On Fri, Aug 12, 2011 at 1:53 PM, Janet Young <jayoung@fhcrc.org> wrote:

> 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.
>
>
Is there a reason to gzip a bigWig file? I think it already supports gzipped
data blocks (but not a gzipped header, which is why this fails).

See: http://comments.gmane.org/gmane.science.biology.ucscgenome.general/8900


> 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
>
>
I just added support for automatic decompression of gzip files, so this
would no longer fail, in general.


>
> ## 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)))
>
>
>
rtracklayer now catches exceptions thrown by Jim Kent's library, so R should
no longer be aborted when things go wrong. In this case, since gzipped files
are not supported, R will issue a warning and error to that effect.

Thanks for this report,
Michael


> #### 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
>
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