rm gwasglue2 functions

[ritarasteiro]

Start preparing resubmission.

• rm all functions related with gwasglue2

[ritarasteiro]

@explodecomputer I rm all mentions of gwasglue2 from this branch. I also added a gwasglue2 branch with all gwasglue2 functionalities.

[remlapmot]

In last week's commits @explodecomputer used an anonymous function in zzz.R on lin 53

https://github.com/MRCIEU/ieugwasr/blob/83f47ddfdfc1c3b8fc2326903d51ed1312075777/R/zzz.R#L53

Anonymous functions were only introduced in R 4.1.0 . So either we need to fix that back to a standard function call or bump the version of R in the DESCRIPTION to 4.1.0. My preference is to use a standard function here.

[remlapmot]

Please remove the version check on startup.

This is because once on CRAN you/we should bump the version of the package in the GitHub repo to a development version number, i.e., ending .9000 . If you leave the version check in it will trigger every time and people will be confused because they have the CRAN version, so why should they need to then go and install the GitHub version.

[remlapmot]

Great news it seems CRAN accepted a resubmission Gib https://cran.r-project.org/package=ieugwasr well done!

But is the version on master the version that was accepted? I'm guessing maybe not as the accepted CRAN version says 0.2.0 and master says 0.1.8.

So we need to get the accepted version onto master. And add the appropriate git tag and do a GitHub release. Is it up to commit https://github.com/MRCIEU/ieugwasr/pull/57/commits/72ed9e93e0b2da703b0638c94b6bbef0d42df9e0 that is the CRAN version?

Then you can add commits subsequent to the accepted version into this PR (or an additional PR), as the package build is still broken on R 4.0.5 as I noted above so that simple fix needs adding (or the R version needs bumping).

[ritarasteiro]

Congratulations @explodecomputer!

[explodecomputer]

Many thanks @ritarasteiro @remlapmot I've created the releases for the 3 (!) versions that have been submitted to CRAN. Unfortunately there was really bad timing because of some issues with the new API, so 0.2.0 was pointing to that and became available on CRAN at exactly the wrong moment when that API version developed some problems, so I then submitted an updated version to 0.2.1 thinking it would be some time before that would be fixed but 2 days later it was fixed and I then submitted 0.2.2. So a bit of a mess!

I've fixed the anonymous function issue now also thanks for spotting that! And codecov seems to have started working again, I don't know why.

[remlapmot]

Great.

But I would still prefer it if we could remove the version check on package load for packages that are on CRAN (it's fair enough to do it in packages just on GitHub).

Look what happens when someone installs this from CRAN - they instantly get the message telling them to reinstall from GitHub - not a great user experience.

install.packages('ieugwasr')
#> 
#> The downloaded binary packages are in
#>  /var/folders/kt/7xskrb1n4_x2jkd9lt0rhybh0000gp/T//RtmpCmFnaW/downloaded_packages
library(ieugwasr)
#> 
#> Warning:
#> You are running an old version of the ieugwasr package.
#> This version:   0.2.2
#> Latest version: 0.2.2-9000
#> Please consider updating using remotes::install_github('MRCIEU/ieugwasr')
#> OpenGWAS updates:
#>   Date: 2024-03-07
#>   [>] There is exceptional load on the OpenGWAS servers.
#>   [>] Urgent infrastructure development being performed.
#>   [>] See local options for analysis: https://mrcieu.github.io/gwasvcf/.

^{Created on 2024-04-03 with reprex v2.1.0}

(To update packages we should teach people the standard methods, i.e., that they should run update.packages(), remotes::update_packages(), and BiocManager::install() regularly.)

[remlapmot]

Also for packages on CRAN for the pkgdown site it's good to turn on pkgdown's development mode https://pkgdown.r-lib.org/reference/build_site.html?q=mode#development-mode.

To do this to _pkgdown.yml simply add these 2 lines

development:
  mode: auto

Then the main site will be for versions with release numbers, and there will be a dev subdirectoty in the site with the pages for the development version.

[remlapmot]

To show you what you get with development mode set to auto:

• main site for released version: https://remlapmot.github.io/OneSampleMR/
• site in dev subdirectoty for development version: https://remlapmot.github.io/OneSampleMR/dev/

done automagically by pkgdown 🪄