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renv::restore with pak errors when using a custom git package #1974

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LeeMendelowitz opened this issue Aug 25, 2024 · 8 comments
Open

renv::restore with pak errors when using a custom git package #1974

LeeMendelowitz opened this issue Aug 25, 2024 · 8 comments

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@LeeMendelowitz
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When using pak with renv 1.0.7, I'm getting in error when trying to renv::restore() using a custom git repo. I'm able to renv::install the package with pak, it's just the restore that fails with an error.

Here's an example of how I installed from a custom git repo (where I replaced my actual url with a dummy url). The install with pak worked fine, and update the renv.lock:

renv::install('git::https://gitlab.example.net/path/example.git')

# Or could use a local repo:
# renv::install("~/projects/example")

renv::snapshot()

The renv.lock has:

    "example": {
      "Package": "example",
      "Version": "1.0.0",
      "Source": "git",
      "RemoteType": "git",
      "RemoteUrl": "https://gitlab.example.net/path/example.git",
      "RemotePkgRef": "git::https://gitlab.example.net/path/example.git",
      "RemoteRef": "HEAD",
      "RemoteSha": "xxx",
      "Requirements": [
        "DBI",
        "R",
        "tibble"
      ],
      "Hash": "xxx"
    },

To test the renv::restore(), I rm -rf renv/library. But a call to renv::restore() with this lock file will fail with:

# Installing packages --------------------------------------------------------
- Installing pak ...                            OK [linked from cache]
Successfully installed 1 package in 13 milliseconds.
✔ Loading metadata database ... done
Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
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* [email protected]: dependency conflict
* [email protected]: dependency conflict
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* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
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* [email protected]: dependency conflict
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* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: Can't find package called [email protected].
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
* [email protected]: dependency conflict
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* [email protected]: dependency conflict
* [email protected]: dependency conflict
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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)

The same error occurs if I try installing a local git repo (i.e. renv::install("~/projects/example").

SessionInfo

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.7.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

loaded via a namespace (and not attached):
[1] compiler_4.3.2 tools_4.3.2    renv_1.0.7     pak_0.8.0
@kevinushey
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This sounds somewhat similar to

renv/NEWS.md

Lines 68 to 70 in fcfe748

* Fixed an issue with `renv`'s `pak` integration where `renv` could install the
wrong version of a GitHub package during restore if
`options(renv.config.pak.enabled = TRUE)` was set. (#1883)
-- do you see the same issue in the development version of renv?

@LeeMendelowitz
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@kevinushey

Yes, this is still an issue in the latest development version of renv. When I try to restore an renv.lock that was generated without pak enabled that uses the custom git repo, I get the error above.

@kevinushey
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kevinushey commented Sep 26, 2024 •
edited
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Thanks -- do you by any chance have a standalone reproducible example I could use for testing? (Can the issue be reproduced readily using any publicly-available R packages on GitHub, but using git references to access those?)

@LeeMendelowitz
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Yup I was able to get a reproducible example using the gt package. Interestingly, calling renv::install("git::[email protected]:rstudio/gt.git") with pak enabled errors out, which might be the heart of the issue. The restore of a lockfile with pak enabled also errors out.

export RENV_CONFIG_CACHE_ENABLED=FALSE


# Step A: Install gt package from GitHub over SSH
# This works fine.
R --no-save <<EOF
renv::init()
renv::install("git::[email protected]:rstudio/gt.git")
renv::snapshot(type="all")
EOF


# Step B: Try restoring with pak enabled. This fails.
RENV_CONFIG_PAK_ENABLED=TRUE R --no-save <<EOF
renv::restore()
EOF


# Step C: Repeat without pak enabled. This works fine.
# It says "The library is already synchronized with the lockfile."
RENV_CONFIG_PAK_ENABLED=FALSE R --no-save <<EOF
renv::restore()
EOF


# Step D: Calling renv::install() with pak enabled also fails.
RENV_CONFIG_PAK_ENABLED=TRUE R --no-save <<EOF
renv::install("git::[email protected]:rstudio/gt.git")
EOF

@LeeMendelowitz
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@kevinushey Sorry forgot to mention you in last comment - I added a reproducible example above.

@kevinushey
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Thanks @LeeMendelowitz -- I'm going to take a look.

@kevinushey
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kevinushey commented Oct 11, 2024 •
edited
Loading

That example fails for me with:

> pak::pkg_install("git::[email protected]:rstudio/gt.git")
Error: 
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* git::[email protected]:rstudio/gt.git: ! pkgdepends resolution error for git::[email protected]:rstudio/gt.git.
Caused by error: 
! Failed to download DESCRIPTION from git repo at <://[email protected]:rstudio/gt.git>.
Caused by error in `(function (e) …`:
! URL rejected: Port number was not a decimal number between 0 and 65535
Type .Last.error to see the more details.

so I think this is not yet supported in pak.

@kevinushey
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r-lib/pak#705 (comment)

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@kevinushey @LeeMendelowitz