[R] how to unzip files in R

Luke Miller millerlp at gmail.com
Wed Feb 1 02:04:15 CET 2012


Try the bzfile() function instead of unz(). You'll find that you're
taken to the same help page for both of those functions.

?bzfile

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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