how to unzip files in R

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