Hey Nuno,
Thanks so much, see below.
Kind regards,
Alan.
name: R GitHub Actions
on:
push:
branches:
- main
- master
- dev-am
pull_request:
branches:
- main
- master
jobs:
R-CMD-check:
name: R-CMD-check
runs-on: ubuntu-latest
container: almurphy/scfdev:latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
RGL_USE_NULL: TRUE
steps:
- uses: actions/checkout@v2
- name: Setup R
uses: r-lib/actions/setup-r@v1
with:
install-r: false
- name: Install dependencies
run: |
install.packages(c("remotes", "rcmdcheck"))
remotes::install_deps(dependencies = TRUE)
shell: Rscript {0}
- name: Check
run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
shell: Rscript {0}
- name: Get R package version
run: |
version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
echo "packageVersion=${version}" >> $GITHUB_ENV
shell: bash {0}
- name: Build and push
uses: docker/build-push-action@v2
with:
push: true
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_TOKEN }}
repository: almurphy/scfdev
tag_with_ref: true
tag_with_sha: true
tags: ${{ github.repository }}:${{ env.packageVersion }}
________________________________
From: Nuno Agostinho <nunodanielagosti...@gmail.com>
Sent: 03 June 2021 20:15
To: Murphy, Alan E <a.mur...@imperial.ac.uk>
Cc: bioc-devel@r-project.org <bioc-devel@r-project.org>
Subject: Re: [Bioc-devel] Add dockerhub push to github repository
Hey Alan,
is that installing the master branch or the current branch that has been pushed
to?
It is based on the current branch.
Building image [***/scfdev:combiz/scFlow:0.7.1 ***/scfdev:dev-am
***/scfdev:sha-658a6af]
invalid argument "***/scfdev:combiz/scFlow:0.7.1" for "-t, --tag" flag: invalid
reference format
I don't think the problem is the Dockerfile, but the GitHub Actions workflow
itself (specifically, the issue seems to be related with the tag of the image).
Could you show me your GitHub Actions workflow file to check what is going on?
Cheers,
Nuno
On 3 Jun 2021, at 20:05, Murphy, Alan E
<a.mur...@imperial.ac.uk<mailto:a.mur...@imperial.ac.uk>> wrote:
Hey Nuno,
Thank you very much for your comprehensive explanation!
I have a question regarding the `remotes::install_local()` approach in the
dockerfile, is that installing the master branch or the current branch that has
been pushed to? I ask as I'm working on 'dev-am' branch and I got the following
error:
Building image [***/scfdev:combiz/scFlow:0.7.1 ***/scfdev:dev-am
***/scfdev:sha-658a6af]
invalid argument "***/scfdev:combiz/scFlow:0.7.1" for "-t, --tag" flag: invalid
reference format
See 'docker build --help'.
Error: Error: exit status 125
Usage:
github-actions build-push [flags]
Flags:
-h, --help help for build-push
exit status 125
Obviously, this may not be down to this but I'm just trying to rule things out
since this was the only change I made to the dockerfile. The docker file has
this added following your dockerfile:
## Install scFlow package
# Copy description
WORKDIR scFlow
ADD . .
# Install R package from source
RUN Rscript -e "remotes::install_local()"
RUN rm -rf *
Cheers,
Alan.
________________________________
From: Nuno Agostinho
<nunodanielagosti...@gmail.com<mailto:nunodanielagosti...@gmail.com>>
Sent: 03 June 2021 11:57
To: Murphy, Alan E <a.mur...@imperial.ac.uk<mailto:a.mur...@imperial.ac.uk>>
Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
<bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Add dockerhub push to github repository
This email from
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from outside Imperial. Do not click on links and attachments unless you
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Hey Alan,
I would like to automatically create a new image and push to dockerhub with
github actions when I push changes to the github repository. Does anyone have
an example of this process in their repositories?
Well, I use GitHub actions to build a Docker image and push it to GitHub
Container Registry, maybe this could help somehow:
https://github.com/nuno-agostinho/psichomics/blob/master/.github/workflows/docker.yml
I use GitHub releases to release a new package version and, every time I
release a new version, a new Docker image is built (this image also gets
automatically tagged with the latest tag). I also build Docker images every
time I push changes to the dev branch.
Regarding DockerHub, I have DockerHub set up to automatically build Docker
images every time I push to master (to create the latest tag) and dev branches
in GitHub, as well as every time I create a new tag (which I do when creating
new releases). I could put this in the GitHub actions, but I didn't bother yet.
I would ideally like the tag of this dockerhub push to be the R package version
(from the DESCRIPTION) to differentiate between images, is this possible?
I think you can run some bash script in your GitHub Actions based on your
DESCRIPTION file. I would have to test but maybe something like:
- name: Get R package version
run: |
version=$(grep Version DESCRIPTION | grep -o "[0-9.]\+")
echo "packageVersion=${version}" >> $GITHUB_ENV
shell:
bash {0}
You can then access this variable in other steps via ${{ env.packageVersion }}
like so:
- name: Build and push
uses: docker/build-push-action@v2
with:
push: true
tags: ${{ github.repository }}:${{ env.packageVersion }}
Is there a way to tell the Dockerfile to install the R package in the current
repository?
To build the image, I use ADD . . to put the GitHub repository content in the
Docker image and then install the package using remotes::install_local(), as
you can see from my Dockerfile:
https://github.com/nuno-agostinho/psichomics/blob/master/Dockerfile
I hope I was clear and helpful. Please tell me if you need help with anything
else! :)
Best,
Nuno Agostinho
On 3 Jun 2021, at 07:52, Murphy, Alan E
<a.mur...@imperial.ac.uk<mailto:a.mur...@imperial.ac.uk>> wrote:
Hi all,
I'm working on developing an R package with the aim to eventually submit to
Bioconductor. I would like to automatically create a new image and push to
dockerhub with github actions when I push changes to the github repository.
Does anyone have an example of this process in their repositories?
Two things to also consider, I would ideally like the tag of this dockerhub
push to be the R package version (from the DESCRIPTION) to differentiate
between images, is this possible? Secondly, I currently have the dockerfile
created but, since my R package repository is private I have been building the
R package and using the tar.gz file in the dockerfile to install the package
(rather than using devtools::install_github()). Is there a way to tell the
Dockerfile to install the R package in the current repository?
Kind regards,
Alan.
Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
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