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reconhub

This packages installs and loads all stable RECON packages similiar to the tidyverse package.

Installing the package

To install the current stable, CRAN version of the package, type:

install.packages("reconhub")

To benefit from the latest features and bug fixes, install the development, github version of the package using:

devtools::install_github("reconhub/reconhub")

Note that this requires the package devtools installed.

What does it do?

# attaches all stable recon packages
library(reconhub)
## Attaching package epicontacts

## Attaching package outbreaks

## Attaching package incidence

Also, you can install all development versions of RECON packages:

reconhub::install_dev_versions()

Getting help online

Bug reports and feature requests should be posted on github using the issue system. All other questions should be posted on the RECON forum:
http://www.repidemicsconsortium.org/forum/

Contributions are welcome via pull requests.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

recontools's People

Contributors

dirkschumacher avatar jrcpulliam avatar thibautjombart avatar zkamvar avatar

Stargazers

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Watchers

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Forkers

jrcpulliam disenodc jimsforks

recontools's Issues

Use *reconhub* as default username

So that in the README:

devtools::install_github("<github_username>/projections")

will be by default

devtools::install_github("reconhub/projections")

Feature list for first version

The package should help to get up to speed when developing a package. It should contain helper functions to:

  • create the basic package infrastructure, with a toy example of code including roxygen2 documentation
  • support for continuous integration tools: travis, appveyor, codecov.io
  • create a README.Rmd / README.md containing tags for the above, CRAN release status, and basic package information, along the lines of: https://github.com/reconhub/outbreaker2
  • create a basic vignette template
  • create a website generated by pkgdown
  • create a default lintr file
  • git clone all existing RECON repositories
  • install all existing RECON packages, either from CRAN (stable versions) or github (devel versions)
  • ....

It should also help to adhere to the RECON guidelines http://www.repidemicsconsortium.org/resources/guidelines/

init

I am currently thinking of having a central init function that guides you through configuring a first package template similar to devtools::release(). If the folder is empty, it could simply create template files like readme/vignette without asking 🤔

This central function relies on small, public helper functions like configuring travis or creating a README.

The init function could do the following:

  • git initif no git repo (ask?)
  • Create .Rbuildignore and .gitignore
  • Create a DESCRIPTION file (ask for package name and license)
  • Check if the package name is already taken on CRAN
  • Create a testthat folder
  • Create a sample R file with roxygen2 code
  • Create a sample vignette (ask for it)
  • Create a readme.Rmd
  • Create travis.yml (ask for it)
  • Create appveyor file (ask for it)
  • Create a default .lintr file
  • Register coverage in travis (ask for it)
  • Create news file
  • Run devtools::document()
  • ...

check

In addition there could be a checkfunction that performs various checks. Some ideas:

  • R cmd check
  • lintr::lint_package
  • goodpractice::gp
  • Check if travis/appveyor are setup
  • Does the DESCRIPTIONcontain a URL/BugTracker URL?
  • Is there a vignette?
  • Is roxygen2 being used?
  • Any @importFrom / importFrom in NAMESPACE?
  • Is there a docs folder / gh-pages branch? if not, ask the user if he/she has a public documentation page somewhere.
  • Snake case?
  • Is there a code of conduct?
  • Is there a news file?
  • Are there tests? Test coverage?
  • ...

Other functions:

Identify deps in R / Rmd / Rnw files

This would be useful for RECON learn, but more generally for blogdown websites and other projects where a number of packages are required without being formally declared anywhere. This is fairly generic so may exist somewhere, but the idea is:

  1. identify recursively all files containing code, i.e. extensions: R, Rmd, Rnw, Snw etc. (handling different capitalisation)

  2. in each file, identify references to R packages, including: library("foo"), require("foo"), loadNamespace("foo") (with or without quotes), foo::bar, foo:::bar, etc. and extract the library names

  3. output a list of required packages, identifying those available on CRAN

A sister function to this one would be use the output of 3. to install all available packages.

`devtools::install()` fails on created package

I get:

> install()
Installing projections
'/usr/local/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore  \
  --quiet CMD INSTALL '/home/thibaut/dev/recon/projections'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘projections’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (projections)
Error in git_branch(path = x$path) : 
  trying to get slot "name" from an object of a basic class ("NULL") with no slots

Add files to .Rbuildignore

Getting this off a novel package skeleton and running devtools::check():

Non-standard files/directories found at top level:
  ‘CONDUCT.md’ ‘README.Rmd’ ‘appveyor.yml’

init_package no workie

Devtools just updated and messed up everything :(

recontools::init_package("hey")
#> * Initializing git repository
#> * Add default .gitignore
#> * Add sample R file
#> * Add .Rbuildignore
#> * Add DESCRIPTION
#> Warning: 'devtools::use_mit_license' is deprecated.
#> Use 'usethis::use_mit_license()' instead.
#> See help("Deprecated") and help("devtools-deprecated").
#> Warning in warn_unless_current_dir(pkg): `pkg` is not `.`, which is now unsupported.
#>   Please use `usethis::proj_set()` to set the project directory.
#> Error in usethis::use_mit_license(copyright_holder = copyright_holder): unused argument (copyright_holder = copyright_holder)

Created on 2018-10-24 by the reprex package (v0.2.1)

Session info 
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.5.1 (2018-07-02)
#>  os       Ubuntu 18.04.1 LTS          
#>  system   x86_64, linux-gnu           
#>  ui       X11                         
#>  language en_GB:en                    
#>  collate  en_GB.UTF-8                 
#>  ctype    en_GB.UTF-8                 
#>  tz       Europe/London               
#>  date     2018-10-24                  
#> 
#> ─ Packages ──────────────────────────────────────────────────────────────
#>  package     * version    date       lib
#>  assertthat    0.2.0      2017-04-11 [1]
#>  backports     1.1.2      2017-12-13 [1]
#>  base64enc     0.1-3      2015-07-28 [1]
#>  callr         3.0.0      2018-08-24 [1]
#>  cli           1.0.1      2018-09-25 [1]
#>  clisymbols    1.2.0      2017-05-21 [1]
#>  crayon        1.3.4      2017-09-16 [1]
#>  debugme       1.1.0      2017-10-22 [1]
#>  desc          1.2.0      2018-05-01 [1]
#>  devtools      2.0.0      2018-10-19 [1]
#>  digest        0.6.18     2018-10-10 [1]
#>  evaluate      0.12       2018-10-09 [1]
#>  fs            1.2.6      2018-08-23 [1]
#>  git2r         0.23.0     2018-07-17 [1]
#>  glue          1.3.0      2018-07-17 [1]
#>  hms           0.4.2      2018-03-10 [1]
#>  htmltools     0.3.6      2017-04-28 [1]
#>  knitr         1.20       2018-02-20 [1]
#>  magrittr      1.5        2014-11-22 [1]
#>  memoise       1.1.0      2017-04-21 [1]
#>  pillar        1.3.0      2018-07-14 [1]
#>  pkgbuild      1.0.2      2018-10-16 [1]
#>  pkgconfig     2.0.2      2018-08-16 [1]
#>  pkgload       1.0.1      2018-10-11 [1]
#>  prettyunits   1.0.2      2015-07-13 [1]
#>  processx      3.2.0      2018-08-16 [1]
#>  ps            1.2.0      2018-10-16 [1]
#>  R6            2.3.0      2018-10-04 [1]
#>  Rcpp          0.12.19    2018-10-01 [1]
#>  readr         1.1.1      2017-05-16 [1]
#>  recontools    0.0.0.9000 2018-10-24 [1]
#>  remotes       2.0.1      2018-10-19 [1]
#>  rlang         0.3.0      2018-10-22 [1]
#>  rmarkdown     1.10       2018-06-11 [1]
#>  rprojroot     1.3-2      2018-01-03 [1]
#>  sessioninfo   1.1.0      2018-09-25 [1]
#>  stringi       1.2.4      2018-07-20 [1]
#>  stringr       1.3.1      2018-05-10 [1]
#>  testthat      2.0.1      2018-10-13 [1]
#>  tibble        1.4.2      2018-01-22 [1]
#>  usethis       1.4.0.9000 2018-10-02 [1]
#>  withr         2.1.2      2018-03-15 [1]
#>  yaml          2.2.0      2018-07-25 [1]
#>  source                              
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  Github (reconhub/recontools@df25821)
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#>  Github (r-lib/usethis@1e3c6a6)      
#>  CRAN (R 3.5.1)                      
#>  CRAN (R 3.5.1)                      
#> 
#> [1] /home/zkamvar/Documents/RLibrary
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

Add more license options

It would be cool to have more options and navigate using the arrow keys to select the license.
MIT + file LICENSE
GPL + file LICENSE
...

Use `knitr` by default for compiling `README.Rmd`?

Currently it looks like the template supposes rmarkdown. I personally prefer to use knit(), but I may be missing some reason why rmarkdown should be preferred. If so, I would add README.html to .gitignore as it will be produced when calling rmarkdown.

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