Working through Travis...

One good thing - as soon as a Github commit is synced online - Travis will check the build.

Latest build #11 has been running for over 10 minutes without an error.
Preparing the Vignettes takes a while - maybe worth simplifying....

Good news is that 2 warnings and 2 notes is what I get with my local build check. 

Undocumented code objects:

  ‘draw_mol_horiz’ ‘draw_phosphosites’ ‘extract_names’

  ‘extractFeaturesList’ ‘extractFeaturesListwithAcc’ ‘five_rel_list’

  ‘geom_motif’ ‘geom_region’ ‘geom_repeat’ ‘prot_data’ ‘protein_json’

  ‘rel_A_features’

Undocumented data sets:

  ‘five_rel_list’ ‘prot_data’ ‘protein_json’ ‘rel_A_features’

AND

* checking Rd \usage sections ... WARNING

Undocumented arguments in documentation object 'geom_chains'

  ‘label_chains’

Documented arguments not in \usage in documentation object 'geom_chains':

  ‘label_chain’



Functions with \usage entries need to have the appropriate \alias

entries, and all their arguments documented.

The \usage entries must correspond to syntactically valid R code.

See chapter ‘Writing R documentation files’ in the ‘Writing R

Extensions’ manual.

I checked the .travis.yml on ggtree (https://github.com/GuangchuangYu/ggtree).

ggtree Travis info would seem to be in the public domain:
https://ci.appveyor.com/project/GuangchuangYu/ggtree/branch/master

Lots of good info on Travis website:
https://docs.travis-ci.com/user/notifications/

Also these link:
https://docs.travis-ci.com/user/languages/r/
http://jtleek.com/protocols/travis_bioc_devel/
https://github.com/craigcitro/r-travis/wiki


Travis examples:
https://github.com/csgillespie/travis-examples/blob/master/bioconductor/.travis.yml



Need to get Coverage done as well:
Maybe: https://codecov.io/
OR:

https://coveralls.io/github/brennanpincardiff/drawProteins


Also info on badges:
https://shields.io/

Troubleshooting in Travis

Problem:

* creating vignettes ... ERROR

Error: processing vignette 'drawProteins_BiocStyle_pdf_output.Rmd' failed with diagnostics:

there is no package called ‘BiocStyle’

Execution halted

Some advice here:
http://jtleek.com/protocols/travis_bioc_devel/

https://github.com/craigcitro/r-travis/wiki



This is interesting too:
http://lint.travis-ci.org/

Some colour links....

R Colour Cheat Sheet
https://www.nceas.ucsb.edu/~frazier/RSpatialGuides/colorPaletteCheatsheet.pdf

R blogger piece about colour
https://www.r-bloggers.com/r-using-rcolorbrewer-to-colour-your-figures-in-r/