Hi, Dear developer I try to run code in BiocParallel manual, but there is error about it

library(RNAseqData.HNRNPC.bam.chr14)
library(GenomicAlignments)
library(BiocParallel)

fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES


gr <- GRanges("chr14", IRanges((1000:3999)*5000, width=1000))

param <- ScanBamParam(which=range(gr))

FUN <- function(fl, param) {
  gal <- readGAlignments(fl, param = param)
  sum(countOverlaps(gr, gal))
}

> SnowParam()
class: SnowParam
  bpisup: FALSE; bpnworkers: 10; bptasks: 0; bpjobname: BPJOB
  bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
  bpRNGseed: ; bptimeout: 2592000; bpprogressbar: FALSE
  bpexportglobals: TRUE
  bplogdir: NA
  bpresultdir: NA
  cluster type: SOCK

> bplapply(fls[1:3], FUN, BPPARAM = SnowParam(), param = param)
Error: BiocParallel errors
  element index: 1, 2, 3
  first error: could not find function "readGAlignments"
In addition: Warning messages:
1: In serialize(data, node$con) :
  'package:stats' may not be available when loading
2: In serialize(data, node$con) :
  'package:stats' may not be available when loading
3: In serialize(data, node$con) :
  'package:stats' may not be available when loading

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] BiocParallel_1.22.0                GenomicAlignments_1.24.0          
 [3] Rsamtools_2.4.0                    Biostrings_2.56.0                 
 [5] XVector_0.28.0                     SummarizedExperiment_1.18.2       
 [7] DelayedArray_0.14.1                matrixStats_0.57.0                
 [9] Biobase_2.48.0                     GenomicRanges_1.40.0              
[11] GenomeInfoDb_1.24.2                IRanges_2.22.2                    
[13] S4Vectors_0.26.1                   BiocGenerics_0.34.0               
[15] RNAseqData.HNRNPC.bam.chr14_0.26.0

loaded via a namespace (and not attached):
 [1] rstudioapi_0.11        zlibbioc_1.34.0        lattice_0.20-41       
 [4] tools_4.0.2            grid_4.0.2             snow_0.4-3            
 [7] crayon_1.3.4           Matrix_1.2-18          GenomeInfoDbData_1.2.3
[10] bitops_1.0-6           RCurl_1.98-1.2         compiler_4.0.2

You have a set of packages that shouldn't be installed for the version of R you are using. The first step for you should be to do

library(BiocManager)
BiocManager::valid()

And do whatever valid says you need to do to fix your installation. Then try your code again.

The 'snow' workers are independent processes and do not 'know' about the packages loaded on the main node. Load the packages on the workers, e.g.,

FUN <- function(fl, param) {
  library(GenomicAlignments)
  gal <- readGAlignments(fl, param = param)
  sum(countOverlaps(gr, gal))
}

But note also that the workers don't know about gr either, so make sure to pass that as part of the function

FUN <- function(fl, gr, param) {
  library(GenomicAlignments)
  gal <- readGAlignments(fl, param = param)
  sum(countOverlaps(gr, gal))
}
bplapply(fls[1:3], FUN, BPPARAM = SnowParam(), gr = gr, param = param)

The bpvalidate() function is meant to help with this, and it indicates the two problems mentioned in this case, but is not entirely satisfactory.

> bpvalidate(FUN)
$inPath
$inPath$countOverlaps
[1] "package:GenomicRanges"

$inPath$gr
[1] ".GlobalEnv"

$inPath$readGAlignments
[1] "package:GenomicAlignments"


$unknown
character(0)

Warning message:
In bpvalidate(FUN) : function references symbol(s) in .GlobalEnv