doEnirchment error after upgrade of R and biocondcutor

[biojiangke]

Running the example in the tutorial (https://rdrr.io/bioc/InterMineR/f/vignettes/Enrichment_Analysis_and_Visualization.Rmd) does not work any more after upgrading bioconductor to 3.13. It throws out the following error:

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘doEnrichment’ for signature ‘"missing"’

Could be some dependency issues but could not find much information on this message.

[rachellyne]

@biojiangke

Thanks for pointing this out.

I don't know why this has changed, but this seems to work:

Go_enrichResult <- doEnrichment(
im.human,
ids = hsa_gene_entrez,
widget = "go_enrichment_for_gene"

)

(instead of im = im.human, just im.human)

[biojiangke]

Thanks for the update! Changing "im=im.human" to "im.human" takes away the previous error, but now when I run doEnrichment I got:

Error in .local(object, ...) : Unauthorized (HTTP 401).

Does this mean the "im.human" object does not have proper authentication to access InterMine? Any advice?

The code before this chunk is this:

# load intermine instance for human genome
im.human = initInterMine(listMines()["HumanMine"])
# get all HumanMine widgets
human.widgets = as.data.frame(getWidgets(im.human))
human.widgets
# only gene related widgets
# get enrichment, gene-related widgets for HumanMine
subset(human.widgets, widgetType == 'enrichment' & targets == "Gene")

Checking results from the above lines, the "human.widgets" object seems to be fine. Using the example data "data("PL_DiabetesGenes")" in the documentation instead of my own gene list gave the same authorization error. Could this a problem on the InterMine side?