Handling multtest dependency (BioC build error)

[sneumann]

Hi, I think we have leftover historic misuse in our dependency handling.

In the old days, we avoided bloating dependencies, because some default behaviour was to recursively install all Suggested packages, and e.g. multtest pulled in a lot of that. So, we have

https://github.com/sneumann/xcms/blob/fcab3c6b00de176fd7613f6c290f0b2469756af7/R/methods-xcmsSet.R#L1565

Which in turn triggers a build error on BioC builds with new R-devel (r83996) Error report on https://master.bioconductor.org/checkResults/3.17/bioc-LATEST/CAMERA/nebbiolo1-checksrc.html

  Test files with failing tests:
     test_annotateDiffreport.R 
       test.annotateDiffreport.calcCaS 
       test.annotateDiffreport.calcCiS 
       test.annotateDiffreport.calcIso 
       test.annotateDiffreport.graphMethod 
       test.annotateDiffreport.intval 
       test.annotateDiffreport.pval 
...  
Error in .local(object, ...) : 
  The use of 'diffreport' requires package 'multtest'. Please install with 'Biobase::install("multtest")'

[jorainer]

two solutions:

• change the code from diffreport to use p.adjust instead.
• add multtest to Suggests.

I would prefer solution 1 as I don't see why we should need/use the multtest package at all?

[jorainer]

So, multtest is already in Suggests - so it should work. Note that I've seen recently also dependency problems for other packages on that particular build system. Maybe it might also be related to something not working properly on that build server?

[jorainer]

Seems to have resolved itself.