Hey Alan, I think the line "container: almurphy/scfdev:latest" should be removed, this should only be used if you want to run something within a container (in this case, you just want to create a container).
Also, you are using docker/build-push-action@v2 as if it was version 1, but they changed a lot this action in the new version, as you can see here: https://github.com/docker/build-push-action/blob/master/UPGRADE.md <https://github.com/docker/build-push-action/blob/master/UPGRADE.md> I would remove the > - 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 }} and replace it with the following: - name: Set up Docker Buildx uses: docker/setup-buildx-action@v1 - name: Login to DockerHub uses: docker/login-action@v1 with: username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_TOKEN }} - name: Build and push uses: docker/build-push-action@v2 with: push: true tags: ${{ github.repository}}:${{ env.packageVersion }} Basically, the steps are more discrete now, tell me if it works and if you need help with anything else. Cheers, Nuno > On 3 Jun 2021, at 20:17, Murphy, Alan E <a.mur...@imperial.ac.uk> wrote: > > 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 > <mailto:nunodanielagosti...@gmail.com>> > Sent: 03 June 2021 20:15 > 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 > > 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 nunodanielagosti...@gmail.com >> <mailto: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 >> >> <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 >> <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 >>> <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
