first error: could not find function "readGAlignments" in BiocParallel
1
Entering edit mode
@shangguandong1996-21805
Last seen 9 hours ago

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
BiocParallel • 84 views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States

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.

1
Entering edit mode
@martin-morgan-1513
Last seen 3 days ago
United States

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
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0
Entering edit mode

Thanks your reply, I make it :).

But my bpvalidate(FUN) message is different from yours. It seems that there is no "package:GenomicAlignments" in bpvalidate(FUN) output.

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

fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES

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

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


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

> bplapply(fls[1:3], FUN, BPPARAM = SnowParam(), gr = gr, param = param)
$ERR127306
[1] 1185

$ERR127307
[1] 1123

$ERR127308
[1] 1241

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


$unknown
character(0)
> 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] GenomicAlignments_1.26.0           Rsamtools_2.6.0                   
 [3] Biostrings_2.58.0                  XVector_0.30.0                    
 [5] SummarizedExperiment_1.20.0        Biobase_2.50.0                    
 [7] MatrixGenerics_1.2.0               matrixStats_0.57.0                
 [9] GenomicRanges_1.42.0               GenomeInfoDb_1.26.2               
[11] IRanges_2.24.1                     S4Vectors_0.28.1                  
[13] BiocGenerics_0.36.0                BiocParallel_1.24.1               
[15] RNAseqData.HNRNPC.bam.chr14_0.28.0

loaded via a namespace (and not attached):
 [1] rstudioapi_0.13        zlibbioc_1.36.0        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_1.2.4
[10] codetools_0.2-18       bitops_1.0-6           RCurl_1.98-1.2        
[13] DelayedArray_0.16.0    compiler_4.0.2
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