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RemoteSha being added to internally-create packages causing renv::status to fail #2014

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fh-mthomson opened this issue Oct 11, 2024 · 11 comments
Closed

RemoteSha being added to internally-create packages causing renv::status to fail #2014

fh-mthomson opened this issue Oct 11, 2024 · 11 comments

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@fh-mthomson
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I'm finding a subtle regression b/w renv 1.0.7 -> 1.0.10 that I suspect is related to RemoteSha changes discussed in #1961.

When running in:

  1. Workbench: renv::status() shows no issues
  2. GitLab CI: renv::status() returns
- The project is out-of-sync -- use `renv::status()` for details.
The following package(s) are out of sync [lockfile != library]:
# RSPM -----------------------------------------------------------------------
- searchr             [0.2.6: unchanged]
- myinternals         [0.4.0: unchanged]

When I downgrade to 1.0.7, then renv::snapshot() removes the RemoteSha entries for each, which allows the CI to again pass with renv::status() showing no issues.

Details:

  • Both Workbench/GitLab CI are using the same Docker image + version, and I've cleared the CI cache to confirm that re-installing (from binary) doesn't resolve the issue.
  • Each of searchr and myinternals (masked names for internal packages) are installed from tag-based git builders on Package Manager.
  • I'm not currently using pak with renv.
@fh-mthomson fh-mthomson changed the title RemoteSha being added to internally-create packages causing RemoteSha being added to internally-create packages causing renv::status to fail Oct 11, 2024
@kevinushey
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Any chance you can prepare a reproducible example, just so I can investigate more easily?

@fh-mthomson
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Any chance you can prepare a reproducible example, just so I can investigate more easily?

Not easily, unfortunately, since it's only happening for private packages on our private PM instance.

Do you have a PM instance with git-backed packages that would be publicly accessible? That's the only way I could think of getting closer to something to help me give you more details.

If you prefer, I can submit a Posit Support ticket with more detailed logs, but figured I'd start here in case you have thoughts.

@kevinushey
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kevinushey commented Oct 11, 2024 •
edited
Loading

Can you try running the following:

trace(renv:::renv_lockfile_diff_record, quote({
  if (identical(before$Package, "searchr")) {
    writeLines("Before:")  
    str(before)
    writeLines("")

    writeLines("After:")
    str(after)
    writeLines("")
  }
}), print = FALSE)

renv::status()

and let me know what output you see?

@fh-mthomson
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fh-mthomson commented Oct 14, 2024 •
edited
Loading

I got a bit closer to ~reproducible:

  1. configured the following git-builder on our dev PM:
rspm create git-builder --url=https://github.com/tidyverse/googledrive.git --source=OTHER_Source --build-trigger=tags
  1. Installed (avoiding the cache):
renv::install(
  "googledrive",
  repos = c(OTHER = "https://<internal PM>/OTHER/__linux__/jammy/latest"),
  rebuild = TRUE
)
  1. Created a lockfile - relevant chunk:
    "googledrive": {
      "Package": "googledrive",
      "Version": "2.1.1",
      "Source": "Repository",
      "Repository": "RSPM",
      "RemoteSha": "a33c4ddfbc68e399c6373771e689310791def85c",
      "Requirements": [
        "R",
        "cli",
        "gargle",
        "glue",
        "httr",
        "jsonlite",
        "lifecycle",
        "magrittr",
        "pillar",
        "purrr",
        "rlang",
        "tibble",
        "utils",
        "uuid",
        "vctrs",
        "withr"
      ],
      "Hash": "e99641edef03e2a5e87f0a0b1fcc97f4"
    },
full file (masking our dev URL) 

{
  "R": {
    "Version": "4.1.3",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://packagemanager.posit.co/cran/latest"
      },
      {
        "Name": "OTHER",
        "URL": "https://<internal>/OTHER/latest"
      }
    ]
  },
  "Packages": {
    "R6": {
      "Package": "R6",
      "Version": "2.5.1",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R"
      ],
      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
    },
    "askpass": {
      "Package": "askpass",
      "Version": "1.2.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "sys"
      ],
      "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a"
    },
    "base64enc": {
      "Package": "base64enc",
      "Version": "0.1-3",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R"
      ],
      "Hash": "543776ae6848fde2f48ff3816d0628bc"
    },
    "bslib": {
      "Package": "bslib",
      "Version": "0.8.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "base64enc",
        "cachem",
        "fastmap",
        "grDevices",
        "htmltools",
        "jquerylib",
        "jsonlite",
        "lifecycle",
        "memoise",
        "mime",
        "rlang",
        "sass"
      ],
      "Hash": "b299c6741ca9746fb227debcb0f9fb6c"
    },
    "cachem": {
      "Package": "cachem",
      "Version": "1.1.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "fastmap",
        "rlang"
      ],
      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
    },
    "cli": {
      "Package": "cli",
      "Version": "3.6.3",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "b21916dd77a27642b447374a5d30ecf3"
    },
    "curl": {
      "Package": "curl",
      "Version": "5.2.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "d91263322a58af798f6cf3b13fd56dde"
    },
    "digest": {
      "Package": "digest",
      "Version": "0.6.37",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "33698c4b3127fc9f506654607fb73676"
    },
    "evaluate": {
      "Package": "evaluate",
      "Version": "1.0.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "3fd29944b231036ad67c3edb32e02201"
    },
    "fansi": {
      "Package": "fansi",
      "Version": "1.0.6",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "grDevices",
        "utils"
      ],
      "Hash": "962174cf2aeb5b9eea581522286a911f"
    },
    "fastmap": {
      "Package": "fastmap",
      "Version": "1.2.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
    },
    "fontawesome": {
      "Package": "fontawesome",
      "Version": "0.5.2",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "htmltools",
        "rlang"
      ],
      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
    },
    "fs": {
      "Package": "fs",
      "Version": "1.6.4",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "methods"
      ],
      "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
    },
    "gargle": {
      "Package": "gargle",
      "Version": "1.5.2",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "cli",
        "fs",
        "glue",
        "httr",
        "jsonlite",
        "lifecycle",
        "openssl",
        "rappdirs",
        "rlang",
        "stats",
        "utils",
        "withr"
      ],
      "Hash": "fc0b272e5847c58cd5da9b20eedbd026"
    },
    "glue": {
      "Package": "glue",
      "Version": "1.8.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "methods"
      ],
      "Hash": "5899f1eaa825580172bb56c08266f37c"
    },
    "googledrive": {
      "Package": "googledrive",
      "Version": "2.1.1",
      "Source": "Repository",
      "Repository": "RSPM",
      "RemoteSha": "a33c4ddfbc68e399c6373771e689310791def85c",
      "Requirements": [
        "R",
        "cli",
        "gargle",
        "glue",
        "httr",
        "jsonlite",
        "lifecycle",
        "magrittr",
        "pillar",
        "purrr",
        "rlang",
        "tibble",
        "utils",
        "uuid",
        "vctrs",
        "withr"
      ],
      "Hash": "e99641edef03e2a5e87f0a0b1fcc97f4"
    },
    "highr": {
      "Package": "highr",
      "Version": "0.11",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "xfun"
      ],
      "Hash": "d65ba49117ca223614f71b60d85b8ab7"
    },
    "htmltools": {
      "Package": "htmltools",
      "Version": "0.5.8.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "base64enc",
        "digest",
        "fastmap",
        "grDevices",
        "rlang",
        "utils"
      ],
      "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
    },
    "httr": {
      "Package": "httr",
      "Version": "1.4.7",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "R6",
        "curl",
        "jsonlite",
        "mime",
        "openssl"
      ],
      "Hash": "ac107251d9d9fd72f0ca8049988f1d7f"
    },
    "jquerylib": {
      "Package": "jquerylib",
      "Version": "0.1.4",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "htmltools"
      ],
      "Hash": "5aab57a3bd297eee1c1d862735972182"
    },
    "jsonlite": {
      "Package": "jsonlite",
      "Version": "1.8.9",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "methods"
      ],
      "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
    },
    "knitr": {
      "Package": "knitr",
      "Version": "1.48",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "evaluate",
        "highr",
        "methods",
        "tools",
        "xfun",
        "yaml"
      ],
      "Hash": "acf380f300c721da9fde7df115a5f86f"
    },
    "lifecycle": {
      "Package": "lifecycle",
      "Version": "1.0.4",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "cli",
        "glue",
        "rlang"
      ],
      "Hash": "b8552d117e1b808b09a832f589b79035"
    },
    "magrittr": {
      "Package": "magrittr",
      "Version": "2.0.3",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R"
      ],
      "Hash": "7ce2733a9826b3aeb1775d56fd305472"
    },
    "memoise": {
      "Package": "memoise",
      "Version": "2.0.1",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "cachem",
        "rlang"
      ],
      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
    },
    "mime": {
      "Package": "mime",
      "Version": "0.12",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "tools"
      ],
      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
    },
    "openssl": {
      "Package": "openssl",
      "Version": "2.2.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "askpass"
      ],
      "Hash": "d413e0fef796c9401a4419485f709ca1"
    },
    "pillar": {
      "Package": "pillar",
      "Version": "1.9.0",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "cli",
        "fansi",
        "glue",
        "lifecycle",
        "rlang",
        "utf8",
        "utils",
        "vctrs"
      ],
      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
    },
    "pkgconfig": {
      "Package": "pkgconfig",
      "Version": "2.0.3",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "utils"
      ],
      "Hash": "01f28d4278f15c76cddbea05899c5d6f"
    },
    "purrr": {
      "Package": "purrr",
      "Version": "1.0.2",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "cli",
        "lifecycle",
        "magrittr",
        "rlang",
        "vctrs"
      ],
      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
    },
    "rappdirs": {
      "Package": "rappdirs",
      "Version": "0.3.3",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R"
      ],
      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
    },
    "renv": {
      "Package": "renv",
      "Version": "1.0.10",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "utils"
      ],
      "Hash": "d0387d5687ec933dd7587efd4cfa2d85"
    },
    "rlang": {
      "Package": "rlang",
      "Version": "1.1.4",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
    },
    "rmarkdown": {
      "Package": "rmarkdown",
      "Version": "2.28",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "bslib",
        "evaluate",
        "fontawesome",
        "htmltools",
        "jquerylib",
        "jsonlite",
        "knitr",
        "methods",
        "tinytex",
        "tools",
        "utils",
        "xfun",
        "yaml"
      ],
      "Hash": "062470668513dcda416927085ee9bdc7"
    },
    "sass": {
      "Package": "sass",
      "Version": "0.4.9",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R6",
        "fs",
        "htmltools",
        "rappdirs",
        "rlang"
      ],
      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
    },
    "sys": {
      "Package": "sys",
      "Version": "3.4.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "de342ebfebdbf40477d0758d05426646"
    },
    "tibble": {
      "Package": "tibble",
      "Version": "3.2.1",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "fansi",
        "lifecycle",
        "magrittr",
        "methods",
        "pillar",
        "pkgconfig",
        "rlang",
        "utils",
        "vctrs"
      ],
      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
    },
    "tinytex": {
      "Package": "tinytex",
      "Version": "0.53",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "xfun"
      ],
      "Hash": "9db859e8aabbb474293dde3097839420"
    },
    "utf8": {
      "Package": "utf8",
      "Version": "1.2.4",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R"
      ],
      "Hash": "62b65c52671e6665f803ff02954446e9"
    },
    "uuid": {
      "Package": "uuid",
      "Version": "1.2-1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "34e965e62a41fcafb1ca60e9b142085b"
    },
    "vctrs": {
      "Package": "vctrs",
      "Version": "0.6.5",
      "Source": "Repository",
      "Repository": "RSPM",
      "Requirements": [
        "R",
        "cli",
        "glue",
        "lifecycle",
        "rlang"
      ],
      "Hash": "c03fa420630029418f7e6da3667aac4a"
    },
    "withr": {
      "Package": "withr",
      "Version": "3.0.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "grDevices",
        "graphics"
      ],
      "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
    },
    "xfun": {
      "Package": "xfun",
      "Version": "0.48",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "grDevices",
        "stats",
        "tools"
      ],
      "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f"
    },
    "yaml": {
      "Package": "yaml",
      "Version": "2.3.10",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
    }
  }
}

  1. CI Error:
$ Rscript -e ' # collapsed multi-line command
- The project is out-of-sync -- use `renv::status()` for details.
[1] "hello"
Tracing function "renv_lockfile_diff_record" in package "renv
(not-exported)"
[1] "renv_lockfile_diff_record"
Before:
List of 7
 $ Package     : chr "googledrive"
 $ Version     : chr "2.1.1"
 $ Source      : chr "Repository"
 $ Repository  : chr "RSPM"
 $ RemoteSha   : chr "a33c4ddfbc68e399c6373771e689310791def85c"
 $ Requirements: chr [1:16] "R" "cli" "gargle" "glue" ...
 $ Hash        : chr "e99641edef03e2a5e87f0a0b1fcc97f4"
After:
List of 8
 $ Package     : chr "googledrive"
 $ Version     : chr "2.1.1"
 $ Source      : chr "Repository"
 $ Repository  : chr "RSPM"
 $ RemoteType  : chr "repository"
 $ RemoteSha   : chr "a33c4ddfbc68e399c6373771e689310791def85c"
 $ Requirements: chr [1:16] "R" "cli" "gargle" "glue" ...
 $ Hash        : chr "e135beaf7a1b46c08f9389c56af5df38"
The following package(s) are out of sync [lockfile != library]:
# RSPM -----------------------------------------------------------------------
- googledrive   [2.1.1: unchanged]
See `?renv::status` for advice on resolving these issues.
Error: renv_status$synchronized is not TRUE
Execution halted
GitLab CI config 

default:
  image: rocker/tidyverse:4.1.3
  before_script:
  - |
    Rscript -e '
    install.packages("renv", repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest")
    renv::restore()
    '

stages:
  - test

lint:
  stage: test
  script:
  - |
    Rscript -e '
    print("hello")

    trace(
      renv:::renv_lockfile_diff_record,
      quote({
        if (identical(before$Package, "googledrive")) {
          writeLines("Before:")
          str(before)
          writeLines("")

          writeLines("After:")
          str(after)
          writeLines("")
        }
      }),
      print = FALSE
      )

    renv_status <- renv::status()
    stopifnot(renv_status$synchronized)
    '

For comparison, RemoteSha displayed in the lock file does align with the git-builder output, per the release: https://github.com/tidyverse/googledrive/releases/tag/v2.1.1

- googledrive (Trigger Type: tags)
    Transaction ID: 4634453
    Repository: https://github.com/tidyverse/googledrive.git
    SHA: a33c4ddfbc68e399c6373771e689310791def85c
    Tag: v2.1.1
    Package Version: 2.1.1
    Status: succeeded
    Time: Mon Oct 14 05:54:46 UTC 2024

Perhaps the issue is actually with Hash, not RemoteSha?

kevinushey added a commit that referenced this issue Nov 13, 2024
@kevinushey
also treat 'repository' remote types as cranlike (#2014)
1c8c64c
@kevinushey
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Collaborator

Sorry for the late response. I think the issue here is actually the differing remote types -- in particular, the second record has:

$ RemoteType : chr "repository"

I've pushed a change in 1c8c64c that might alleviate the issue; please let me know if it makes a difference.

@fh-mthomson
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Contributor Author

Thanks for taking a look! I just ran:

  1. renv::install('rstudio/renv')
  2. renv::snapshot()

Then pushed, and getting a different error trying to install via CI. Any suggestions?

# Bootstrapping renv 1.0.11.9000 [sha: b531b02] ------------------------------
- Downloading renv ... FAILED
Error in h(simpleError(msg, call)) : failed to download:
All download methods failed
Calls: source ... bootstrap -> withCallingHandlers -> renv_bootstrap_download

Relevant snippets (lmk if the full files would help):

renv/activate.R:

  # the requested version of renv
  version <- "1.0.11.9000"
  attr(version, "sha") <- "b531b0215fa8edcd80a05af22ec0f85a4dcb027a"

renv.lock:

    "renv": {
      "Package": "renv",
      "Version": "1.0.11.9000",
      "Source": "GitHub",
      "RemoteType": "github",
      "RemoteHost": "api.github.com",
      "RemoteUsername": "rstudio",
      "RemoteRepo": "renv",
      "RemoteRef": "main",
      "RemoteSha": "b531b0215fa8edcd80a05af22ec0f85a4dcb027a",
      "Requirements": [
        "utils"
      ],
      "Hash": "9002c894649542a4ca23e1e6f25f3f82"
    },

@kevinushey
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Hmm, I wasn't able to reproduce locally:

# Bootstrapping renv 1.0.11.9000 [sha: b531b02] ------------------------------
- Downloading renv ... OK
- Installing renv  ... OK

- Project '~/scratch/blah' loaded. [renv 1.0.11.9000; sha: b531b02]

Is it possible that your CI system doesn't have access to GitHub for some reason? (renv is trying to bootstrap itself by downloading the appropriate version of renv from GitHub, but that is apparently failing)

@fh-mthomson
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fh-mthomson commented Nov 13, 2024 •
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hmm looks to be a common issue with remotes - r-lib/remotes#641 (comment)

More minimal example, running this in CI fails:

$ Rscript -e 'remotes::install_github("rstudio/renv")'
Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`
Error: Failed to install 'unknown package' from GitHub:
  HTTP error 401.
  Bad credentials
  Rate limit remaining: 59/60
  Rate limit reset at: 2024-11-14 00:22:12 UTC
  
Execution halted

I tried using pak via renv in GitLab CI:

default:
  image: rocker/tidyverse:4.4.2
  before_script:
  - |
    Rscript -e '
    pak::pak('rstudio/renv')
    options(renv.config.pak.enabled = TRUE)
    renv::restore()
    '

but, I think it's still failing from .Rprofile calling renv/activate.R to bootstrap install from GH.

Error:

# Bootstrapping renv 1.0.11.9000 [sha: b531b02] ------------------------------
- Downloading renv ... FAILED
Error in h(simpleError(msg, call)) : failed to download:
All download methods failed
Calls: source ... bootstrap -> withCallingHandlers -> renv_bootstrap_download
Execution halted

Any suggestions?

@fh-mthomson
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Output of:

    Sys.getenv("GITHUB_TOKEN", unset = NA)
    Sys.getenv("GITHUB_PAT", unset = NA)
    Sys.getenv("GH_TOKEN", unset = NA)

Is:

[1] NA
[1] NA
[1] NA

Setting GITHUB_PAT manually in the CI config allows it to successfully bootstrap install!

# Bootstrapping renv 1.0.11.9000 [sha: b531b02] ------------------------------
- Downloading renv ... 
OK
- Installing renv  ... 
OK

(seems like a separate bug to investigate, since I wouldn't expect GITHUB_PAT to be necessary)

BUT the good news is that I confirmed the latest version of renv does resolve the original reported issue. thank you!!

@kevinushey
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BUT the good news is that I confirmed the latest version of renv does resolve the original reported issue. thank you!!

Phew, that's awesome to hear. Thanks for confirming!

@fh-mthomson
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Thanks again for making this change in this release!

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