Merge pull request #526 from GoekeLab/fix_xgboost_parallel_issue_for_v4

Fix xgboost parallel issue for v4

Author: Chen Ying

R/bambu.R

@@ -181,6 +181,7 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
 
     emParameters <- setEmParameters(emParameters = opt.em)
     bpParameters <- setBiocParallelParameters(reads, ncore, verbose, demultiplexed)
+	xgb.set.config(nthread = 1)
     # only when reads is not NULL, this proceed, otherwise, it will jump to quant step
     if(!is.null(reads)){ 
         rm.readClassSe <- FALSE

R/bambu_utilityFunctions.R

@@ -4,9 +4,6 @@
 #' @importFrom BiocParallel bpparam
 #' @noRd
 setBiocParallelParameters <- function(reads, ncore, verbose, demultiplexed){
-    if(ncore >= 2) message("WARNING - If you change the number of cores (ncore) ",
-    "between Bambu runs and there is no progress please restart your R session ",
-    "to resolve the issue that originates from the XGboost package.")
     bpParameters <- bpparam()
     #===# set parallel options: otherwise use parallel to distribute samples
     # when demultiplexed is FALSE, isFALSE(demultiplexed) is TRUE

README.md

@@ -695,7 +695,7 @@ Minor changes:
 - Resolve process.y.margin.and.object error [issue](https://github.com/GoekeLab/bambu/issues/505)  
 - Resolve xgboost warnings related to argument updates in the recent xgboost version
 - Resolve the dplyr warning related to summarise usage [issue](https://github.com/GoekeLab/bambu/issues/380) 
-
+- Resolve the xgboost related parallel processing restarting with no progress issue
 
 **bambu v3.8.2**