Making new organism packages rnw

[villafup]

@jwokaty -- error below

Build fails. Missing a library?

(base) pvillafuerte@supermicro:~$ R_LIBS_USER="/mnt/STORE1/lib/R/bioc-release" R CMD build AnnotationForge 
* checking for file ‘AnnotationForge/DESCRIPTION’ ... OK
* preparing ‘AnnotationForge’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
*--- re-building ‘MakingNewAnnotationPackages.Rmd’ using knitr
Quitting from lines 2-31 (MakingNewAnnotationPackages.Rmd) 
**Error: processing vignette 'MakingNewAnnotationPackages.Rmd' failed with diagnostics:
could not find function "Biocpkg"**
--- failed re-building ‘MakingNewAnnotationPackages.Rmd’*

SUMMARY: processing the following file failed:
  ‘MakingNewAnnotationPackages.Rmd’

Error: Vignette re-building failed.
Execution halted

[hpages]

Hi @villafup,

2 problems:

• The title of this PR is incorrect and misleading. Note that the AnnotationForge package contains 4 vignettes. This PR converts the MakingNewAnnotationPackages.Rnw vignette to the Rmd format, but the title suggests that it converts the MakingNewOrganismPackages.Rmd vignette (which doesn't need conversion as it is already in the Rmd format).

• I just made a few minor corrections to the MakingNewAnnotationPackages.Rnw vignette. See issue #48 and commit e7cd29cab766972816c4e7c844f28acb8f0e3074. These changes will need to be incorporated in the Rmd version of the vignette.

So I think the easiest thing to do at this point is to close this PR, in order to avoid any confusion.

If you wish to follow up with the conversion of MakingNewAnnotationPackages.Rnw to Rmd, please:

1. Resync your fork of the AnnotationForge repo.
2. Create a new branch e.g. MakingNewAnnotationPackages-Rnw2Rmd.
3. Do your work on this new branch.
4. Commit and push.
5. Submit a new PR and make sure that you use a title that reflects the content of the PR e.g. "Convert MakingNewAnnotationPackages.Rnw to Rmd format".

Thanks!