during some apt installations. That may have overwritten the one already installed. Thank you for the additional info though!
from rocker.
That /bin <-> /usr/bin transition has bitten me too and can create havoc here.
My personal $0.02 is that the whole notion of 'today' pretending that it was '1 1/2 years ago' and I could work as if 4.2.1 is current is very very fraught as the world around does not stand still. Rocker's versioned2 stack also freeze the CRAN repo (via date snapshots at p3m, before that MRAN) so that may help ...
from rocker.
And FYI you can prevent upgrades of packages under apt
and dpkg
via "hold" commands. That is sometimes useful when a 'bad' or 'new' library accidentally slips in though Debian does a very good with library transitions preventing that sort of thing.
from rocker.
Related Issues (20)
- wiki: best practices for creating dockerfiles HOT 6
- `r-base` (Docker Official Image) is not updated HOT 5
- Migrating from Dockerhub? HOT 3
- Container for RStudio (not server) HOT 1
- MRAN repository snapshots were deleted - Failing jobs because packages can't be found anymore HOT 5
- docker v18 & packages repositories & rocker's images HOT 5
- unable to load shared object
- Update results in deletion of all install package...
- installation testing fails HOT 1
- r: error while loading shared libraries: libR.so: cannot open shared object file: No such file or directory
- Installing unstable apt packages? HOT 4
- Local Zotero Integration? HOT 3
- R session terminated HOT 1
- latest r-base breaks install of `curl` package HOT 8
- xz-utils backdoor HOT 4
- Potential high vulnerability in r-base:4.3.1 HOT 3
- Installing packages fails due to broken openssl package in debian testing HOT 2
- Alternative Methods of Extending Images? HOT 5
- update 'latest' version to 4.4.0 RDS security flaw HOT 2
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