diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 802e6fd..bae85ca 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -10,7 +10,9 @@ on: pull_request: branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -26,24 +28,22 @@ jobs: - {os: windows-latest, r: 'devel'} - {os: windows-latest, r: 'release'} - # Use 3.6 to trigger usage of RTools35 - - {os: windows-latest, r: '3.6'} - # use 4.1 to check with rtools40's older compiler - - {os: windows-latest, r: '4.1'} + # use 4.0 or 4.1 to check with rtools40's older compiler + - {os: windows-latest, r: 'oldrel-4'} - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - - {os: ubuntu-latest, r: 'oldrel-2'} - - {os: ubuntu-latest, r: 'oldrel-3'} - - {os: ubuntu-latest, r: 'oldrel-4'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + - {os: ubuntu-latest, r: 'oldrel-2'} + - {os: ubuntu-latest, r: 'oldrel-3'} + - {os: ubuntu-latest, r: 'oldrel-4'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -67,3 +67,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 77f5d83..b692e85 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -9,7 +9,9 @@ on: types: [published] workflow_dispatch: -name: pkgdown +name: pkgdown.yaml + +permissions: read-all jobs: pkgdown: @@ -22,7 +24,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,7 +43,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml index 71f335b..2edd93f 100644 --- a/.github/workflows/pr-commands.yaml +++ b/.github/workflows/pr-commands.yaml @@ -4,7 +4,9 @@ on: issue_comment: types: [created] -name: Commands +name: pr-commands.yaml + +permissions: read-all jobs: document: @@ -13,8 +15,10 @@ jobs: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/pr-fetch@v2 with: @@ -50,8 +54,10 @@ jobs: runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/pr-fetch@v2 with: diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 0368c0c..4765c2a 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,7 +6,9 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -16,7 +18,7 @@ jobs: R_WEBFAKES_PROCESS_TIMEOUT: 50000 steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -24,7 +26,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr + extra-packages: any::covr, any::xml2 needs: coverage - name: "Set environmental variables" @@ -34,23 +36,32 @@ jobs: - name: Test coverage run: | - covr::codecov( + cov <- covr::package_coverage( quiet = FALSE, clean = FALSE, install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") ) + covr::to_cobertura(cov) shell: Rscript {0} + - uses: codecov/codecov-action@v4 + with: + fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} + file: ./cobertura.xml + plugin: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + - name: Show testthat output if: always() run: | ## -------------------------------------------------------------------- - find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package diff --git a/DESCRIPTION b/DESCRIPTION index 72302ef..0c85869 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -43,4 +43,4 @@ Config/testthat/edition: 3 Encoding: UTF-8 Language: en-US Roxygen: list(markdown = TRUE, r6 = FALSE) -RoxygenNote: 7.3.1.9000 +RoxygenNote: 7.3.2 diff --git a/R/repo-set.R b/R/repo-set.R index 9f76f76..c21ef6f 100644 --- a/R/repo-set.R +++ b/R/repo-set.R @@ -59,7 +59,7 @@ repo_get <- function(r_version = getRversion(), bioc = TRUE, #' #' @export #' @examplesIf pkgcache:::run_examples() -#' repo_resolve("PPM@2020-01-21") +#' repo_resolve("PPM@2021-01-21") #' #' repo_resolve("PPM@dplyr-1.0.0") #' #' repo_resolve("PPM@R-4.0.0") diff --git a/man/pkgcache-package.Rd b/man/pkgcache-package.Rd index dc5eeca..33a1193 100644 --- a/man/pkgcache-package.Rd +++ b/man/pkgcache-package.Rd @@ -39,7 +39,7 @@ print nicer, similarly to tibbles.) \if{html}{\out{
}}\preformatted{library(pkgcache) library(pillar) meta_cache_list() -#> # A data frame: 44,780 x 32 +#> # A data frame: 48,094 x 32 #> package version depends suggests license imports linkingto archs enhances #> #> 1 A3 1.0.0 R (>= ~ randomF~ GPL (>~ @@ -50,9 +50,9 @@ meta_cache_list() #> 6 ABCoptim 0.15.0 testtha~ MIT + ~ Rcpp, ~ Rcpp ABCo~ #> 7 ABCp2 1.2 MASS GPL-2 #> 8 ABHgenotyp~ 1.0.1 knitr, ~ GPL-3 ggplot~ -#> 9 ABM 0.3 GPL (>~ R6, Rc~ Rcpp ABM.~ +#> 9 ABM 0.4.1 GPL (>~ R6, Rc~ Rcpp ABM.~ #> 10 ABPS 0.3 testthat GPL (>~ kernlab -#> # i 44,770 more rows +#> # i 48,084 more rows #> # i 23 more variables: license_restricts_use , priority , #> # license_is_foss , os_type , repodir , rversion , #> # platform , needscompilation , ref , type , @@ -84,36 +84,35 @@ The \verb{pkg_cache_*} API is high level, and uses a user level cache: #> [1] "/Users/gaborcsardi/Library/Caches/org.R-project.R/R/pkgcache/pkg" #> #> $files -#> [1] 176 +#> [1] 40 #> #> $size -#> [1] 204562277 +#> [1] 61300737 }\if{html}{\out{
}} \if{html}{\out{
}}\preformatted{pkg_cache_list() -#> # A data frame: 176 x 11 +#> # A data frame: 40 x 11 #> fullpath path package url etag sha256 version platform built vignettes #> -#> 1 /Users/gab~ bin/~ diffvi~ http~ "\"2~ e8869~ 0.1.1 aarch64~ NA NA -#> 2 /Users/gab~ src/~ testth~ 0.0.0.~ source 1 0 -#> 3 /Users/gab~ src/~ testth~ 0.0.0.~ aarch64~ 1 0 -#> 4 /Users/gab~ bin/~ DT http~ "\"1~ 69c62~ 0.27 aarch64~ NA NA -#> 5 /Users/gab~ bin/~ R6 http~ "\"1~ 00398~ 2.5.1 aarch64~ NA NA -#> 6 /Users/gab~ src/~ cli c37f3~ 3.6.1.~ source 1 0 -#> 7 /Users/gab~ src/~ cli c37f3~ 3.6.1.~ aarch64~ 1 0 -#> 8 /Users/gab~ bin/~ glue http~ "\"2~ 25019~ 1.6.2 aarch64~ NA NA -#> 9 /Users/gab~ src/~ cli f6794~ 3.1.0.~ source 1 0 -#> 10 /Users/gab~ src/~ cli f6794~ 3.1.0.~ aarch64~ 1 0 -#> # i 166 more rows +#> 1 /Users/gab~ arch~ http~ "\"1~ 9da51~ NA NA +#> 2 /Users/gab~ bin/~ cli http~ "\"1~ b24b4~ 3.6.2 x86_64-~ NA NA +#> 3 /Users/gab~ bin/~ jose http~ "\"7~ b1bac~ 1.2.0 aarch64~ NA NA +#> 4 /Users/gab~ src/~ gh 1.4.0.~ source 1 0 +#> 5 /Users/gab~ src/~ gh 1.4.0.~ aarch64~ 1 0 +#> 6 /Users/gab~ bin/~ gh http~ "\"1~ f5daf~ 1.4.0 aarch64~ NA NA +#> 7 /Users/gab~ src/~ tic 11103~ 0 NA +#> 8 /Users/gab~ src/~ tic 11103~ 0.14.0 source 1 0 +#> 9 /Users/gab~ src/~ tic 11103~ 0.14.0 aarch64~ 1 0 +#> 10 /Users/gab~ bin/~ rhub http~ "\"f~ af2d6~ 1.1.2 aarch64~ NA NA +#> # i 30 more rows #> # i 1 more variable: rversion }\if{html}{\out{
}} \if{html}{\out{
}}\preformatted{pkg_cache_find(package = "dplyr") -#> # A data frame: 1 x 11 -#> fullpath path package url etag sha256 version platform built vignettes -#> -#> 1 /Users/gabo~ bin/~ dplyr http~ "\"1~ cb4f7~ 1.1.2 aarch64~ NA NA -#> # i 1 more variable: rversion +#> # A data frame: 0 x 11 +#> # i 11 variables: fullpath , path , package , url , +#> # etag , sha256 , version , platform , built , +#> # vignettes , rversion }\if{html}{\out{
}} \code{pkg_cache_add_file()} can be used to add a file, @@ -132,26 +131,26 @@ all fields from \code{PACKAGES}, \code{PACKAGES.gz} or \code{PACKAGES.rds} files library: \if{html}{\out{
}}\preformatted{parse_installed() -#> # A data frame: 329 x 97 -#> Package Type Title Version Date Author Maintainer Description Copyright -#> -#> 1 AsioHeaders Pack~ "'As~ 1.22.1~ 2022~ "Dirk~ Dirk Edde~ "'Asio' is~ file ins~ -#> 2 BiocGeneri~ "S4 ~ 0.46.0 "The ~ Hervé Pag~ "The packa~ -#> 3 BiocManager "Acc~ 1.30.20 "Mart~ Marcel Ra~ "A conveni~ -#> 4 Biostrings "Eff~ 2.67.2 "Herv~ Hervé Pag~ "Memory ef~ -#> 5 DBI "R D~ 1.1.3 2022~ "R Sp~ Kirill Mü~ "A databas~ -#> 6 DBItest "Tes~ 1.7.3 2022~ "Kiri~ Kirill Mü~ "A helper ~ -#> 7 DT Pack~ "A W~ 0.27 "Yihu~ Yihui Xie~ "Data obje~ -#> 8 Distributi~ "Dis~ 0.6-0 2018~ "Davi~ David Sco~ "Utilities~ -#> 9 Formula "Ext~ 1.2-5 2023~ "Achi~ Achim Zei~ "Infrastru~ -#> 10 GenomeInfo~ "Uti~ 1.35.17 "Sona~ Hervé Pag~ "Contains ~ -#> # i 319 more rows -#> # i 88 more variables: License , URL , BugReports , -#> # NeedsCompilation , Packaged , Repository , -#> # `Date/Publication` , Built , biocViews , Encoding , -#> # Depends , Imports , Suggests , Collate , git_url , -#> # git_branch , git_last_commit , git_last_commit_date , -#> # `Authors@R` , VignetteBuilder , RoxygenNote , ... +#> # A data frame: 888 x 128 +#> Package Type Title Version Date `Authors@R` Maintainer Description Imports +#> +#> 1 AdaptGa~ Pack~ Gaus~ 1.6 2024~ "c(person(~ Michael T~ "Multimoda~ "Rcpp,~ +#> 2 Annotat~ Mani~ 1.64.1 Bioconduc~ "Implement~ "DBI, ~ +#> 3 Annotat~ Tool~ 1.42.2 Bioconduc~ "Provides ~ "DBI, ~ +#> 4 AsioHea~ Pack~ 'Asi~ 1.22.1~ 2022~ Dirk Edde~ "'Asio' is~ +#> 5 AutoQua~ Auto~ 1.0.1 2023~ "\n c(p~ Adrian An~ "R package~ "bit64~ +#> 6 BH Pack~ Boos~ 1.81.0~ 2023~ Dirk Edde~ "Boost pro~ +#> 7 BayesFa~ Pack~ Comp~ 0.9.12~ 2022~ "c(person(~ Richard D~ "A suite o~ "pbapp~ +#> 8 Biobase Biob~ 2.62.0 "c(\n p~ Bioconduc~ "Functions~ "metho~ +#> 9 BiocBas~ Gene~ 1.4.0 "c(\n per~ Marcel Ra~ "The packa~ "metho~ +#> 10 BiocFil~ Mana~ 2.10.1 "c(person(~ Lori Shep~ "This pack~ "metho~ +#> # i 878 more rows +#> # i 119 more variables: Suggests , LinkingTo , Depends , +#> # License , LazyLoad , URL , Encoding , +#> # NeedsCompilation , VignetteBuilder , BugReports , +#> # Packaged , Author , Repository , `Date/Publication` , +#> # Built , Archs , RemoteType , RemotePkgRef , +#> # RemoteRef , RemoteRepos , RemotePkgPlatform , ... }\if{html}{\out{
}} } diff --git a/man/repo_get.Rd b/man/repo_get.Rd index d285384..f0af80f 100644 --- a/man/repo_get.Rd +++ b/man/repo_get.Rd @@ -140,7 +140,7 @@ will trigger an error. \examples{ repo_get() \dontshow{if (pkgcache:::run_examples()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf} -repo_resolve("PPM@2020-01-21") +repo_resolve("PPM@2021-01-21") #' repo_resolve("PPM@dplyr-1.0.0") #' repo_resolve("PPM@R-4.0.0") \dontshow{\}) # examplesIf} diff --git a/tests/async/test-call-function.R b/tests/async/test-call-function.R index 4ff4143..9442f7a 100644 --- a/tests/async/test-call-function.R +++ b/tests/async/test-call-function.R @@ -57,6 +57,7 @@ test_that("calls that error", { test_that("calls that crash", { skip_without_package("processx", "3.4.1.9001") + skip_without_package("callr", "3.7.6.9000") afun <- async(function(x) { when_all( call_function(function() Sys.getpid()),