In my package
I am having trouble with github action
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
The reason is the /tmp directory, however I don’t know how to change it in github action
Using R — Package Installation Problems | Working With Data (mazamascience.com)
Does someone have a working example for a rstan-based package?
Here my file at GitHub - stemangiola/ppcseq: Posterior predictive check for bulk RNA sequencing differential abundance analyses
## Acronyms:
## * GHA: GitHub Action
## * OS: operating system
## Specify which branches you want this GHA to run on.
## Bioconductor uses branches such as master (bioc-devel) and RELEASE_* like
## RELEASE_3_10. For more details check
## http://bioconductor.org/developers/how-to/git/
on:
push:
branches:
- master
- 'RELEASE_*'
pull_request:
branches:
- master
- 'RELEASE_*'
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'
jobs:
## This first job uses the GitHub repository branch name to infer what
## version of Bioconductor we will be working on.
define-docker-info:
runs-on: ubuntu-latest
outputs:
imagename: ${{ steps.findinfo.outputs.imagename }}
biocversion: ${{ steps.findinfo.outputs.biocversion }}
steps:
- id: findinfo
run: |
## Find what Bioconductor RELEASE branch we are working on
## otherwise, assume we are working on bioc-devel.
if echo "$GITHUB_REF" | grep -q "RELEASE_"; then
biocversion="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')"
else
biocversion="devel"
fi
## Define the image name and print the information
imagename="bioconductor/bioconductor_docker:${biocversion}"
echo $imagename
echo $biocversion
## Save the information for the next job
echo "::set-output name=imagename::${imagename}"
echo "::set-output name=biocversion::${biocversion}"
R-CMD-check-bioc:
## This job then checks the R package using the Bioconductor docker that
## was defined by the previous job. This job will determine what version of
## R to use for the macOS and Windows builds on the next job.
runs-on: ubuntu-latest
needs: define-docker-info
## Name shown on the GHA log
name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }})
## Information used by the next job that will run on macOS and Windows
outputs:
rversion: ${{ steps.findrversion.outputs.rversion }}
biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}
## Environment variables unique to this job.
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
TZ: UTC
NOT_CRAN: true
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
## The docker container to use. Note that we link a directory on the GHA
## runner to a docker directory, such that we can then cache the linked
## directory. This directory will contain the R packages used.
container:
image: ${{ needs.define-docker-info.outputs.imagename }}
volumes:
- /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library
steps:
- name: Install latest git
run: |
## git version provided
git --version
## to be able to install software properties
sudo apt-get update -y
## to be able to use add-apt-repository
sudo apt-get install software-properties-common -y
## to use stable releases of git that are already in a PPA at
## https://launchpad.net/~git-core/+archive/ubuntu/candidate
sudo add-apt-repository ppa:git-core/candidate -y
## Update
sudo apt-get update -y
## Upgrade git and other tools
sudo apt-get upgrade -y
## latest git version
git --version
shell: bash {0}
## Related to https://github.com/rocker-org/rocker-versioned2/issues/52
## Most of these steps are the same as the ones in
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- uses: actions/checkout@v2
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
## Find the corresponding R version based on the Bioconductor version
## to use for the macOS and Windows checks by the next GHA job
- id: findrversion
name: Find Bioc and R versions
run: |
## Find what branch we are working on
if echo "$GITHUB_REF" | grep -q "RELEASE_"; then
biocversion="release"
else
biocversion="devel"
fi
## Define the R and Bioconductor version numbers
biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))")
rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))")
## Print the results
echo $biocversion
echo $biocversionnum
echo $rversion
## Save the info for the next job
echo "::set-output name=rversion::${rversion}"
echo "::set-output name=biocversionnum::${biocversionnum}"
shell:
bash {0}
- name: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache')"
uses: actions/cache@v1
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-
- name: Install dependencies
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
## issues described at
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
local_deps <- remotes::local_package_deps(dependencies = TRUE)
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(local_deps[local_deps %in% deps$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$diff != 0])
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_: false
run: |
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
shell: Rscript {0}
- name: Reveal testthat details
if: env.has_testthat == 'true'
run: find . -name testthat.Rout -exec cat '{}' ';'
- name: Run RUnit tests
if: env.has_RUnit == 'true'
run: |
## Install BiocGenerics
BiocManager::install("BiocGenerics")
BiocGenerics:::testPackage()
shell: Rscript {0}
- name: BiocCheck
run: |
## This syntax works on Windows as well as other OS
## plus it doesn't break the GHA workflow in case BiocCheck finds
## an error (for example, the package is bigger than the maximum
## allowed size). We want the rest of the GHA to proceed even if
## there is a BiocCheck error in order to see the full output and
## run the tests on all operating systems.
BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE)
## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html
shell: Rscript {0}
- name: Install covr
if: github.ref == 'refs/heads/master' && env.run_covr == 'true'
run: |
remotes::install_cran("covr")
shell: Rscript {0}
- name: Test coverage
if: github.ref == 'refs/heads/master' && env.run_covr == 'true'
run: |
covr::codecov()
shell: Rscript {0}
- name: Install pkgdown
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'
run: |
remotes::install_github("r-lib/pkgdown")
shell: Rscript {0}
- name: Install package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'
run: R CMD INSTALL .
- name: Deploy package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'
run: |
git config --local user.email "action@github.com"
git config --local user.name "GitHub Action"
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: ${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results
path: check
## Run R CMD check on both macOS and Windows. You can also run the
## tests on Linux outside of the Bioconductor docker environment. If you
## do so, you might have to install system dependencies on Linux
## Bioconductor's docker includes all the system dependencies required by
## Bioconductor packages and their dependencies (which includes many CRAN
## dependencies as well, thus making this workflow useful beyond Bioconductor)
R-CMD-check-r-lib:
runs-on: ${{ matrix.config.os }}
needs: [define-docker-info, R-CMD-check-bioc]
name: ${{ matrix.config.os }} (r-${{ needs.R-CMD-check-bioc.outputs.rversion }} bioc-${{ needs.define-docker-info.outputs.biocversion }})
strategy:
fail-fast: false
matrix:
config:
## Comment/Un-comment in case you also want to run other versions
- {os: windows-latest}
- {os: macOS-latest}
# - {os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
BIOCVERSIONNUM: ${{ needs.R-CMD-check-bioc.outputs.biocversionnum }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- name: Setup R from r-lib
uses: r-lib/actions/setup-r@master
with:
r-version: ${{ needs.R-CMD-check-bioc.outputs.rversion }}
- name: Setup pandoc from r-lib
uses: r-lib/actions/setup-pandoc@master
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- name: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache')"
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-
- name: Install Linux system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
sudo -s eval "$sysreqs"
- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
run: |
## Enable installing XML from source if needed
brew install libxml2
echo "::set-env name=XML_CONFIG::/usr/local/opt/libxml2/bin/xml2-config"
## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
brew install imagemagick@6
- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
## Edit below if you have any Windows system dependencies
shell: Rscript {0}
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
- name: Set BiocVersion
run: |
BiocManager::install(version = Sys.getenv('BIOCVERSIONNUM'), ask = FALSE)
shell: Rscript {0}
- name: Install dependencies
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
## issues described at
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Pass #1 at installing dependencies
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
local_deps <- remotes::local_package_deps(dependencies = TRUE)
deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
BiocManager::install(local_deps[local_deps %in% deps$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$diff != 0])
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_: false
run: |
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
shell: Rscript {0}
- name: Reveal testthat details
if: env.has_testthat == 'true'
run: find . -name testthat.Rout -exec cat '{}' ';'
- name: Run RUnit tests
if: env.has_RUnit == 'true'
run: |
## Install BiocGenerics
BiocManager::install("BiocGenerics")
BiocGenerics:::testPackage()
shell: Rscript {0}
- name: BiocCheck
run: |
## This syntax works on Windows as well as other OS
## plus it doesn't break the GHA workflow in case BiocCheck finds
## an error (for example, the package is bigger than the maximum
## allowed size). We want the rest of the GHA to proceed even if
## there is a BiocCheck error in order to see the full output and
## run the tests on all operating systems.
BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE)
## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html
shell: Rscript {0}
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-results
path: check
Thanks a lot.
