Depending on what you want to do with that file, there may be no need to
uncompress
read.table(), e.g., works fine with the compressed version.
Benno
On Feb 1, 2012, at 2:04 AM, Luke Miller wrote:
> 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 <[email protected]> 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
>>
>> ______________________________________________
>> [email protected] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> [email protected] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Benno Pütz
Statistical Genetics
MPI of Psychiatry
Kraepelinstr. 2-10
80804 Munich, Germany
T: ++49-(0)89-306 22 222
F: ++49-(0)89-306 22 601
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