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()),