WIP: Newsubmission

[zachcp]

@rajarshi ,

I wanted to prepare for a new submission to CRAN as stated in https://github.com/CDK-R/cdkr/issues/99. When I started to run through devtools:check() I ended up encountering a number of documentation related issues that this attempts to address. There are, as of this PR, 2 WARNINGs left (down from 5 + test fails) that deal with building the vignettes. There are a few other odds-and-ends that need to be addressed (see below) but the vignette code is the core bit that could use some work/eyes. For build_error_log see this gist.

I can keep working on this branch until the issues below are fixed, or, if you like, we can merge and tackle the issues piecemeal.

Issues Addressed in this PR

• [x] add files needed for tests to inst/molfiles
• [x] use roxygen to document bpdata
• [x] add roxygen metadatafunctions for a large number of functions and update Rd
• [x] update for pkdgown and vignettes: usethis:;use_vignette() and usethis::pkgdown()
• [x] modify imports for S3 itertools to conform with new Roxygen (no @@S3 tag)

Needed Before Resubmission to CRAN

• [ ] Update Docs/params for a number of functions
• [ ] get vignettes to build and apply appropriate tests
• [ ] address any inconsistencies with previous Roxygen tests.
• [ ] version bump
• [ ] News.md/changelog

Desired before Resubmisison to CRAN

• [ ] CI Testing (use travis)
• [ ] CI/CD build of pkgdown website (use travis +pkgdown)

[rajarshi]

Started fixing the issues, but I can't get devtools::check() to run. I'm getting

** testing if installed package can be loaded
Error: package or namespace load failed for ‘rcdk’:
 object 'do' not found whilst loading namespace 'rcdk'
Error: loading failed
Execution halted

Any idea why this happens?