[Bioc-devel] bgzip does not seem to close all file handles

[Martin Morgan]

On 04/11/2012 07:35 AM, Hahne, Florian wrote:
> Hi all, Martin,
> I just realized that bgzip does not seem to properly clean up after it has
> finished:
>
> library(Rsamtools)
> dir.create("test")
> write.table(data.frame(seq="chr1", start=1, end=2, data=10),
> file="test/test.txt", sep="\t",  row.names=FALSE, quote=FALSE)
> bgzip("test/test.txt", "test/test.tabix")
>
> Now if I try to delete 'test' on an NFS mounted file system I get:
> rm -rf test/
> rm: cannot remove `test': Directory not empty

Thanks Florian should be fixed in 1.8.1 / 1.9.1 and svn. Martin
>
>
> And in there I find an NFS file handler:
> ls -lah test
> total 12
> drwxr-xr-x  2 itox 4096 Apr 11 16:27 .
> drwxr-xr-x 16 itox 4096 Apr 11 16:25 ..
> -rw-r--r--  1 itox   87 Apr 11 16:26 .nfs00000000001675a200000130
>
> This handler remains in 'test' until I close the R session. I know from
> previous experience that our NFS setup is a bit funky, but since I could
> clearly pin this down to bgzip I thought it might be something that is
> fixable in there. This will not happen on local file systems because they
> don't seem to care about open file handles (at least on my Mac)
>
>
>> sessionInfo()
> R Under development (unstable) (2012-04-03 r58904)
> Platform: x86_64-unknown-linux-gnu/x86_64 (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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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] Rsamtools_1.8.0     Biostrings_2.24.0   GenomicRanges_1.8.2
> [4] IRanges_1.14.2      BiocGenerics_0.2.0  BiocInstaller_1.4.3
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1 stats4_2.16.0  tools_2.16.0   zlibbioc_1.2.0
>
>
>
>
> Thanks,
> Florian
>
>
>
>
>
>
>
>
> Florian Hahne
> Novartis Institute For Biomedical Research
> Translational Sciences / Preclinical Safety / PCS Informatics
> Expert Data Integration and Modeling Bioinformatics
> CHBS, WKL-135.2.26
> Novartis Institute For Biomedical Research, Werk Klybeck
> Klybeckstrasse 141
> CH-4057 Basel
> Switzerland
> Phone: +41 61 6967127
> Email : florian.hahne at novartis.com
>


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