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/

Some links to remember including some Arduino stuff....

Geomapping London
http://spatialanalysis.co.uk/wp-content/uploads/2013/04/james_cheshire_ggplot_intro_blog.pdf

Graph Theory
https://dev.to/vaidehijoshi/a-gentle-introduction-to-graph-theory


Arduino
https://create.arduino.cc/projecthub/Arduino_Genuino/getting-started-with-the-arduino-web-editor-4b3e4a
https://www.arduino.cc/en/Reference/HomePage

https://github.com/punkplod23/CodeClubArduino

Making robots
http://www.instructables.com/id/How-To-Make-an-Obstacle-Avoiding-Arduino-Robot/
http://makezine.com/projects/building-a-simple-arduino-robot/




https://www.bps.ac.uk/news-events/future-scientific-meetings

http://www.mathematicshed.com/the-gender-neutral-shed.html

Reading Hadley's Package chapter about Documentation

Key point:

Use Roxygen comments in the R files - then the documentation takes care of itself!


Cut and pasted from: http://r-pkgs.had.co.nz/man.html

The documentation workflow

In this section, we’ll first go over a rough outline of the complete documentation workflow. Then, we’ll dive into each step individually. There are four basic steps:

1. Add roxygen comments to your .R files.
2. Run devtools::document() (or press Ctrl/Cmd + Shift + D in RStudio) to convert roxygen comments to .Rd files. (devtools::document() calls roxygen2::roxygenise() to do the hard work.)
3. Preview documentation with ?.
4. Rinse and repeat until the documentation looks the way you want.

Roxygen comments start with #'

For functions:

As well as the introduction block, most functions have three tags: @param, @examples and @return.

Introduction is the first part!

Each block includes some text before the first tag.1 This is called the introduction, and is parsed specially:

• The first sentence becomes the title of the documentation. That’s what you see when you look at help(package = mypackage) and is shown at the top of each help file. It should fit on one line, be written in sentence case, and end in a full stop.
• The second paragraph is the description: this comes first in the documentation and should briefly describe what the function does.
• The third and subsequent paragraphs go into the details: this is a (often long) section that is shown after the argument description and should go into detail about how the function works.

All objects must have a title and description. Details are optional.

Well happy days (or evenings), I just completed my first documentation of a function!

Hi res images for blog...

https://xomisse.com/blog/how-to-fix-blurry-images-on-blogger/

and

https://danieljhocking.wordpress.com/2013/03/12/high-resolution-figures-in-r/

aim - get drawProteins on Bioconductor

need unit testing
need vignette

found this style on github

https://github.com/juliangehring/vignettes



This is also very important:

https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html

https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html


Unit Test Guidelines:
https://www.bioconductor.org/developers/how-to/unitTesting-guidelines/

Information on making Bioconductor contributions through Github
https://github.com/Bioconductor/Contributions


This link is important too:
https://cran.r-project.org/web/packages/ggplot2/vignettes/extending-ggplot2.html