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CRAN prep #19
CRAN prep #19
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Hi Austin, thanks for getting this started. At a glance, I like your first round of changes. Our GitHub actions are failing:
Could I please ask you to go ahead and make these changes to the presto/.github/workflows/R-CMD-check.yaml Line 36 in 052085d
This should be:
presto/.github/workflows/R-CMD-check.yaml Line 40 in 052085d
This should be:
I think the branch called |
A few changes to the GHA:
I played around with the GHA on my fork of the repo and checks passed on windows and macOS but not yet on ubuntu which I'm still sorting out |
Hey Austin, Thanks for working on this. Below, I share some notes on what I could observe from the logs. In summary, I think we're on the right track, and I believe many potential GHA failures are out of your control. I might suggest running R CMD check on your laptop to avoid losing time due to these GHA issues. Thanks for your help and patience, DetailsI noticed in your repo that macOS passed the GHA but the others did not. Weird. I looked at one of the failed GHA runs and found this:
Here are the lines: presto/vignettes/getting-started.Rmd Lines 116 to 120 in 51eefa7
At first I thought maybe we failed to add SingleCellExperiment to the dependencies. But I checked DESCRIPTION and see that we include the package in Then I checked the log file in GHA and found this:
This indicates that the package is not downloading successfully. Maybe we are unlucky. Just now, I was able to reproduce the 503 error in my web browser. A few moments later, I am now able to successfully download this file: https://bioconductor.org/packages/3.14/bioc/src/contrib/SingleCellExperiment_1.16.0.tar.gz I might conclude that the bioconductor server was momentarily unavailable. Then, I decided to launch the GHA jobs in this pull request and I saw a new error message:
According to this comment, the error might go away if we just re-run the GHA jobs: Conclusions
How to run R CMD check quicklyRecently, I had to run CRAN check on ggrepel a few times, and I was frustrated that each run took a lot of time. Then I found a comment by Jim Hester:
After setting the environment variable |
Thanks for investigating the logs and suggestions. I've been running R checks locally without any errors warnings or notes on an ubuntu 20.04 system with R 4.1.3, so the GHA errors were indeed perplexing. Since the GHA errors seem to be due to inconsistency in dependency installation, I can focus a bit more on documentation. Anything else I'm missing before merging and CRAN submission? |
Thank you, Austin! Would you like to make more changes (e.g. clearer error messages, documentation)? One thing that users might appreciate is a pkgdown website with some usage examples and tips. I think an appropriate URL for this page would be https://immunogenomics.github.io/presto If you're ready for a merge, please let me know and I'll take it from here. |
I've made a few changes to the docs and examples and added a |
@AustinHartman I forgot to ask, could you please provide your information so we can add you as a contributor in the DESCRIPTION file? Here's mine (I will add myself, too, since I'm contributing):
|
Thanks - here's my info: |
Work in progress preparing presto for CRAN submission. Looking for any feedback related to styling, documentations, etc.
I moved DESeq2 from imports to suggests given it's used for the pseudobulk testing, but not for the main wilcox rank sum workflow. Also, since DESeq2 is a bioconductor package it will make it easier for CRAN packages, like Seurat, to import presto.