gerstung-lab / deepsnv Goto Github PK

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Error in counts[i, , ] <- c[[i]] : 
  number of items to replace is not a multiple of replacement length
In addition: Warning message:
In mclapply(files, function(f) { :
  scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected

> library(deepSNV)
> regions <- GRanges("chr6", IRanges(start = 45422511, end=45422911))
> files <- c("/home/nicholas_calicolabs_com/test_ref.bam", "/home/nicholas_calicolabs_com/test_test.bam")
> loadAllData(files, regions, q=30)

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: bam2R(f, regions$chr[j], regions$start[j], regions$stop[j], ...)
 2: FUN(X[[i]], ...)
 3: lapply(X = X, FUN = FUN, ...)
 4: mclapply(files, function(f) {    test.matrix <- matrix(0, ncol = length(nucleotides), nrow = rows)    for (j in 1:nrow(regions)) {        test.matrix[beg[j]:end[j], ] = bam2R(f, regions$chr[j],             regions$start[j], regions$stop[j], ...)[, nucleotides]    }    mode(test.matrix) <- "integer"    test.matrix}, mc.cores = mc.cores)
 5: loadAllData(files, regions, q = 30)

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data deepSNV
###
##############################################################################
##############################################################################


* checking for file ‘deepSNV/DESCRIPTION’ ... OK
* preparing ‘deepSNV’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘shearwaterML.Rmd’ using rmarkdown
[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

Quitting from lines 35-39 (shearwaterML.Rmd) 
Error: processing vignette 'shearwaterML.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'x' in selecting a method for function 'as.list': no 'header' line "#CHROM POS ID..."?
--- failed re-building ‘shearwaterML.Rmd’

--- re-building ‘deepSNV.Rnw’ using knitr
--- finished re-building ‘deepSNV.Rnw’

--- re-building ‘shearwater.Rnw’ using knitr
[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tabs:
	#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT

Quitting from lines 348-353 (shearwater.Rnw) 
Error: processing vignette 'shearwater.Rnw' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'x' in selecting a method for function 'as.list': no 'header' line "#CHROM POS ID..."?
--- failed re-building ‘shearwater.Rnw’

SUMMARY: processing the following files failed:
  ‘shearwaterML.Rmd’ ‘shearwater.Rnw’

Error: Vignette re-building failed.
Execution halted