[pak] Use pak for package installation

[hadley]

Related issues:

• Cannot install from the cellar with pak #1268
• Why aren't packages installed with pak synchronized to renv cache? #1331
• Make pak upgrade option configurable #1330
• renv_pak_restore tries to move packages to cache instead of installing from cache #1334

[kevinushey]

Note that partial support is available if one sets in their .Renviron:

RENV_CONFIG_PAK_ENABLED = TRUE

But we'll probably want to scope out what work needs to be done to let us turn this on by default.

[mnlang]

I'm encountering a problem with renv::restore() when using pak with a Remotes section in the DESCRIPTION file that includes dependencies on a self-maintained GitLab instance, which, to my knowledge, has not been reported.

Everything works correctly without these dependencies when setting RENV_CONFIG_PAK_ENABLED = TRUE and directly installing the package via:

pak::pkg_install("gitlab::https://boulangerie.thinkr.fr/mygroup/mysubgroup/mypackage")

as described in this comment, runs as well.

It seems that it cannot resolve to the GitLab instance, as it throws the error ! Could not solve package dependencies and attempts to download the DESCRIPTION files from gitlab.com:

Caused by error: 
! Failed to download DESCRIPTION from git repo at
<https://gitlab.com/...

[kevinushey]

Any chance you could provide a standalone, reproducible example?

[mnlang]

I'm sorry, but providing a standalone, reproducible example on a company GitLab instance is rather difficult. However, I started from scratch and, to my surprise, encountered different error messages. Here's what I tried:

First Attempt Using pak

After successfully installing via:

pak::pkg_install("gitlab::https://gitlab.company.com/user/demopackage2")
renv::snapshot()

The renv.lock file appears as follows:

{
  "R": {
    "Version": "4.1.2",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "demopackage2": {
      "Package": "demopackage2",
      "Version": "0.0.0.9000",
      "Source": "GitLab",
      "RemoteType": "gitlab",
      "RemoteUrl": "https://gitlab.company.com/user/demopackage2.git",
      "RemotePkgRef": "gitlab::https://gitlab.company.com/user/demopackage2",
      "RemoteRef": "HEAD",
      "RemoteSha": "6a013a17b0898d52289c6cd370011a50da29792a",
      "RemoteHost": "gitlab.company.com",
      "RemoteRepo": "demopackage2",
      "RemoteUsername": "user",
      "Hash": "0608030528c9f1423fb36ab185cdaa4d"
    },
    "renv": {
      "Package": "renv",
      "Version": "1.0.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "utils"
      ],
      "Hash": "41b847654f567341725473431dd0d5ab"
    }
  }
}

However, the following error occurs when calling renv::restore:

! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
Error:                                                                
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* user/demopackage2@HEAD: ! pkgdepends resolution error for user/demopackage2@HEAD.
Caused by error: 
! Can't find GitHub repo user/demopackage2.
Type .Last.error to see the more details.
Traceback (most recent calls last):
6: renv::restore()
5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude, 
       project = project)
4: pak$pkg_install(remotes)
3: remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), 
       list(pkg = pkg, lib = lib, upgrade = upgrade, ask = ask, 
           start = start, dependencies = dependencies, loaded = loaded_packages(lib)))
2: err$throw(res$error)
1: base::stop(cond)

Second Attempt Using pak

Alternatively, after successful installation via:

pak::pkg_install("git::https://gitlab.company.com/user/demopackage2.git")
renv::snapshot()

The renv.lock file appears as follows:

{
  "R": {
    "Version": "4.1.2",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "demopackage2": {
      "Package": "demopackage2",
      "Version": "0.0.0.9000",
      "Source": "git",
      "RemoteType": "git",
      "RemoteUrl": "https://gitlab.company.com/user/demopackage2.git",
      "RemotePkgRef": "git::https://gitlab.company.com/user/demopackage2.git",
      "RemoteRef": "HEAD",
      "RemoteSha": "6a013a17b0898d52289c6cd370011a50da29792a",
      "RemoteHost": "gitlab.company.com",
      "RemoteRepo": "demopackage2",
      "RemoteUsername": "user",
      "Hash": "8538f3274f87fc9bf3793017f7d1ee6a"
    },
    "renv": {
      "Package": "renv",
      "Version": "1.0.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "utils"
      ],
      "Hash": "41b847654f567341725473431dd0d5ab"
    }
  }
}

And the following error occurs when calling renv::restore:

> renv::restore()
! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
Error:                                                                
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* user/demopackage2@HEAD: ! pkgdepends resolution error for user/demopackage2@HEAD.
Caused by error: 
! Can't find GitHub repo user/demopackage2.
Type .Last.error to see the more details.
Traceback (most recent calls last):
6: renv::restore()
5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude, 
       project = project)
4: pak$pkg_install(remotes)
3: remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), 
       list(pkg = pkg, lib = lib, upgrade = upgrade, ask = ask, 
           start = start, dependencies = dependencies, loaded = loaded_packages(lib)))
2: err$throw(res$error)
1: base::stop(cond)

Installation via remotes

Again, successful installation now via:

remotes::install_gitlab("user/demopackage2", host = "https://gitlab.company.com")

The snapshot looks like this:

{
  "R": {
    "Version": "4.1.2",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "demopackage2": {
      "Package": "demopackage2",
      "Version": "0.0.0.9000",
      "Source": "GitLab",
      "RemoteType": "gitlab",
      "RemoteHost": "https://gitlab.company.com",
      "RemoteRepo": "demopackage2",
      "RemoteUsername": "user",
      "RemoteRef": "HEAD",
      "RemoteSha": "6a013a17b0898d52289c6cd370011a50da29792a",
      "Hash": "82cef80084224e734eb15b302e0b7fb6"
    },
    "renv": {
      "Package": "renv",
      "Version": "1.0.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "utils"
      ],
      "Hash": "41b847654f567341725473431dd0d5ab"
    }
  }
}

And the following error is produced:

renv::restore()

! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
Error:                                                                
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* user/demopackage2@HEAD: ! pkgdepends resolution error for user/demopackage2@HEAD.
Caused by error: 
! Can't find GitHub repo user/demopackage2.
Type .Last.error to see the more details.
Traceback (most recent calls last):
6: renv::restore()
5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude, 
       project = project)
4: pak$pkg_install(remotes)
3: remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), 
       list(pkg = pkg, lib = lib, upgrade = upgrade, ask = ask, 
           start = start, dependencies = dependencies, loaded = loaded_packages(lib)))
2: err$throw(res$error)
1: base::stop(cond)

Finally, by removing RENV_CONFIG_PAK_ENABLED = TRUE from the .Renviron file, it works:

renv::restore()

The following package(s) will be updated:

# GitLab ---------------------------------------------------------------------
- demopackage2   [* -> user/demopackage2@HEAD]

Do you want to proceed? [Y/n]: Y

# Downloading packages -------------------------------------------------------
- Downloading demopackage2 from GitLab ...      OK [602 bytes in 0.38s]
Successfully downloaded 1 package in 0.42 seconds.

# Installing packages --------------------------------------------------------
- Installing demopackage2 ...                   OK [built from source and cached in 0.38s]

[alethor]

Can confirm that I also had the same issue as @mnlang for a private repo hosted on gitlab.com

[kevinushey]

Can you please file a separate issue with details, so that this doesn't get lost?

Is there any chance this could be reproduced using an R package available on a publicly-visible Gitlab project?