[BioC] rtracklayer import.bw on gz file makes R crash

[Janet Young]

Hi there,

By trying to do something that's not supposed to be done, I accidentally found a fatal R-killing issue with import.bw: I tried using import.bw on a bigWig file while it was still gzipped.

You never know, sometimes these things work - I've since found an email thread that might help me avoid unpacking the file ( https://stat.ethz.ch/pipermail/bioconductor/2011-April/038734.html ) but in the meantime I thought I should tell you about how I made R die.  

Code to reproduce this, details and sessionInfo are all below.

thanks,

Janmet

########

library(rtracklayer)

test.bw.file <- system.file("tests", "test.bw", package = "rtracklayer")

## import works, as it's supposed to
bw <- import(test.bw.file, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7)))

### I copied that test.bw file to a local dir and used gzip to compress it
test.bw.file.gz <- "temp/test.bw.gz"

### import gives error if I try to read in the gz file directly - that's OK
bw2 <- import(test.bw.file.gz, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7)))
##  Error in .importForFormat(format) : No import function for 'gz' found


## import.bw also works as its supposed to on the uncompressed file
bw3 <- import.bw(test.bw.file, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7)))

## here's sessionInfo output, before I kill off R:
sessionInfo()
# R version 2.13.1 (2011-07-08)
# Platform: i386-apple-darwin9.8.0/i386 (32-bit)
#
# locale:
# [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
#
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
#
# other attached packages:
# [1] rtracklayer_1.12.4 RCurl_1.6-7        bitops_1.0-4.1    
#
# loaded via a namespace (and not attached):
# [1] Biostrings_2.20.2   BSgenome_1.20.0     GenomicRanges_1.4.6 IRanges_1.10.5     
# [5] XML_3.4-2          


##### now, using import.bw on the gz file makes R crash with no error report on Mac 
bw4 <- import.bw(test.bw.file.gz, ranges = GenomicRanges::GRanges("chr19", IRanges(1, 6e7)))


#### also see the same problem on linux, where my sessionInfo is as follows:
# R version 2.13.1 (2011-07-08)
# Platform: x86_64-unknown-linux-gnu (64-bit)
# 
# locale:
#  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
#  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
# [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] rtracklayer_1.12.4 RCurl_1.6-5        bitops_1.0-4.1    
# 
# loaded via a namespace (and not attached):
# [1] Biostrings_2.20.2   BSgenome_1.20.0     GenomicRanges_1.4.6
# [4] IRanges_1.10.5      XML_3.4-2