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Merge branch 'release/0.15.0'
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@HenrikBengtsson
HenrikBengtsson committed Oct 29, 2024
2 parents a65e447 + 4fb8744 commit e436385
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -68,3 +68,4 @@ Rplots.pdf$
^docs
^pkgdown

^CRAN-SUBMISSION$
112 changes: 56 additions & 56 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -6,7 +6,7 @@ jobs:
R-CMD-check:
if: "! contains(github.event.head_commit.message, '[ci skip]')"

timeout-minutes: 45
timeout-minutes: 30

runs-on: ${{ matrix.config.os }}

Expand All @@ -18,77 +18,57 @@ jobs:
config:
- {os: windows-latest, r: 'devel' }
- {os: windows-latest, r: 'release' }
- {os: macOS-latest, r: 'devel' }
- {os: macOS-latest, r: 'release' }
- {os: ubuntu-22.04, r: 'devel' }
- {os: ubuntu-22.04, r: 'release' }
- {os: ubuntu-22.04, r: 'oldrel' }
- {os: ubuntu-22.04, r: 'oldrel-1' }
- {os: ubuntu-22.04, r: 'oldrel-2' }
- {os: ubuntu-22.04, r: '3.5' }
- {os: ubuntu-22.04, r: 'release' , language: ko, label: ko }
- {os: ubuntu-22.04, r: 'release' , language: zh_CN, label: zh_CN }
- {os: ubuntu-22.04, r: 'release' , language: zh_TW, label: zh_TW }

# - {os: macOS-latest, r: 'devel' }
# - {os: macOS-latest, r: 'release' }
# - {os: macOS-latest, r: 'oldrel' }
- {os: ubuntu-latest, r: 'devel' }
- {os: ubuntu-latest, r: 'release' }
- {os: ubuntu-latest, r: 'oldrel' }
- {os: ubuntu-latest, r: 'oldrel-1' }
- {os: ubuntu-latest, r: 'oldrel-2' }
- {os: ubuntu-latest, r: '3.6' }
- {os: ubuntu-latest, r: 'release' , language: ko, label: ko }
- {os: ubuntu-latest, r: 'release' , language: zh_CN, label: zh_CN }
- {os: ubuntu-latest, r: 'release' , language: zh_TW, label: zh_TW }
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
R_KEEP_PKG_SOURCE: yes
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
## Test in other locale (optional)
LANGUAGE: ${{ matrix.config.language }}
## R CMD check
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_LENGTH_1_CONDITION_: true
_R_CHECK_LENGTH_1_LOGIC2_: true
_R_CHECK_MATRIX_DATA_: true
_R_CHECK_SUGGESTS_ONLY_: true
_R_CHECK_THINGS_IN_TEMP_DIR_: true
RCMDCHECK_ERROR_ON: note
## Test in other locale (optional)
LANGUAGE: ${{ matrix.config.language }}

## R (>= 4.4.0) Note, no trailing underscore (sic!)
_R_COMPARE_LANG_OBJECTS: eqonly

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-tinytex@v2

- name: Install system dependencies (Linux)
if: runner.os == 'Linux'
run: sudo apt-get install -y tidy

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

- name: Query R package dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v3
- uses: r-lib/actions/setup-r-dependencies@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
extra-packages: any::rcmdcheck
needs: check

- name: Install R package system dependencies (Linux)
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
sudo apt install -y libcurl4-openssl-dev
- name: Install R package dependencies
run: |
remotes::install_deps(dependencies = TRUE)
install.packages(".", repos = NULL, type = "source") ## self vignette engine
shell: Rscript {0}

- name: Install 'rcmdcheck'
- name: Install itself (to build vignettes)
run: |
remotes::install_cran("rcmdcheck")
library(rcmdcheck) ## triggers an error, if installation failed
install.packages(".", repos=NULL, type="source")
shell: Rscript {0}

- name: Session info
Expand All @@ -97,15 +77,35 @@ jobs:
capabilities()
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
## Verify LANGUAGE settings by generating a translatable error
cat(sprintf("LANGUAGE=%s\n", sQuote(Sys.getenv("LANGUAGE"))))
cat(sprintf("locales: %s\n", sQuote(Sys.getlocale())))
tryCatch(log("a"), error = conditionMessage)
shell: Rscript {0}

- name: Check
run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", if (.Platform$OS.type == "windows" && getRversion() >= "4.2.0") "--no-multiarch"), check_dir = "check")
- name: Check (!Windows)
if: runner.os != 'Windows'
run: |
rcmdcheck::rcmdcheck(
args = "--as-cran",
error_on = "note",
check_dir = "check"
)
shell: Rscript {0}

- name: Check (Windows)
if: runner.os == 'Windows'
run: |
rcmdcheck::rcmdcheck(
args = c("--no-manual", "--as-cran"),
error_on = "note",
check_dir = "check"
)
shell: Rscript {0}

- name: Upload check results
if: failure()
uses: actions/upload-artifact@v3
uses: actions/upload-artifact@v4
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
82 changes: 0 additions & 82 deletions .github/workflows/covr.yaml
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69 changes: 36 additions & 33 deletions .github/workflows/revdepcheck-top.yaml
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Expand Up @@ -8,22 +8,32 @@ jobs:

timeout-minutes: 30

runs-on: ubuntu-22.04
runs-on: ubuntu-latest

name: ${{ matrix.config.pkg }} (${{ matrix.config.r }})

strategy:
fail-fast: false
matrix:
config:
- { r: "release", pkg: "cSEM" }
- { r: "release", pkg: "dipsaus" }
- { r: "release", pkg: "EFAtools" }
- { r: "release", pkg: "fxTWAPLS" }
# - { r: "release", pkg: "gtfs2gps" }
- { r: "release", pkg: "cSEM" }
- { r: "release", pkg: "dipsaus" }
- { r: "release", pkg: "EFAtools" }
# - { r: "release", pkg: "EGAnet" } ## libglpk.so missing
# - { r: "release", pkg: "elevatr" } ## libproj.so missing
- { r: "release", pkg: "fabletools" }
- { r: "release", pkg: "fxTWAPLS" }
# - { r: "release", pkg: "lava" } ## req's Bioc pkgs
# - { r: "release", pkg: "nflfastR" }
# - { r: "release", pkg: "poppr" } ## fails to install
# - { r: "release", pkg: "Seurat" }
- { r: "release", pkg: "SimDesign" }
# - { r: "release", pkg: "tidySEM" } ## fails to install
- { r: "release", pkg: "tsdistributions" }
- { r: "release", pkg: "tsgarch" }

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
## R CMD check
_R_CHECK_LENGTH_1_CONDITION_: true
Expand All @@ -32,43 +42,35 @@ jobs:
_R_CHECK_CRAN_INCOMING_: false

steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-tinytex@v2

- name: Install system dependencies (Linux)
if: runner.os == 'Linux'
run: sudo apt-get install -y tidy

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
use-public-rspm: true

- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}

- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v3
- uses: r-lib/actions/setup-r-dependencies@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

- name: Install system dependencies (Linux)
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
extra-packages: |
any::rcmdcheck
any::remotes
any::sessioninfo
any::covr
needs: check

- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
remotes::install_cran("${{ matrix.config.pkg }}", dependencies=TRUE)
install.packages(".", repos=NULL, type="source")
install.packages("${{ matrix.config.pkg }}", dependencies=TRUE)
shell: Rscript {0}

- name: Session info
Expand All @@ -82,11 +84,12 @@ jobs:
run: |
url=$(Rscript -e "cat(remotes:::download_version_url('${{ matrix.config.pkg }}', version=NULL, repos='https://cloud.r-project.org', type='source'))")
wget "$url"
R_PROGRESSR_ENABLE=true
R CMD check --no-manual --as-cran "$(basename "$url")"
- name: Upload check results
if: failure()
uses: actions/upload-artifact@v3
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-revdep${{ matrix.config.pkg }}-results
path: check
path: ${{ matrix.config.pkg }}.Rcheck
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