Installation issue

[MatthewMaher]

Trying to do a first-ever install of this package. I'm using R-4.0.0

I did the recommended command: devtools::install_github("mrcieu/gwasglue") But it failed with:

Error: Failed to install 'gwasglue' from GitHub:
  Failed to install 'gwasvcf' from GitHub:
  HTTP error 404.
  No commit found for the ref master

Did you spell the repo owner (`mrcieu`) and repo name (`gwasglue2`) correctly?

I can't help note that final message acts like I type 'gwasglue2' in the command, but I did not include that '2'.

FWIW, I earlier had a "Bad credentials" error, which I got around by creating a GITHUB PAT, so this new error does not seem to be permissions related, as far as I can tell.

Please advise.
Thanks

[remlapmot]

If you can't get the devtools::install_github() command to work, we distribute binary versions of packages for some operating systems through our mrcieu.r-universe.dev but you need to be using the latest (R 4.3.2) or previous minor version release of R (4.2.3) (unless you are in some locked down system, you really don't want to be on such an old version of R anyway).

To use this, for Windows and Intel Macs (and for Apple Silicon Macs but the packages will build from source), the installation code is

install.packages(
  'gwasglue',
  repos = c(
    'https://mrcieu.r-universe.dev',
    'https://cloud.r-project.org'
  )
)

If you are on Ubuntu Jammy Jellyfish Linux adapt the installation code given here by swapping the package name with the one you require.

[MatthewMaher]

Thanks for the tip on the binaries. I don't currently have access to the latest R (so I've requested it and am waiting).

But on the error message, I looked a bit and yes, I see that the package 'mrcieu/gwasglue' has a DESCRIPTION that references 'mrcieu/gwasvcf' but then that has a DESCRIPTION that references 'mrcieu/gwasglue2' (which appears to be some new, in-progress development version?) and that package 'gwasglue2' truly does not have a 'master' branch in the repo (as the message complains).

The README for gwasglue2 says that "It aims to replace the original gwasglue package but it is still in early development."

Given that, should gwasvcf really be referencing it? the gwasvcf change that added the reference to gwasglue2 was made in Aug 2023.

Is gwasglue (without the '2') now considered deprecated?

Thanks for any assistance

[remlapmot]

With a relatively up to date version of either the devtools or remotes packages the name of the default branch of a repository should not matter, i.e., whether that be master or main or something else. So you should try installing a more recent version of devtools/remotes. Git and most web based Git hosts switched from calling the default branch master to main a few years ago and I've never experienced a problem because of this.

Well spotted, the gwasglue2 package is in development. I am not sure if it's ready for others to use yet; @ritarasteiro or @explodecomputer can tell you more.