Pre-submission tasks to rOpenSci

[jasdumas]

To do list

• Contact rOpenSci about interest and inclusion: pre-submission inquiry for shinyGEO

  • Refactor as an R package
  • Include a test suite
  • Address the maintenance issue for updating GEO data

• Format into a R package: move package into inst/ folder, add DESCRIPTION, run documentation for man/ folder

• Figure out how to have Bioconductor dependencies alongside CRAN packages for the DESCRIPTION. Current RMD check status, with 1 error from this:

checking package dependencies ... ERROR
Packages required but not available: ‘limma’ ‘affy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
R CMD check results
1 error  | 0 warnings | 0 notes

R CMD check succeeded

• Add runshinyGEO() function to load shiny app when the package is installed

• include Travis CI button and setup for testing

• Include a unit tests for the new functions added

• Add update_GEOdata() function to let the user update the data from the client-side

[jasdumas]

package were not installed on my local machine. I also did an update of the Bioconductor installer

https://www.bioconductor.org/install/

[jasdumas]

@gdancik wanted to ping you on these current things i'm working on! 😄

• Currently working on the update_GEOdata() function and getting Travis CI to get a passing build
• the only NOTE for RMD check is that fact that the package is large:

Status: 1 NOTE
checking installed package size ... NOTE
  installed size is 54.5Mb
  sub-directories of 1Mb or more:
    shiny-apps  54.5Mb

See
  ‘/Users/jasminedumas/Desktop/R-directory/shinyGEO.Rcheck/00check.log’
for details.


R CMD check results
0 errors | 0 warnings | 1 note 

R CMD check succeeded

[gdancik]

Thanks for the update and I'm excited to see the you are making progress on this. For the update_GEOdata() function, right now that functionality is in bash scripts which will be shell / OS dependent. We have (or at least had) versions working on Mac and Linux but they are slightly different versions. To include this in the R package, you could implement this as a pure R function using RCurl.

[jasdumas]

@gdancik whenever you get a chance, please feel free to review my last commit which added the updateGEOdata() function here: https://github.com/jasdumas/shinyGEO/blob/master/R/updateGEOdata.R which uses the rvest and readr packages.

• R CMD check passed with No Errors, Messages or Notes 🎉

[gdancik]

This is amazing! Great job! I will merge this soon with the other shinyGEO so we have this functionality in R.