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carpentries-incubator / high-dimensional-stats-r

High-dimensional statistics with R
https://carpentries-incubator.github.io/high-dimensional-stats-r
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review comments: setup.md #34

Closed 3mmaRand closed 2 years ago

3mmaRand commented 2 years ago

destfile argument is missing from download.file() command e.g destfile = "dependencies.csv"

Maybe add a few comments to the set up and give an indication of time taken?

For ref: I did in a fresh RStudio Cloud Project (public: https://rstudio.cloud/project/3121818), attempted package installation of all 50 packages took 30 mins and I had several fails: 1: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'stats' 'MASS' 'cluster' 'BiocManager' 'utils' 2: In .inet_warning(msg) : installation of package ‘scran’ had non-zero exit status 3: In .inet_warning(msg) : installation of package ‘GenomicFeatures’ had non-zero exit status 4: In .inet_warning(msg) : installation of package ‘bumphunter’ had non-zero exit status 5: In .inet_warning(msg) : installation of package ‘ensembldb’ had non-zero exit status 6: In .inet_warning(msg) : installation of package ‘minfi’ had non-zero exit status 7: In .inet_warning(msg) : installation of package ‘scRNAseq’ had non-zero exit status 8: In .inet_warning(msg) : installation of package ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’ had non-zero exit status 9: In .inet_warning(msg) : installation of package ‘IlluminaHumanMethylationEPICmanifest’ had non-zero exit status 10: In .inet_warning(msg) : installation of package ‘FlowSorted.Blood.EPIC’ had non-zero exit status

alanocallaghan commented 2 years ago

Good points. May also see if I can thin down the list of needed packages (eg, the illumina packages shouldn't be necessary for running the lesson)

scran install is Killed so I think that's a memory issue on the Rstudio cloud (although if I remember well they're also missing a lot of system dependencies for Bioc)

catavallejos commented 2 years ago

Thanks @3mmaRand for the feedback. Here is what we plan to do:

1) Edit setup.md with an expectation of how long setup takes. 2) Check whether dependency list can be made shorter. 3) Check setup runs smoothly in different environments.

We will also explore whether to provide a Docker container with all the requirements for the course.

I will close this issue for now as I have moved these to our master to-do list in #64

Of course, just re-open this issue if you have further comments.