Writting eigenvectors table to analyze their functions #52
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
on: | |
push: | |
branches: [master] | |
pull_request: | |
branches: [master] | |
name: R-CMD-check-bioc | |
## These environment variables control whether to run GHA code later on that is | |
## specific to testthat, covr, and pkgdown. | |
## | |
## If you need to clear the cache of packages, update the number inside | |
## cache-version as discussed at https://github.com/r-lib/actions/issues/86. | |
## Note that you can always run a GHA test without the cache by using the word | |
## "/nocache" in the commit message. | |
env: | |
has_testthat: 'true' | |
run_covr: 'true' | |
run_pkgdown: 'true' | |
has_RUnit: 'false' | |
cache-version: 'cache-v1' | |
run_docker: 'false' | |
#ESTO HAY QUE ACTIVARLO SI QUEREMOS TESTEAR EN DOCKER | |
jobs: | |
build-check: | |
runs-on: ${{ matrix.config.os }} | |
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
container: ${{ matrix.config.cont }} | |
## Environment variables unique to this job. | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest", http-user-agent: 'release' } | |
## Check https://github.com/r-lib/actions/tree/master/examples | |
## for examples using the http-user-agent | |
env: | |
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
RSPM: ${{ matrix.config.rspm }} | |
NOT_CRAN: true | |
TZ: UTC | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
steps: | |
## Set the R library to the directory matching the | |
## R packages cache step further below when running on Docker (Linux). | |
- name: Set R Library home on Linux | |
if: runner.os == 'Linux' | |
run: | | |
mkdir /__w/_temp/Library | |
echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | |
## Most of these steps are the same as the ones in | |
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
## If they update their steps, we will also need to update ours. | |
- name: Checkout Repository | |
uses: actions/checkout@v3 | |
## R is already included in the Bioconductor docker images | |
- name: Setup R from r-lib | |
if: runner.os != 'Linux' | |
uses: r-lib/actions/setup-r@v2 | |
with: | |
r-version: ${{ matrix.config.r }} | |
http-user-agent: ${{ matrix.config.http-user-agent }} | |
## pandoc is already included in the Bioconductor docker images | |
- name: Setup pandoc from r-lib | |
if: runner.os != 'Linux' | |
uses: r-lib/actions/setup-pandoc@v2 | |
- name: Query dependencies | |
run: | | |
install.packages('remotes') | |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
shell: Rscript {0} | |
- name: Restore R package cache | |
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | |
uses: actions/cache@v3 | |
with: | |
path: ${{ env.R_LIBS_USER }} | |
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3- | |
- name: Cache R packages on Linux | |
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | |
uses: actions/cache@v3 | |
with: | |
path: /home/runner/work/_temp/Library | |
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }} | |
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3- | |
- name: Install Linux system dependencies | |
if: runner.os == 'Linux' | |
run: | | |
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') | |
echo $sysreqs | |
sudo -s eval "$sysreqs" | |
- name: Install BiocManager | |
run: | | |
message(paste('****', Sys.time(), 'installing BiocManager ****')) | |
remotes::install_cran("BiocManager") | |
shell: Rscript {0} | |
- name: Set BiocVersion | |
run: | | |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | |
shell: Rscript {0} | |
- name: Install dependencies pass 1 | |
run: | | |
## 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. | |
## For running the checks | |
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | |
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | |
## Pass #1 at installing dependencies | |
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | |
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | |
continue-on-error: false | |
shell: Rscript {0} | |
- name: Install dependencies pass 2 | |
run: | | |
## Pass #2 at installing dependencies | |
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | |
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | |
shell: Rscript {0} | |
- name: Install BiocGenerics | |
if: env.has_RUnit == 'true' | |
run: | | |
## Install BiocGenerics | |
BiocManager::install("BiocGenerics") | |
shell: Rscript {0} | |
- name: Install covr | |
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | |
run: | | |
remotes::install_cran("covr") | |
shell: Rscript {0} | |
- name: Install pkgdown | |
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
run: | | |
remotes::install_cran("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 | |
DISPLAY: 99.0 | |
run: | | |
options(crayon.enabled = TRUE) | |
rcmdcheck::rcmdcheck( | |
args = c("--no-manual", "--no-vignettes", "--timings"), | |
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | |
error_on = "warning", | |
check_dir = "check" | |
) | |
shell: Rscript {0} | |
#, "--no-suggests"), ADD THIS TO AVoid the instatation of suggested packages | |
## 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 | |
# env: | |
# DISPLAY: 99.0 | |
# 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: Install package | |
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
run: R CMD INSTALL . | |
- name: Install deploy dependencies | |
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | |
run: | | |
apt-get update && apt-get -y install rsync | |
- name: Upload check results | |
if: failure() | |
uses: actions/upload-artifact@master | |
with: | |
name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results | |
path: check |