[R] how to unzip files in R

[Henrik Bengtsson]

I may be wrong, but I don't think unz() handles bz2 files - only zip files.

See bunzip2() of the R.utils package (which utilizes bzfile connections).

/Henrik


On Tue, Jan 31, 2012 at 2:34 PM, ql16717 <ql16717 at gmail.com> wrote:
> Hi,
>
> I have downloaded a bunch of bz2 files. I wonder if R will be able to
> unzip them in a batch mode or even one at a time?
>
> I was looking at the unz function. But it didn't work well. Say I have
> a bz2 file in H:/Temp/65502805_532.pair.bz2. Anyone has any
> suggestion?
>
> thanks
> John
>
>> setwd("H:\\Temp\\")
>> getwd()
> [1] "H:/Temp"
>> fn<-list.files(pattern="bz2", full.names=TRUE)
>> fn
> [1] "./65502805_532.pair.bz2"
>> unz(description=fn, filename="65502805_532.pair", open="r")
> Error in unz(description = fn, filename = "65502805_532.pair", open = "r") :
>  cannot open the connection
> In addition: Warning message:
> In unz(description = fn, filename = "65502805_532.pair", open = "r") :
>  cannot open zip file './65502805_532.pair.bz2'
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pdInfoBuilder_1.18.0 oligo_1.18.1         oligoClasses_1.16.0
> affxparser_1.26.2    RSQLite_0.10.0
> [6] DBI_0.2-5            Biobase_2.12.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.22.0         Biostrings_2.22.0     bit_1.1-8
> ff_2.2-4              IRanges_1.12.1
> [6] preprocessCore_1.16.0 splines_2.14.0        tools_2.14.0
> zlibbioc_1.0.0
>
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