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test again GHA workflow with modifs (wip)
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@phauchamps
phauchamps committed Jan 9, 2024
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Showing 1 changed file with 163 additions and 163 deletions.
326 changes: 163 additions & 163 deletions .github/workflows/check-bioc.yml
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Expand Up @@ -162,175 +162,175 @@ jobs:
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}

# - name: Manually install vdiffr in version 1.0.5 to avoid compil error
# run: |
# BiocManager::install("remotes")
# remotes::install_version("vdiffr", version = "1.0.5")
# shell: Rscript {0}

- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
shell: Rscript {0}

- name: Install dependencies
run: |
withr::with_makevars(
c(CFLAGS = "-w",
CXXFLAGS = "-w"),
{
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
## issues described at
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
local_deps <- remotes::local_package_deps(dependencies = TRUE)
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])

## Pass #2 at installing dependencies
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(deps$package[deps$diff != 0])

## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
},
assignment = "+=")

shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

## Fix error: The magick package is required to crop "...png" but not available.
- name: Manually install magick
run: BiocManager::install("magick")
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

- name: Install BiocGenerics
if: env.has_RUnit == 'true'
run: |
## Install BiocGenerics
BiocManager::install("BiocGenerics")
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

- name: Install covr
##if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

- name: Install pkgdown
##if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_github("r-lib/pkgdown")
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
- pre-install cytolib
run: |
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
BiocManager::install("cytolib")
shell: Rscript {0}


## Might need an to add this to the if: && runner.os == 'Linux'
- name: Reveal testthat details
if: env.has_testthat == 'true'
run: find . -name testthat.Rout -exec cat '{}' ';'

- name: Run RUnit tests
if: env.has_RUnit == 'true'
run: |
BiocGenerics:::testPackage()
shell: Rscript {0}

- name: Run BiocCheck
if: env.has_BiocCheck == 'true'
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
`quit-with-status` = TRUE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = TRUE
)
shell: Rscript {0}

- name: Test coverage
#if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov(quiet = FALSE)
shell: Rscript {0}

- name: Install package
#if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .

- name: Deploy package
#if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --global user.email "[email protected]"
git config --global user.name "GitHub Actions"
git config --global --add safe.directory /__w/CytoMDS/CytoMDS
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
## at least one locally before this will work. This creates the gh-pages
## branch (erasing anything you haven't version controlled!) and
## makes the git history recognizable by pkgdown.

- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-devel-r-devel-results
path: check
# - name: Install dependencies
# run: |
# withr::with_makevars(
# c(CFLAGS = "-w",
# CXXFLAGS = "-w"),
# {
# ## Try installing the package dependencies in steps. First the local
# ## dependencies, then any remaining dependencies to avoid the
# ## issues described at
# ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
# ## https://github.com/r-lib/remotes/issues/296
# ## Ideally, all dependencies should get installed in the first pass.
#
# ## Pass #1 at installing dependencies
# message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
# local_deps <- remotes::local_package_deps(dependencies = TRUE)
# deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
# BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
#
# ## Pass #2 at installing dependencies
# message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
# deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
# BiocManager::install(deps$package[deps$diff != 0])
#
# ## For running the checks
# message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
# remotes::install_cran("rcmdcheck")
# BiocManager::install("BiocCheck")
# },
# assignment = "+=")
#
# shell: Rscript {0}
#
# - name: Session info
# run: |
# options(width = 100)
# pkgs <- installed.packages()[, "Package"]
# sessioninfo::session_info(pkgs, include_base = TRUE)
# shell: Rscript {0}
#
# ## Fix error: The magick package is required to crop "...png" but not available.
# - name: Manually install magick
# run: BiocManager::install("magick")
# shell: Rscript {0}
#
# - name: Session info
# run: |
# options(width = 100)
# pkgs <- installed.packages()[, "Package"]
# sessioninfo::session_info(pkgs, include_base = TRUE)
# shell: Rscript {0}
#
# - name: Install BiocGenerics
# if: env.has_RUnit == 'true'
# run: |
# ## Install BiocGenerics
# BiocManager::install("BiocGenerics")
# shell: Rscript {0}
#
# - name: Session info
# run: |
# options(width = 100)
# pkgs <- installed.packages()[, "Package"]
# sessioninfo::session_info(pkgs, include_base = TRUE)
# shell: Rscript {0}
#
# - name: Install covr
# ##if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
# if: env.run_covr == 'true' && runner.os == 'Linux'
# run: |
# remotes::install_cran("covr")
# shell: Rscript {0}
#
# - name: Session info
# run: |
# options(width = 100)
# pkgs <- installed.packages()[, "Package"]
# sessioninfo::session_info(pkgs, include_base = TRUE)
# shell: Rscript {0}
#
# - name: Install pkgdown
# ##if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
# if: env.run_pkgdown == 'true' && runner.os == 'Linux'
# run: |
# remotes::install_github("r-lib/pkgdown")
# shell: Rscript {0}
#
# - name: Session info
# run: |
# options(width = 100)
# pkgs <- installed.packages()[, "Package"]
# sessioninfo::session_info(pkgs, include_base = TRUE)
# shell: Rscript {0}
#
# - name: Run CMD check
# env:
# _R_CHECK_CRAN_INCOMING_: false
# run: |
# rcmdcheck::rcmdcheck(
# args = c("--no-build-vignettes", "--no-manual", "--timings"),
# build_args = c("--no-manual", "--no-resave-data"),
# error_on = "warning",
# check_dir = "check"
# )
# shell: Rscript {0}
#
# ## Might need an to add this to the if: && runner.os == 'Linux'
# - name: Reveal testthat details
# if: env.has_testthat == 'true'
# run: find . -name testthat.Rout -exec cat '{}' ';'
#
# - name: Run RUnit tests
# if: env.has_RUnit == 'true'
# run: |
# BiocGenerics:::testPackage()
# shell: Rscript {0}
#
# - name: Run BiocCheck
# if: env.has_BiocCheck == 'true'
# run: |
# BiocCheck::BiocCheck(
# dir('check', 'tar.gz$', full.names = TRUE),
# `quit-with-status` = TRUE,
# `no-check-R-ver` = TRUE,
# `no-check-bioc-help` = TRUE
# )
# shell: Rscript {0}
#
# - name: Test coverage
# #if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
# if: env.run_covr == 'true' && runner.os == 'Linux'
# run: |
# covr::codecov(quiet = FALSE)
# shell: Rscript {0}
#
# - name: Install package
# #if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
# if: env.run_pkgdown == 'true' && runner.os == 'Linux'
# run: R CMD INSTALL .
#
# - name: Deploy package
# #if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
# if: env.run_pkgdown == 'true' && runner.os == 'Linux'
# run: |
# git config --global user.email "[email protected]"
# git config --global user.name "GitHub Actions"
# git config --global --add safe.directory /__w/CytoMDS/CytoMDS
# Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
# shell: bash {0}
# ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
# ## at least one locally before this will work. This creates the gh-pages
# ## branch (erasing anything you haven't version controlled!) and
# ## makes the git history recognizable by pkgdown.
#
# - name: Upload check results
# if: failure()
# uses: actions/upload-artifact@master
# with:
# name: ${{ runner.os }}-biocversion-devel-r-devel-results
# path: check

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