Error message in CreateSinglerObject

[ChaDuss]

I am in trouble with the function CreateSinglerObject. I got those "Warning messages" several times with different counts and I don't understand why.

I work with R3.6 and Ubuntu.

singler = CreateSinglerObject(pbmc.raw.data, annot = NULL, project.name = "hay_35_pop", min.genes = 0,

•                           technology = "10X", species = "Human", citation = "cool",
  

•                           ref.list = list(ref), normalize.gene.length = F, variable.genes = "de",
  

•                           fine.tune = T, do.signatures = T, clusters = pbmcsmall@active.ident, do.main.types = F,
  

•                           reduce.file.size = T, numCores = SingleR.numCores)
  

[1] "Dimensions of counts data: 18934x2647"
[1] "Annotating data with refCD34-..."
[1] "Variable genes method: de"
[1] "Number of DE genes:1599"
[1] "Number of cells: 2647"
[1] "Fine-tuning round on top cell types (using 16 CPU cores):"
|===================================================================================================================================| 100%, Elapsed 00:07
[1] "Number of DE genes:1599"
[1] "Number of clusters: 13"
[1] "Fine-tuning round on top cell types (using 16 CPU cores):"
|===================================================================================================================================| 100%, Elapsed 00:02
Warning messages:
1: In selectChildren(pids[!fin], -1) :
cannot wait for child 6345 as it does not exist
2: In parallel::mccollect(...) : 1 parallel job did not deliver a result
3: In selectChildren(pids[!fin], -1) :
cannot wait for child 6363 as it does not exist
4: In parallel::mccollect(...) : 1 parallel job did not deliver a result

Do you know what can I do to fix it ?

Than you very much.

Bests,

[dviraran]

Try using numCores=4 instead of 16. Seems like an issue with the multi threading.

[ChaDuss]

Thanks but it did not work with numCores = 4 or numCores =1 :
Warning messages:
1: In selectChildren(pids[!fin], -1) :
cannot wait for child 6006 as it does not exist
2: In parallel::mccollect(...) : 1 parallel job did not deliver a result
3: In selectChildren(pids[!fin], -1) :
cannot wait for child 6017 as it does not exist
4: In parallel::mccollect(...) : 1 parallel job did not deliver a result

[dviraran]

I tried looking for this error online (HenrikBengtsson/future#218) and it seems its a problem with R 3.5.0. Maybe update R to 3.6.0?

Anyway, according to this thread, these warnings are harmless.