Proxy-Setting/Prevent R from Internet Search

[dansteiert]

Description of feature

Hi differentialabundance Team,

I tried running the pipeline, and got an error, that R/Bioconductor is trying to retrieve/verify packages, accompanied by a "Couldn't conncet to server", which I assume is due to my proxy settings.

I am using the singularity profile.
Is there an option to set my proxy or prevent R from searching the interenet in the first place?

Below is my error message:

Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:AFFY_JUSTRMA_RAW (study)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:AFFY_JUSTRMA_RAW (study)` terminated with an error exit status (1)

The full R script ...

Command exit status:
  1

Command output:
  (empty)

Command error:
  Loading required package: BiocGenerics

  Attaching package: ‘BiocGenerics’

  The following objects are masked from ‘package:stats’:

      IQR, mad, sd, var, xtabs

  The following objects are masked from ‘package:base’:

      anyDuplicated, aperm, append, as.data.frame, basename, cbind,
      colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
      get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
      match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
      Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
      table, tapply, union, unique, unsplit, which.max, which.min

  Loading required package: Biobase
  Welcome to Bioconductor

      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.

  Error: Bioconductor version cannot be validated; no internet connection?  See
    #troubleshooting section in vignette
  In addition: Warning messages:
  1: In file(con, "r") :
    URL 'https://bioconductor.org/config.yaml': status was 'Couldn't connect to server'
  2: In file(con, "r") :
    URL 'http://bioconductor.org/config.yaml': status was 'Couldn't connect to server'
  Execution halted

[pinin4fjords]

Yeah, I was worried this would happen when I wrote the culprit module (issue is this).

The issue is that Affy needs the CDFs etc for the array design. We can't bake every possible one into an upstream image (at l'm not prepared to create and maintain such a thing), so we currently rely on dynamically fetching the right ones at run time.

Apologies, but I'm not seeing any easy way to fix this right now. I wonder if any @nf-core/maintainers might have cunning plans?

[dansteiert]

Thank you anyway for having a look into it!

I was hoping there is some nextflow config, where I can pass all my proxy information into, such that each container can access the interenet if there is a need for it, but apparently this is not the case, right?

[SPPearce]

If you (as the user) build a singularity container with the required packages then you could override the container directive for that process locally via a config. The script might need updating to check if the package already exists before trying to download it though.

Alternatively there could be an optional file location which could be staged into the progress to be checked in case the file exists before going to the internet.

[pinin4fjords]

Closing this for lack of activity for now. @dansteiert if you tried the container override and it didn't work, indicating we need some code changes, reopen this and I'll take a closer look.