Dependency on deprecated xcmsClusterApply

[sneumann]

Hi,

we are getting an error xcmsClusterApply in findAdducts (the only place in CAMERA calling this function):

> an <- findAdducts(an,
+                   rules=rs@rules,
+                   polarity="positive")
Generating peak matrix for peak annotation!
Found and use user-defined ruleset!
Calculating possible adducts in 216 Groups... 
Parallel mode: There are 15 tasks.
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'xcmsClusterApply' not found
> traceback()
4: get(name, envir = asNamespace(pkg), inherits = FALSE)
3: xcms:::xcmsClusterApply
2: findAdducts(an, rules = rs@rules, polarity = "positive")
1: findAdducts(an, rules = rs@rules, polarity = "positive")

xcmsClusterApply was rightfully removed from xcms in
sneumann/xcms@944e73b#diff-79ec150cf995556015ba23f2a591ee68d5968adce487a08d2522e083a5c91112L303

But it is still called in

CAMERA/R/xsAnnotate.R

Line 966 in 0ff0ebf

result <- xcms:::xcmsClusterApply(cl=object@runParallel$cluster,

The proper way is to go BPPARAM in CAMERA as well.
@jorainer, I need some hand-holding if I don't get this fixed this weekend myself.

Yours, Steffen

[sneumann]

A second place that needs fixing is

CAMERA/R/xsAnnotate.R

Line 963 in 0ff0ebf

result <- xcmsPapply(argList, annotateGrpMPI2, paramsGlobal)

Yours, Steffen

[jorainer]

Sure, I'll fix that.

[jorainer]

Uh, had a look at the code. Replacing xcmsPapply with bplapply looks like a much larger change as expected. Due to the short time period to fix this I would rather re-add the xcmsPapply in xcms.

[jorainer]

I've re-enabled the deprecated functionality in xcms (just merged into the xcms master branch - version 3.11.8) - this should fix it, but it would be better if you could verify that @sneumann .