Investigate the "there is no package called xx" issue

[lorraine-dev]

Is this a version conflict with R, does this happen for every instance of a particular library?
Is it a Binder issue, ie, is gesis.notebooks also unable to install the library?

[lorraine-dev]

Possible explanation:

While testing the project "uhma8" that failed with the log,

Error in FUN(X[[i]], ...) : there is no package called ‘car’

I noticed that 'car' was not included in the DESCRIPTION file. On checking it further, found that flowR doesn't identify this package as a dependency.

Cross checked with flowR team and this is indeed an open issue at flowr-analysis/flowr#1259

In summary, flowR fails to extract dependencies when the library is loaded like so:

Will continue to work on #13 once the parent issue is resolved.

[tobihol]

Does the issue only appear in the case where its not in the DESCRIPTION file?

[lorraine-dev]

Probably not, but a large portion of errors from our last execution can be attributed to this issue. I'm investigating a few other cases to see if there are other reasons as well.

[lorraine-dev]

More findings:

Project# 92e6c, error from execution log:
Error in library(rethinking) : there is no package called ‘rethinking’

However, this dependency has been identified by flowR and added to DESCRIPTION.

From the docker build logs-> successful call for devtools::install_local(getwd()) indicating DESCRIPTION file is being read properly.

However, at the end of package list, there is an error,

#30 3.943 Skipping 1 packages not available: rethinking

Further info from the logs:

#30 221.3 ERROR: dependency ‘rethinking’ is not available for package ‘repo2dockerProject’
#30 221.3 * removing ‘/srv/rlibs/repo2dockerProject’
#30 221.4 Warning messages:
#30 221.4 1: package ‘rethinking’ is not available for this version of R
#30 221.4 
#30 221.4 A version of this package for your version of R might be available elsewhere,
#30 221.4 see the ideas at
#30 221.4 https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 

Exploring this further, I looked into the package rethinking. From it's readme here, https://github.com/rmcelreath/rethinking

Note that the rethinking package is not on CRAN, just on github. The rethinking package is never going to be on CRAN. So if you get an error about rethinking not being available for your version of R, it is because you tried to install from CRAN. Use the github code above.

We can only assume that there might be multiple cases where the user installs a package not available in CRAN. Further discussions needed to decide whether this should be supported in our automated pipeline.