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> Sent: 03 June 2021 11:57 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 This email from nunodanielagosti...@gmail.com originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. 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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
