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NESCent / MINOTAUR

Multivariate vIsualisatioN and OuTlier Analysis Using R
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pull request to pass R CMD check and Travis CI #9

Closed thierrygosselin closed 8 years ago

thierrygosselin commented 8 years ago

Package now pass R CMD check and Travis CI

Again... awesome work, congratulations to the R hackathon team!

caitiecollins commented 8 years ago

Hi Thierry,

Wow. These look like great changes. Thanks very much!

Have we met, by the way? Did you come across MINOTAUR through NESCent or by way of contact with other members of our group?

I'd like to accept your commit, especially because it looks like you put in quite a bit of work combing through the code making useful changes (some of which have been on my neglected to-do list!). I may need to first check with the other co-contributors to the package, but are you interested in continuing to contribute to the project?

I should also say that we have just submitted the main initial paper describing the package, and this is still in the review process, so we have forked the project onto a "develop" branch in addition to the "master" branch. The reviewers have been directed to use the master branch (which we have promised to keep as stable and un-changing as possible), so we are trying to make all new changes on the develop branch (particularly changes that might break the package or affect the performance/appearance of the package). That said, it looks like the changes you have suggested are more likely to improve than threaten the stability of the package, so for this time I think it's fine if they are made to the master branch.

Thanks again for taking the time to make those changes. And please do tell me a little about yourself, your interests, and whether you would like to continue to contribute to MINOTAUR.

All the best, Caitlin Collins.

Department of Infectious Disease Epidemiology Imperial College London

On Thu, Jul 28, 2016 at 5:56 AM, Thierry Gosselin notifications@github.com wrote:

  • Removed the misc folder because you probably don’t want to show this to users
  • Removed require(“package_name”) in various places because it shouldn't be use inside package. Instead, I used :: and modified the Depends and Imports fields in the DESCRIPTION
  • Added short name, title, description and keyword for the cpp function
  • Added #' \dontrun{} to @examples to go through R CMD check quickly
  • Because package size was > 5 MB, I resized the figures in the vignettes and changed to .PNG. These modifications don't affect reading of the vignette. The package is now = 5 MB, this might throw some notes or warnings, if submitted to CRAN. Consequently, you might want to reduce the size of the data (use less markers maybe?)
  • Added a few lines in the .travis.yml file to use remotes packages
  • new version to trigger a Travis build

Package now pass R CMD check and Travis CI

Again... awesome work, congratulations to the R hackathon team!

You can view, comment on, or merge this pull request online at:

https://github.com/NESCent/MINOTAUR/pull/9 Commit Summary

  • * deleted, not necessary
  • * deleted, move outside package
  • * added citation file
  • * new fields and modified some fields to be more accurate with names of authors and creator
  • * replaced images in vignette for .png images of smaller size to have a package less than 5 MB
  • * new travis CI
  • * new appveyor badge
  • Included documentation
  • * removed unnecessary parts
  • encoding problem in the reference: non-ASCII
  • * removed require that shouldn't be used inside package
  • small edits
  • * removed require that shouldn't be used inside package
  • * Added #' \dontrun{} to @examples to go through R CMD check quickly
  • encoding problem with non-ASCII character
  • * TRAVIS CI and APPVEYOR badge
  • edit
  • * new version to trigger a travis build
  • * using :: for external package dependencies
  • * added just a tiny description of what the package does, based on the shiny description provided
  • * include :: for packages dependencies
  • * added :: for required packages
  • simple
  • * numerous edit to add :: to functions
  • * numerous edit to pass: R CMD check
  • test
  • * remotes specification for Travis
  • edit travis ci remotes
  • * github::Bioconductor-mirror/BiocInstaller is required for github::Bioconductor-mirror/OmicCircos to work...
  • * edit remotes
  • * removing APPVEYOR until further testing

File Changes

Patch Links:

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thierrygosselin commented 8 years ago

Hi Caitlin, I was at the R hackathon ... not top shape at the time had a huge cold and snoozing all the time ;) I'm actually the editor at MER, with Emmanuel Paradis, for the R special issue and I was in charge of the MINOTAUR paper (btw... it's accepted)

as for the proposed change, feel free to modify! These were there to help pass R CMD check and travis CI ... now it should work fine Best Thierry

caitiecollins commented 8 years ago

Hi,

Ok, well that makes sense. I'm sorry I wasn't sure if we had met. Now that you mention the cold, I do think I remember!

I'm really glad to hear the paper was accepted. That's excellent news!

I looked over the changes and they look good to me (I've merged them in now). I'm new to using travis and I just added it to the package, so I'm very grateful for the helping hand from someone more familiar with it than I.

Many thanks, Caitlin.