Stuck with package '<package name>' was installed by an R version with different internals...

[rocker-org]

Stuck with package '' was installed by an R version with different internals...

from shiny.

[eddelbuettel]

You are mixing R 3.4.* and R 3.5.*. You need to be more careful about which repositories, and R versions, you are accessing. That is an error that is likely entirely entirely on your side.

[Emelieh21]

@cboettig Thanks a lot for clarifying! Looking a bit deeper I see the stable r-cran-rjava came with R 3.2.3... I took apt-get install r-cran-rjava out now and replaced it with:

apt-get install -y default-jdk && \
apt-get install -y libicu-dev && \
apt-get install -y libbz2-dev && \
apt-get install liblzma-dev && \
R -e "install.packages('rJava')"  &&\

Stuff seems to look normal again :) Thanks again for the quick reactions from your side.

[eddelbuettel]

(You can combine those calls as

apt-get install -y default-jdk ibicu-dev libbz2-dev liblzma-dev && \
     R -e "install.packages('rJava')"  &&\

and of course line-break the packages. Another trick is install.r or install2.r

apt-get install -y default-jdk ibicu-dev libbz2-dev liblzma-dev && \
     install.r rJava  &&\

and both tricks are all over our Dockerfiles ...)

[perrystephenson]

For anyone else landing on this page when trying to install rJava on the rocker images, the response from @eddelbuettel above has a typo: ibicu-dev should be libicu-dev.

Which means the final one-liner install should be something like:

apt-get install -y default-jdk ibicu-dev libbz2-dev liblzma-dev && install.r rJava

[Emelieh21]

Thanks @eddelbuettel for the fast response! Maybe a stupid question, but how do you know I am mixing R3.4.* and R3.5.*? I didn't realize it, I am just using the same docker file as before.

[eddelbuettel]

Launch your container with bash and at the prompt do apt-cache policy r-base-core. You'll see where it comes from. Do the same with any package that goes belly up: apt-cache cache policy r-cran-curl (to name one).

There is no Docker bug here. You have an issue in your add-on work, so I will gently close this. If you find a reproducible issue from our side by all means please reopen and document.

[cboettig]

@Emelieh21 Sorry, this is my fault. I've transitioned the shiny image to build on debian:stable rather than debian:testing (to align with RStudio and provide the versioned images that were requested). So indeed they are not the same images as ~ 1 month ago (see PR #24)

This approach does not play nicely with apt-get r-cran-* because in the versioned stack, R is installed from source. I recommend installing R packages directly from CRAN (e.g. the r-cran-rjava) or otherwise you'll pull in a copy of the older R that ships in debian:stable (at /usr/bin/R) in addition the the already installed latest R (at /usr/local/bin/R), which you probably don't want.

[eddelbuettel]

@cboettig Can you detail what you mean by r-cran-rjava? That is (again) a binary build and as such susceptible to mixing R 3.4.* and R 3.5.*. If you have backports in mind, point to the relevant URL and apt add-repo lines. Else say you meant install.packages("rJava") with all its dependency issues.

Maybe use Ubuntu LTS instead? We'd get the Rutter repo there.... Or stick with testing instead?

[cboettig]

@eddelbuettel Right, @Emelieh21 's Dockerfile includes r-cran-rjava in the apt-get line above. It he changed it to install.packages("rJava") like you say (and handled the dependency issues, e.g. default-jdk) then I think the above problem mixing versions would go away.

I don't see how Ubuntu LTS would help.I'm not sure how to take a vanilla Debian or Ubuntu image, install the desired version of R from source only, and still have things so that users can apt-get install R binaries from anywhere. Any r-cran- binary is going to depend on the binary build of R and so it's going to install a second version of R into /usr/bin in addition to the one I installed manually from source at /usr/local/bin, right?

[eddelbuettel]

You can definitely mix-and-match 'R from source' with r-cran-* provided you use the same R version (or "newer than"). That is what everybody does who builds R from svn or git anyway -- it happily uses packages from anywhere in .libPaths() provided they come from a compatible version. There are times when you could not do that -- i.e. a year ago when what is now r-release was r-devel and was imposing a change to the then r-release. Right now we don't have that problem. And obviousy if you rebuild the same r-release from source you get the same r-release and they match.

Devil, as always, in the detail. Happy to take off-line and poke at particular Dockerfiles.

[Emelieh21]

That does looks much nicer. Thanks for the tip :)

[HarshGrandeur]

You must have upgraded to a newer version of R, but R did not automatically update packages. You first need to find packages with older version and update them.
Find the
new_packages <- installed.packages()
this will store all the package installed inside a data frame
convert into a dataframe
df <- as.data.frame(new_packages)
find older package versions , replace the list with packages which are of latest version and you dont want to update
D2 = subset(df, !(Built %in% c('4.0.0','4.0.2')))
D2 <- as.data.frame(D2)
Finally install the packages :
install.packages(D2$Package)