fix: cran warnings about packages

[mihai-sysbio]

This PR aims to resolve the CRAN warning about the 2 packages that are not yet available on CRAN. Once they are, the 2 suggested packages should be added back.

note: pinging @mro100 about this as well

[mihai-sysbio]

Based on the latest build log from CRAN there is still one pending warning (locally reported as error):

* checking dependencies in R code ... WARNING
‘::’ or ‘:::’ imports not declared from:
  ‘clpAPI’ ‘cplexAPI’

It seems these 2 packages should be listed as imports in the DESCRIPTION file. However, these packages seem to have been archived long ago, so importing them would be of any help:

• https://cran.r-project.org/web/packages/cplexAPI/index.html
• https://cran.r-project.org/web/packages/clpAPI/index.html

Given that sybil is risking archiving as well, is there any way out short of purging the use of these packages?

[mro100]

I assume that was the result after you erased the two packages from suggests. Yes, that was too easily thought. The following R files contain clpAPI:: and cplexAPI:: calls: optObj_basicfunc.R optObj_clpAPIClass.R optsolClass.R optObj_cplexAPIClass.R I do not think it is a good idea to remove the calls and all references to cplexAPI and clpAPI, because if people manage to install the clpAPI and cplexAPI package on their machines from source code, they can still use sybil with it. The idea to erase the packages from the Suggests was not a good idea, then. The thing is, that sybil package is programmed in a way that it runs also totally fine without clpAPI and cplexAPI packages present, that is why they are only Suggests. If they are present, they can be used. If they are not present, they cannot be used. That being said, maybe the best strategy is to keep the two packages in the Suggests and on submission, mention in the comment field (regarding to the NOTE that will be received in the building process about suggested packages that are not present) that we are working on a resubmission of clpAPI and cplexAPI, and that the package also works fine without these packages present (this is why they are only Suggests and not Depends, so I would think it will not be a problem). I will try to write a question to the mailing list these days asking about the issue environment variables for Clp and CPLEX installations anyways. In the end, it is your decision. I assume that we will not have a problem on submission that way.