Drive-by comment; Be careful when passing secrets/credentials via command-line arguments as is:

docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 YOURDOCKERIMAGENAME

If this is done on a computer to which others have a access, e.g. computer clusters, then they can see your password with a simple ps aux call.

I was getting this error in the deploy step - "Error: The deploy step encountered an error: The process '/usr/bin/git' failed with exit code 128".

In case anyone else encounters this error, adding write permissions to the workflow file fixed it for me. Here is the thread with the solution: JamesIves/github-pages-deploy-action#1110 (comment)

Hi Sean, @seandavi
Whenever you get a chance, could you rename the branch so that it conforms to Bioconductor guidelines?
See here for more information: http://contributions.bioconductor.org/branch-rename-faqs.html
Thank you!

Hello @seandavi and team,

I already opened an issue on the sysreqs repo about this, see: r-hub/sysreqs#24. Starting last night, the GHA workflow to build my workshop started failing even though I had only incremented the package version number.

Wondering if this is happening to anyone else? I am pretty sure it is due to an expired SSL certification for the sysreq website, see the issue for more details.

Best,
Christopher Eeles
Software Developer
Haibe-Kains Lab
PM-Research | UHN

I have an issue that is slightly related to #10 . I too had issues with my docker credentials failing after 10+ minutes of the action (although in my case I am glad it failed after making the pkgdown website, not before). I think my problem is that I am not formatting the DOCKER_USERNAME and DOCKER_PASSWORD properly and I cannot find an example anywhere. My action fails with

Pushing image [jdrnevich/buildacarpentriesworkshop:latest jdrnevich/buildacarpentriesworkshop:latest jdrnevich/buildacarpentriesworkshop:sha-38bb549]
The push refers to repository [docker.io/jdrnevich/buildacarpentriesworkshop]
60176156405e: Preparing
... # removed a bunch of Preparing and Waiting lines
30691b678e1c: Waiting
denied: requested access to the resource is denied
Error: exit status 1
Usage:
  github-actions build-push [flags]

I created a docker account and got an access token. How exactly should I enter them in the secrets? I have tried:

DOCKER_USERNAME: jdrnevich
DOCKER_PASSWORD: mytokenid

and

DOCKER_USERNAME jdrnevich
DOCKER_PASSWORD mytokenid

Both failed. Instead of trying lots of combos and waiting 10 min to see, I thought I'd ask here and also request you add the formatting to Section 6 of HOWTO_BUILD_WORKSHOP.Rmd. Thanks!

Hi Sean, @seandavi
Thanks so much for making a template for this!

I was able to run the GH Action using the template provided but at some step
the push to gh-pages did not include a .nojekyll file which was not letting
my website be served.

Perhaps this is an issue for one of the steps?

PS. This could be an interaction that I don't fully understand with a custom CNAME
and gh-pages. I see other pages rendered fine without one:
https://github.com/PeteHaitch/BioC2020_DelayedArray_workshop/tree/gh-pages
https://PeteHaitch.github.io/BioC2020_DelayedArray_workshop

Thanks.
-Marcel

Both https://seandavi.github.io/BuildABiocWorkshop and https://app.orchestra.cancerdatasci.org/ are throwing 404s at the moment.

To make the repository more consistent with Rule 9 of https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854

Additionally, add github magic so that new issues create an appropriate template for contributing FAIRly.

https://github.com/seandavi/BuildABiocWorkshop/blob/45827935dd767b31d1ac79efa00a82d5ba9640c2/.github/workflows/basic_checks.yaml#L143-L154

Hi there,

Following the instructions in the package exactly leads to failing GH Action checks at the "Deploy" phase of r-build-and-check. This is presumably due to an error introduced within the past month causing the workflow to be unable to initialize a repository (see Issue #1110, Issue #1083). This has subsequently been fixed in later releases, but the workflow bundled in the template repository doesn't seem to work.

The fixes for this are:

• update JamesIves/github-pages-deploy-action@releases/v3 -> JamesIves/github-pages-deploy-action@releases/v4 in basic_checks.yaml:68
• Add an entry in the README to tell users to ensure "Read and Write permissions" are checked under Settings > Actions > General > Workflow permissions

Hi,

I had some issues getting the action to run without error--nothing too serious but I did have to wait 13 minutes to find out that I had entered the wrong docker username/password (visible here: https://github.com/cmirzayi/EpiForBioWorkshop2020/runs/774158738?check_suite_focus=true) and 19 minutes before failure because I had not added pkgdown as a dependency (https://github.com/cmirzayi/EpiForBioWorkshop2020/runs/774201957?check_suite_focus=true). If possible, it would be good if the action checked for these sorts of errors before running for 10+ minutes.

Thanks!
Chloe

• Similar to: tesselle/khroma@1dcd9ad

Hi,

I'm getting the following error in the install dependencies step:

The following packages have unmet dependencies: libgit2-dev : Depends: libcurl4-gnutls-dev but it is not going to be installed E: Unable to correct problems, you have held broken packages. ##[error]Process completed with exit code 100.

any help?
dario

Hi @seandavi,

when I reach the docker step it gives me an error on the installation of the AnnotationDbi package.

Here the log error section:

Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help

• installing source package ‘AnnotationDbi’ ...
  ** using staged installation
  ** R
  ** inst
  ** tests
  ** byte-compile and prepare package for lazy loading
  Bioconductor version 3.12 (BiocManager 1.30.10), ?BiocManager::install for help
  Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object '/usr/local/lib/R/site-library/Rcpp/libs/Rcpp.so':
  /usr/local/lib/R/site-library/Rcpp/libs/Rcpp.so: undefined symbol: EXTPTR_PTR
  Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
  Execution halted
  ERROR: lazy loading failed for package ‘AnnotationDbi’
• removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
  Error in i.p(...) :
  (converted from warning) installation of package ‘AnnotationDbi’ had non-zero exit status
  Calls: ... with_rprofile_user -> with_envvar -> force -> force -> i.p
  Execution halted
  The command '/bin/sh -c Rscript -e "devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())"' returned a non-zero code: 1
  Error: exit status 1
  Usage:
  exit status 1

It seems that some Rcpp shared library is missing, any suggestion on how to solve it?

Thanks,
Dario

As of 12 June 2023, we are getting warnings about Node 12 deprecation in the following:

• r-build-and-check actions/checkout@v2, actions/cache@v1
• docker-build-and-push actions/checkout@v2, docker/setup-buildx-action@79abd3f

We are getting warnings about save-state or set-output in docker-build-and-push. See this run, for instance.

It looks like fixes for all of these might just involve bumping the actions version, as I don't see any calls to the deprecated APIs directly in the workflow. I may take a crack at fixing this when I get a couple hours to play around.

Is this an issue? You can see this in the log for job1, under the docker/build-push-action section.

WARNING! Using --password via the CLI is insecure. Use --password-stdin.
WARNING! Your password will be stored unencrypted in /github/home/.docker/config.json.
Login Succeeded
Configure a credential helper to remove this warning. See
https://docs.docker.com/engine/reference/commandline/login/#credentials-store

I don't know where /github/home/.docker/config.json is (on GitHub? On DockerHub?, in the Docker container itself?) I assume the latter, but can't actually find it.

Is there a potential issue with conflict with pre-existing github.io site?

github.com/vjcitn/intmmo is an attempt to produce a workshop site
with minimal changes to the template. i already have vjcitn.github.io and
attempt to produce vjcitn.github.io/intmmo by altering DESCRIPTION, basic_checks.yaml,
and _pkgdown.yml, and having a vignette with the name of the repo.
The actions workflow succceeds, the gh-pages branch of intmmo seems properly populated, but vjcitn.github.io/intmmo generates 404 next to some pre-existing content in my gh-pages.

I will try to learn more about pkgdown but I wonder if there is a simple explanation and
workaround.

Hi,

is there a way to create a dataset and include it into the workshop material?

I tried to include an .rda file into the package data folder and recalling it with the data("datasetname") function, but this is not working.

Do you know why? Is there any idea to do something like that?

Thanks!

Move docker build and deploy to end of workflow
to prioritize github pages push. Does not change
logic at all.

By default, BiocManager::repositories() on the Bioconductor docker images (now) uses the RStudio package manager for fast binary installation of CRAN packages. Does this line
https://github.com/seandavi/BuildABiocWorkshop/blob/5ba55a4f6ae3df095f89d71643e05fb2f0082f2c/.github/workflows/basic_checks.yaml#L44 defeat that behavior, replacing BiocManager's repository with the CRAN source repository? Whatever the case, CRAN packages are being installed from source...

Also, setting options(Ncpus = 8) (or however many CPUs are available) installs packages in parallel, potentially quite a bit faster (even Ncpus = 2 on a single CPU machine would speed things up, I think...)

I see that removing the options() in the Dockerfile might also be appropriate? https://github.com/seandavi/BuildABiocWorkshop/blob/5ba55a4f6ae3df095f89d71643e05fb2f0082f2c/Dockerfile#L7-L9

Hi,

Thanks for making a convenient workshop template.
The creation of our vignette is getting killed without an interpretable error message (https://github.com/kstreet13/bioc2020trajectories/runs/736248107?check_suite_focus=true).
Compilation of the vignette works fine locally.
Any idea what could be causing this?

Thanks!

Table 2 of https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854 suggests metadata to describe resources and facilitate FAIR sharing of training material. These can be included as DESCRIPTION dcf ('debian control format') fields