Error in (function () : unused argument (x = 3)
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Description
Hi,
I am having an issue with getting batchtools to work. I am following this tutorial and have edited the function to work with my phyloseq function. When I just the function on it on and get the results it works. However, when I submit it with batchtools it always fails. Can you please help.
Here is my complete code and errors:
#Create function
myFct<- function() {
Fun <- tax_glom(physeq, "Function")
Fun1<-psmelt(Fun)
FunTrt <- merge_samples(Fun, "Treatment")
FunTrt1<-psmelt(FunTrt)
names(FunTrt1)[2]<-"Trt"
return(FunTrt1)
}
#Run function to make sure it actually works
myFctNam()
**#Submit slurm job **
reg <- makeRegistry(file.dir="myregdir", conf.file=".batchtools.conf.R")
Njobs <- 1:4 # Define number of jobs (here 4)
ids <- batchMap(fun=myFct, x=Njobs)
done <- submitJobs(ids, reg=reg, resources=list(partition="short", walltime=60, ntasks=10, ncpus=1, memory=1024))
waitForJobs()
``` # Wait until jobs are completed
**#Results**
**waitForJobs() # Wait until jobs are completed
[1] FALSE **
**getStatus()**
Status for 4 jobs at 2023-01-13 21:27:41:
Submitted : 4 (100.0%)
-- Queued : 0 ( 0.0%)
-- Started : 4 (100.0%)
---- Running : 0 ( 0.0%)
---- Done : 0 ( 0.0%)
---- Error : 4 (100.0%)
---- Expired : 0 ( 0.0%)
**> getErrorMessages(ids, reg = getDefaultRegistry())**
job.id terminated error message
1: 1 TRUE TRUE Error in (function () : unused argument (x = 1)
2: 2 TRUE TRUE Error in (function () : unused argument (x = 2)
3: 3 TRUE TRUE Error in (function () : unused argument (x = 3)
4: 4 TRUE TRUE Error in (function () : unused argument (x = 4)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the batchMap(fun=myFct, x=Njobs) call and compare it with the tutorial, then inspect the recorded failures using getErrorMessages(ids, reg = getDefaultRegistry()). Check the .batchtools.conf.R and Slurm submission settings as well. Done means identifying whether the error comes from the submitted function arguments or batchtools and documenting a reproducible resolution.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- distributed-systems
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100