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Could not find R package in . or its parent directories. #576

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rjake opened this issue Dec 27, 2023 · 12 comments
Closed

Could not find R package in . or its parent directories. #576

rjake opened this issue Dec 27, 2023 · 12 comments

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@rjake
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rjake commented Dec 27, 2023

I am trying to adapt the pkgdown.yml workflow from r-lib/actions and it started failing on the step setup-r-dependencies@v2. I think it related to this commit that was released with version 0.7.1 on 12/11/23. I posted on Stack Overflow but didn't get any responses. I'm not sure if there is something in pak that can help, if the r-lib/actions workflow example needs to be updated, or if there is a better place to get help. Any advice is appreciated.

on:
  push:
    branches:
      - main
  workflow_dispatch:

jobs:
  pkgdown:
    runs-on: self-hosted   # <---- self hosted
    container: ...

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    permissions:
      contents: write

    steps:
      - name: Install Required Packages
        run: apt-get update && apt-get install -y gdebi-core pandoc

      - uses: actions/checkout@v1
        
      - uses: r-lib/actions/setup-renv@v2

      - uses: r-lib/actions/setup-r-dependencies@v2   # <--- fails here
        with:
          extra-packages: any::pkgdown, local::.
          needs: website
  Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * deps::.: ! pkgdepends resolution error for deps::..
  Caused by error: 
  ! Could not find R package in `.` or its parent directories.
  * any::pak=: ! pkgdepends resolution error for any::pak=.
  Caused by error: 
  ! missing value where TRUE/FALSE needed
  * local::.: ! pkgdepends resolution error for local::..
  Caused by error: 
  ! Could not find R package in `.` or its parent directories.
  ---
  Backtrace:
  1. pak::lockfile_create(c(deps, extra_deps), lockfile = ".github/pkg.lock", …
  2. pak:::remote(function(...) { …
  3. err$throw(res$error)
  ---
  Subprocess backtrace:
  1. base::withCallingHandlers(cli_message = function(msg) { …
  2. get("lockfile_create_internal", asNamespace("pak"))(...)
  3. prop$stop_for_solution_error()
  4. private$plan$stop_for_solve_error()
  5. pkgdepends:::pkgplan_stop_for_solve_error(self, private)
  6. base::throw(new_error("Could not solve package dependencies:\n", msg, …
  7. | base::signalCondition(cond)
  8. global (function (e) …
  Execution halted
@gaborcsardi
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Please include a link to your workflow file, and to a failed build.

@rjake
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rjake commented Dec 27, 2023 •
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It's on our enterprise server so I don't have any links. Here is what we are running and the log for the setup-r-dependencies step. Also, I just barely understand actions.

pkgdown.yaml 
# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
on:
  # because there is no "on merge" option, this workflow will run anytime a PR is closed or when manually triggered
  # if the PR is closed but not merged, the logic 'github.event.pull_request.merged == false' will be used during 
  # 'actions/checkout@v3' and the workflow will rebuild pages off of the main branch. This is an uneccessary build
  # but I can't find an alternative
  push:
    branches:
      - main
  workflow_dispatch: # run manually
    inputs:
      which-branch:
        description: "Which branch should be used to generate pages?"
        type: choice
        default: 'main'
        options:
        - main
        - this-pr

name: pkgdown

jobs:
  pkgdown:
    runs-on: self-hosted
    container: *****
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    permissions:
      contents: write

    steps:
      - name: Install Required Packages
        run: apt-get update && apt-get install -y gdebi-core pandoc

      - uses: actions/checkout@v1
        if: github.event.inputs.which-branch == 'main' # manually triggered + main selected
        with:
            ref: ${{ github.event.pull_request.head.sha }}
      
      - name: Increase timeout
        shell: Rscript {0}
        run: options(timeout = max(300, getOption("timeout")))
        
      - uses: r-lib/actions/setup-renv@v2

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.
          needs: website

      - name: Build site
        shell: Rscript {0}
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        
      - name: Install rsync 📚
        run: |
          apt-get update && apt-get install -y rsync
      
      - name: Deploy to GitHub pages 🚀
        uses: JamesIves/[email protected]
        with:
          clean: false
          branch: gh-pages
          folder: docs # this is the location from pkgdown::build_site_github_pages() and not Settings > Pages
log & error 
Run r-lib/actions/setup-r-dependencies@v[2](<server>/actions/runs/131606/job/220237#step:8:2)
  with:
    extra-packages: any::pkgdown, local::.
    needs: website
    cache: true
    cache-version: 1
    packages: deps::., any::sessioninfo
    pak-version: stable
    working-directory: .
    dependencies: "all"
    upgrade: FALSE
  env:
    GITHUB_PAT: ***
    R_KEEP_PKG_SOURCE: yes
    RENV_PATHS_ROOT: /runner/_work/_temp/renv
Run # Set site library path
  # Set site library path
  cat("::group::Set site library path\n")
  if (Sys.getenv("RENV_PROJECT") != "") {
    message("renv project detected, no need to set R_LIBS_SITE")
    cat(sprintf("R_LIB_FOR_PAK=%s\n", .libPaths()[1]), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
    q("no")
  }
  lib <- Sys.getenv("R_LIBS_SITE")
  if (lib == "") {
    lib <- file.path(dirname(.Library), "site-library")
    cat(sprintf("R_LIBS_SITE=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
    cat(sprintf("R_LIB_FOR_PAK=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
    message("Setting R_LIBS_SITE to ", lib)
  } else {
    message("R_LIBS_SITE is already set to ", lib)
    cat(sprintf("R_LIB_FOR_PAK=%s\n", strsplit(lib, .Platform$path.sep)[[1]][[1]]), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
  }
  cat("::endgroup::\n")
  shell: Rscript {0}
  env:
    GITHUB_PAT: ***
    R_KEEP_PKG_SOURCE: yes
    RENV_PATHS_ROOT: /runner/_work/_temp/renv
Set site library path
  renv project detected, no need to set R_LIBS_SITE
Run # Install pak
  # Install pak
  echo "::group::Install pak"
  if which sudo >/dev/null; then SUDO="sudo -E --preserve-env=PATH env"; else SUDO=""; fi
  $SUDO R -q -e 'dir.create(Sys.getenv("R_LIB_FOR_PAK"), recursive = TRUE, showWarnings = FALSE)'
  $SUDO R -q -e 'install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable/", lib = Sys.getenv("R_LIB_FOR_PAK"))'
  echo "::endgroup::"
    upgrade = (FALSE),
    dependencies = c(needs, ("all"))
  )
  cat("::endgroup::\n")
  cat("::group::Show Lockfile\n")
  writeLines(readLines(".github/pkg.lock"))
  cat("::endgroup::\n")
  shell: Rscript {0}
  env:
    GITHUB_PAT: ***
    R_KEEP_PKG_SOURCE: yes
    RENV_PATHS_ROOT: /runner/_work/_temp/renv
    R_LIB_FOR_PAK: /__w/rocqi/rocqi/renv/library/R-4.2/x86_64-pc-linux-gnu
Dependency resolution
  Warning message:
  package ‘pak’ was built under R version 4.2.[3](<server>/actions/runs/131606/job/220237#step:8:3) 
  ℹ Creating lockfile '.github/pkg.lock'
  
  ✔ Updated metadata database: [4](<server>/actions/runs/131606/job/220237#step:8:4).43 MB in 9 files.
  
  ℹ Creating lockfile '.github/pkg.lock'
  ℹ Updating metadata database
  ✔ Updating metadata database ... done
  
  ℹ Creating lockfile '.github/pkg.lock'
  ✖ Creating lockfile '.github/pkg.lock' [11.2s]
  
  Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * deps::.: ! pkgdepends resolution error for deps::..
  Caused by error: 
  ! Could not find R package in `.` or its parent directories.
  * local::.: ! pkgdepends resolution error for local::..
  Caused by error: 
  ! Could not find R package in `.` or its parent directories.
  ---
  Backtrace:
  1. pak::lockfile_create(c(deps, extra_deps), lockfile = ".github/pkg.lock", …
  2. pak:::remote(function(...) { …
  3. err$throw(res$error)
  ---
  Subprocess backtrace:
  1. base::withCallingHandlers(cli_message = function(msg) { …
  2. get("lockfile_create_internal", asNamespace("pak"))(...)
  3. prop$stop_for_solution_error()
  4. private$plan$stop_for_solve_error()
  [5](<server>/actions/runs/131606/job/220237#step:8:5). pkgdepends:::pkgplan_stop_for_solve_error(self, private)
  [6](<server>/actions/runs/131606/job/220237#step:8:6). base::throw(new_error("Could not solve package dependencies:\n", msg, …
  [7](<server>/actions/runs/131606/job/220237#step:8:7). | base::signalCondition(cond)
  [8](<server>/actions/runs/131606/job/220237#step:8:8). global (function (e) …
  Execution halted
  Error: Process completed with exit code 1.
DESCRIPTION 
Package: rocqi
Title: CHOP Analytics R package
Version: 2.1.0
Authors@R: c(
  person("Joe", "Mirizio", role = c("aut", "cre"), email = "[email protected]"),
  person("Paul", "Wildenhain", role = "aut", email = "[email protected]"),
  person("Jake", "Riley", role = "aut", email = "[email protected]")
)
Description: Gather, explore, analyze, and present data for CHOP.
License: MIT + file LICENSE
Language: en-US
Depends:
    R (>= 4.1)
Imports:
    dplyr (>= 0.7.0),
    ggplot2 (>= 3.4.0),
    glue (>= 1.3.0),
    highcharter (>= 0.7.0),
    httr,
    knitr,
    lifecycle (>= 1.0.0),
    methods,
    odbc (>= 1.2.0),
    plotly,
    purrr,
    qicharts2 (>= 0.7.2),
    readr,
    rlang,
    skimr (>= 2.0),
    stringr,
    tidyr (> 1.0)
Suggests:
    DBItest,
    devtools,
    lintr (>= 3.0),
    lubridate,
    mockery,
    rmarkdown,
    scales,
    testthat (>= 3.1.5)
VignetteBuilder:
    knitr
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
LazyData: true
Repository: CHOPRAN
RoxygenNote: 7.2.3
Roxygen: list(markdown = TRUE)
renv.lock 
{
  "R": {
    "Version": "4.1.3",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://packagemanager.posit.co/cran/latest"
      },
      {
        "Name": "CHOPRAN",
        "URL": "https://github.research.chop.edu/pages/CQI/chopran"
      }
    ]
  },
  "Packages": {
    "BH": {
      "Package": "BH",
      "Version": "1.81.0-1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "68122010f01c4dcfbe58ce7112f2433d"
    },
    "DBI": {
      "Package": "DBI",
      "Version": "1.1.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "methods"
      ],
      "Hash": "b2866e62bab9378c3cc9476a1954226b"
    },
    "DBItest": {
      "Package": "DBItest",
      "Version": "1.7.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "DBI",
        "R",
        "R6",
        "blob",
        "callr",
        "desc",
        "hms",
        "lubridate",
        "methods",
        "palmerpenguins",
        "rlang",
        "testthat",
        "utils",
        "vctrs",
        "withr"
      ],
      "Hash": "0ff95dd4be706690f3ad0e5ae9e7937d"
    },
    "DT": {
      "Package": "DT",
      "Version": "0.27",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "crosstalk",
        "htmltools",
        "htmlwidgets",
        "jquerylib",
        "jsonlite",
        "magrittr",
        "promises"
      ],
      "Hash": "3444e6ed78763f9f13aaa39f2481eb34"
    },
    "MASS": {
      "Package": "MASS",
      "Version": "7.3-55",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "grDevices",
        "graphics",
        "methods",
        "stats",
        "utils"
      ],
      "Hash": "c5232ffb549f6d7a04a152c34ca1353d"
    },
    "Matrix": {
      "Package": "Matrix",
      "Version": "1.4-0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "graphics",
        "grid",
        "lattice",
        "methods",
        "stats",
        "utils"
      ],
      "Hash": "130c0caba175739d98f2963c6a407cf6"
    },
    "R6": {
      "Package": "R6",
      "Version": "2.5.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
    },
    "RColorBrewer": {
      "Package": "RColorBrewer",
      "Version": "1.1-3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
    },
    "Rcpp": {
      "Package": "Rcpp",
      "Version": "1.0.10",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "methods",
        "utils"
      ],
      "Hash": "e749cae40fa9ef469b6050959517453c"
    },
    "TTR": {
      "Package": "TTR",
      "Version": "0.24.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "curl",
        "xts",
        "zoo"
      ],
      "Hash": "c553a7be22ec50faaebee27be54a1313"
    },
    "XML": {
      "Package": "XML",
      "Version": "3.99-0.14",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "methods",
        "utils"
      ],
      "Hash": "e5c8af79df616c135b21eaeb1dc6bc5c"
    },
    "anytime": {
      "Package": "anytime",
      "Version": "0.3.9",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "BH",
        "R",
        "Rcpp"
      ],
      "Hash": "74a64813f17b492da9c6afda6b128e3d"
    },
    "askpass": {
      "Package": "askpass",
      "Version": "1.2.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "sys"
      ],
      "Hash": "cad6cf7f1d5f6e906700b9d3e718c796"
    },
    "assertthat": {
      "Package": "assertthat",
      "Version": "0.2.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "tools"
      ],
      "Hash": "50c838a310445e954bc13f26f26a6ecf"
    },
    "backports": {
      "Package": "backports",
      "Version": "1.4.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "c39fbec8a30d23e721980b8afb31984c"
    },
    "base64enc": {
      "Package": "base64enc",
      "Version": "0.1-3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "543776ae6848fde2f48ff3816d0628bc"
    },
    "bit": {
      "Package": "bit",
      "Version": "4.0.5",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "d242abec29412ce988848d0294b208fd"
    },
    "bit64": {
      "Package": "bit64",
      "Version": "4.0.5",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "bit",
        "methods",
        "stats",
        "utils"
      ],
      "Hash": "9fe98599ca456d6552421db0d6772d8f"
    },
    "blob": {
      "Package": "blob",
      "Version": "1.2.4",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "methods",
        "rlang",
        "vctrs"
      ],
      "Hash": "40415719b5a479b87949f3aa0aee737c"
    },
    "brew": {
      "Package": "brew",
      "Version": "1.0-8",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "d69a786e85775b126bddbee185ae6084"
    },
    "brio": {
      "Package": "brio",
      "Version": "1.1.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "976cf154dfb043c012d87cddd8bca363"
    },
    "broom": {
      "Package": "broom",
      "Version": "1.0.5",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "backports",
        "dplyr",
        "ellipsis",
        "generics",
        "glue",
        "lifecycle",
        "purrr",
        "rlang",
        "stringr",
        "tibble",
        "tidyr"
      ],
      "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c"
    },
    "bslib": {
      "Package": "bslib",
      "Version": "0.4.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "base64enc",
        "cachem",
        "grDevices",
        "htmltools",
        "jquerylib",
        "jsonlite",
        "memoise",
        "mime",
        "rlang",
        "sass"
      ],
      "Hash": "a7fbf03946ad741129dc81098722fca1"
    },
    "cachem": {
      "Package": "cachem",
      "Version": "1.0.7",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "fastmap",
        "rlang"
      ],
      "Hash": "cda74447c42f529de601fe4d4050daef"
    },
    "callr": {
      "Package": "callr",
      "Version": "3.7.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "R6",
        "processx",
        "utils"
      ],
      "Hash": "9b2191ede20fa29828139b9900922e51"
    },
    "cellranger": {
      "Package": "cellranger",
      "Version": "1.1.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "rematch",
        "tibble"
      ],
      "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
    },
    "cli": {
      "Package": "cli",
      "Version": "3.6.1",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "utils"
      ],
      "Hash": "89e6d8219950eac806ae0c489052048a"
    },
    "clipr": {
      "Package": "clipr",
      "Version": "0.8.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "utils"
      ],
      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
    },
    "codetools": {
      "Package": "codetools",
      "Version": "0.2-18",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
      "Hash": "019388fc48e48b3da0d3a76ff94608a8"
    },
    "colorspace": {
      "Package": "colorspace",
      "Version": "2.1-0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "grDevices",
        "graphics",
        "methods",
        "stats"
      ],
      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
    },
    "commonmark": {
      "Package": "commonmark",
      "Version": "1.9.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "d691c61bff84bd63c383874d2d0c3307"
    },
    "conflicted": {
      "Package": "conflicted",
      "Version": "1.2.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R",
        "cli",
        "memoise",
        "rlang"
      ],
      "Hash": "bb097fccb22d156624fd07cd2894ddb6"
    },
    "cpp11": {
      "Package": "cpp11",
      "Version": "0.4.3",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "ed588261931ee3be2c700d22e94a29ab"
    },
    "crayon": {
      "Package": "crayon",
      "Version": "1.5.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "grDevices",
        "methods",
        "utils"
      ],
      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
    },
    "credentials": {
      "Package": "credentials",
      "Version": "1.3.2",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "askpass",
        "curl",
        "jsonlite",
        "openssl",
        "sys"
      ],
      "Hash": "93762d0a34d78e6a025efdbfb5c6bb41"
    },
    "crosstalk": {
      "Package": "crosstalk",
      "Version": "1.2.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R6",
        "htmltools",
        "jsonlite",
        "lazyeval"
      ],
      "Hash": "6aa54f69598c32177e920eb3402e8293"
    },
    "curl": {
      "Package": "curl",
      "Version": "5.1.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Requirements": [
        "R"
      ],
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  }
}

@gaborcsardi
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Do you have a DESCRIPTION file at the root of the repository? Can you show that file?

@rjake
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rjake commented Dec 28, 2023

Yes, I have added it in the comment above as well as the renv.lock file

@gaborcsardi
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I don't know why this happens, but if you have an renv.lock file, the correct action to use is setup-renv, not setup-r-dependencies.

@rjake
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rjake commented Dec 28, 2023

Thanks for looking into it. We do have setup-renv as a step before setup-r-dependencies. I'm not sure where these two options need to go as we don't have pkgdown in our DESCRIPTION. I can contact our Posit rep if you think that is a better way to resolve this

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.  # <----
          needs: website                          # <----

@gaborcsardi
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I think the proper renv way to handle this is to put pkgdown into renv.lock and then use setup-renv and not use setup-r-dependencies at all.

I can contact our Posit rep if you think that is a better way to resolve this

That sounds like a good idea.

@rjake rjake closed this as completed Dec 28, 2023
@joelostblom
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joelostblom commented Sep 5, 2024 •
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@rjake did you find a solution to this issue? I'm experiencing the same thing.

@gaborcsardi failed action here and workflow file here in case you are able to provide some guidance. I don't have an env lock file or DESCRIPTION File; I would liketo install the packages directly in the action to use with quarto's knitr engine. I don't have much experience with github actions so might be getting something simple wrong.

@rjake
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rjake commented Sep 5, 2024

@joelostblom our current workflow looks like this:

Details .github/workflows/pkgdown.yaml 
on:
  release:
    types: [published]
  workflow_dispatch: # run manually

name: pkgdown
permissions: read-all

jobs:
  pkgdown:
    runs-on: self-hosted
    container: ... # an R docker container

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    permissions:
      contents: write
      id-token: write
      pages: write
      
    steps:
      - uses: actions/checkout@v4

      - name: Install Linux dependencies
        run: | # may be a better way to do this??
          apt-get clean
          apt-get update 
          apt-get install -y libcurl4-openssl-dev
          apt-get install -y libglpk-dev
          apt-get install -y libgmp3-dev
          apt-get install -y libicu-dev
          apt-get install -y libssl-dev
          apt-get install -y libxml2-dev
          apt-get install -y make
          apt-get install -y pandoc
          apt-get install -y rsync
          apt-get install -y zlib1g-dev
      - uses: r-lib/actions/setup-renv@v2

      - name: Build site
        shell: Rscript {0}
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = TRUE)
        
      - name: Deploy to GitHub pages 🚀
        uses: JamesIves/[email protected]
        with:
          clean: false
          branch: gh-pages
          folder: docs

We do have an R docker container set up so there isn't the r-lib/actions/setup-r@v2 step. We also added pkgdown to the renv.lock file as suggested above

@joelostblom
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joelostblom commented Sep 5, 2024 •
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Thank you for the reply @rjake ! Interesting that you also couldn't get r-lib/actions/setup-r@v2 setup-r-dependencies@v2 working. I tried it out a bit more but could still not get it to work, so I switched to using a micromamba workflow to setup my R dependencies instead. It worked right away and is plenty fast thanks to environment caching, so I think I will stay with that for the time being.

@gaborcsardi
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! Interesting that you also couldn't get r-lib/actions/setup-r@v2 working. I tried it out a bit more but could still not get it to work,

This seems to work fine, no?
https://github.com/joelostblom/viz-oer/actions/runs/10712186374/job/29702168233?pr=25#step:3:1

If you don't have a DESCRIPTION file, then you need to specify the packages directly, in the packages parameter:

    - uses: r-lib/actions/setup-r-dependencies@v2
      with:
        packages: |
          ggplot2
          rcmdcheck

@joelostblom
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joelostblom commented Sep 5, 2024 •
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Thank you for having a look @gaborcsardi

This seems to work fine, no?

Sorry, I meant to say that setup-r-dependencies@v2 is not working.

Thanks for the note about using packages instead of extra-packages, I didn't see that mentioned initially in https://github.com/r-lib/actions/tree/v2-branch/setup-r-dependencies#readme, but I now see that it is actually in the parameter list, just not part of the examples. Will try it out.

Edit: Specifying packages as per the above works, but it was prohibitively slow to build packages like tidyverse from source so I went back to micromamba.

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