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r-lib / pak

A fresh approach to package installation
https://pak.r-lib.org
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Could not find R package in `.` or its parent directories. #576

Closed rjake closed 6 months ago

rjake commented 6 months ago

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 commented 6 months ago

Please include a link to your workflow file, and to a failed build.

rjake commented 6 months ago

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 ```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: ${{ github.event.pull_request.head.sha }} - name: Increase timeout shell: Rscript {0} run: options(timeout = max(300, getOption("timeout"))) - uses: r-lib/actions/setup-renv@v2 - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::pkgdown, local::. needs: website - name: Build site shell: Rscript {0} run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) - name: Install rsync 📚 run: | apt-get update && apt-get install -y rsync - name: Deploy to GitHub pages 🚀 uses: JamesIves/github-pages-deploy-action@v4.4.1 with: clean: false branch: gh-pages folder: docs # this is the location from pkgdown::build_site_github_pages() and not Settings > Pages ```
log & error ```bash Run r-lib/actions/setup-r-dependencies@v[2](/actions/runs/131606/job/220237#step:8:2) with: extra-packages: any::pkgdown, local::. needs: website cache: true cache-version: 1 packages: deps::., any::sessioninfo pak-version: stable working-directory: . dependencies: "all" upgrade: FALSE env: GITHUB_PAT: *** R_KEEP_PKG_SOURCE: yes RENV_PATHS_ROOT: /runner/_work/_temp/renv Run # Set site library path # Set site library path cat("::group::Set site library path\n") if (Sys.getenv("RENV_PROJECT") != "") { message("renv project detected, no need to set R_LIBS_SITE") cat(sprintf("R_LIB_FOR_PAK=%s\n", .libPaths()[1]), file = Sys.getenv("GITHUB_ENV"), append = TRUE) q("no") } lib <- Sys.getenv("R_LIBS_SITE") if (lib == "") { lib <- file.path(dirname(.Library), "site-library") cat(sprintf("R_LIBS_SITE=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE) cat(sprintf("R_LIB_FOR_PAK=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE) message("Setting R_LIBS_SITE to ", lib) } else { message("R_LIBS_SITE is already set to ", lib) cat(sprintf("R_LIB_FOR_PAK=%s\n", strsplit(lib, .Platform$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)' $SUDO R -q -e 'install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable/", lib = Sys.getenv("R_LIB_FOR_PAK"))' echo "::endgroup::" upgrade = (FALSE), dependencies = c(needs, ("all")) ) cat("::endgroup::\n") cat("::group::Show Lockfile\n") writeLines(readLines(".github/pkg.lock")) cat("::endgroup::\n") shell: Rscript {0} env: GITHUB_PAT: *** R_KEEP_PKG_SOURCE: yes RENV_PATHS_ROOT: /runner/_work/_temp/renv R_LIB_FOR_PAK: /__w/rocqi/rocqi/renv/library/R-4.2/x86_64-pc-linux-gnu Dependency resolution Warning message: package ‘pak’ was built under R version 4.2.[3](/actions/runs/131606/job/220237#step:8:3) ℹ Creating lockfile '.github/pkg.lock' ✔ Updated metadata database: [4](/actions/runs/131606/job/220237#step:8:4).43 MB in 9 files. ℹ Creating lockfile '.github/pkg.lock' ℹ Updating metadata database ✔ Updating metadata database ... done ℹ Creating lockfile '.github/pkg.lock' ✖ Creating lockfile '.github/pkg.lock' [11.2s] Error: ! error in pak subprocess Caused by error: ! Could not solve package dependencies: * deps::.: ! pkgdepends resolution error for deps::.. Caused by error: ! Could not find R package in `.` or its parent directories. * local::.: ! pkgdepends resolution error for local::.. Caused by error: ! Could not find R package in `.` or its parent directories. --- Backtrace: 1. pak::lockfile_create(c(deps, extra_deps), lockfile = ".github/pkg.lock", … 2. pak:::remote(function(...) { … 3. err$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](/actions/runs/131606/job/220237#step:8:5). pkgdepends:::pkgplan_stop_for_solve_error(self, private) [6](/actions/runs/131606/job/220237#step:8:6). base::throw(new_error("Could not solve package dependencies:\n", msg, … [7](/actions/runs/131606/job/220237#step:8:7). | base::signalCondition(cond) [8](/actions/runs/131606/job/220237#step:8:8). global (function (e) … Execution halted Error: Process completed with exit code 1. ```
DESCRIPTION ```yaml Package: rocqi Title: CHOP Analytics R package Version: 2.1.0 Authors@R: c( person("Joe", "Mirizio", role = c("aut", "cre"), email = "mirizioj@chop.edu"), person("Paul", "Wildenhain", role = "aut", email = "wildenhaip@chop.edu"), person("Jake", "Riley", role = "aut", email = "rileyj3@chop.edu") ) 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 ```json { "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": 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"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": 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"lifecycle", "magrittr", "methods", "pillar", "purrr", "rlang", "tibble", "tidyr", "tidyselect", "utils", "vctrs", "withr" ], "Hash": "d24305b92db333726aed162a2c23a147" }, "desc": { "Package": "desc", "Version": "1.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "R6", "cli", "rprojroot", "utils" ], "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21" }, "devtools": { "Package": "devtools", "Version": "2.4.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", "desc", "ellipsis", "fs", "lifecycle", "memoise", "miniUI", "pkgbuild", "pkgdown", "pkgload", "profvis", "rcmdcheck", "remotes", "rlang", "roxygen2", "rversions", "sessioninfo", "stats", "testthat", "tools", "urlchecker", "usethis", "utils", "withr" ], "Hash": "ea5bc8b4a6a01e4f12d98b58329930bb" }, "diffobj": { "Package": "diffobj", "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "crayon", "methods", "stats", "tools", "utils" ], "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8" }, "digest": { "Package": "digest", "Version": "0.6.31", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "utils" ], "Hash": "8b708f296afd9ae69f450f9640be8990" }, "downlit": { "Package": "downlit", "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "brio", "desc", "digest", "evaluate", "fansi", "memoise", "rlang", "vctrs", "withr", "yaml" ], "Hash": "79bf3f66590752ffbba20f8d2da94c7c" }, "dplyr": { "Package": "dplyr", "Version": "1.1.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "R6", "cli", "generics", "glue", "lifecycle", "magrittr", "methods", "pillar", "rlang", "tibble", "tidyselect", "utils", "vctrs" ], "Hash": "dea6970ff715ca541c387de363ff405e" }, "dtplyr": { "Package": "dtplyr", "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "cli", "data.table", "dplyr", "glue", "lifecycle", "rlang", "tibble", "tidyselect", "vctrs" ], 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gaborcsardi commented 6 months ago

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

rjake commented 6 months ago

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

gaborcsardi commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

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.