[BioC] Using the untar() with getGEOSuppFiles()

[Sean Davis]

On Sat, Mar 31, 2012 at 5:58 AM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> Hi all,
>
> I'm having a difficult time using the untar() after I retrieve the
> supp files using getGEOSuppFiles(). I tried it with gse15653 and
> gse12643. Both times different errors and I'm not quite sure what else
> to do. My goal is to retrieve the associated .cel files. Please help.

Thanks for the report.  This should be fixed now.  Give things a day
or so to move through the build system.

Sean


> Thanks.
>
> -Avoks
>
>> untar("GSE12643/GSE12643_RAW.tar", files = NULL, list = FALSE, exdir = ".",
> +       compressed = gzip, extras = NULL, verbose = FALSE,
> +       tar = Sys.getenv("TAR"))
> Error in rawToChar(block[seq_len(ns)]) :
>  embedded nul in string:
> '\023Ö\030ÛT×\002@Êe4-\024üWÙ&Ù?i0Ú‡"XRâæCGw÷\001\024uA<°§Êœºb•ýó•6…XR\004Q\036¤\v­4@ÔYÏ=m\020B éÙ9Ô¸ Ÿ²“áŠL €O ¹ô”Ð\0>í}]Dw¨®D\036‘'
>>
>> untar("GSE15653/GSE15653_RAW.tar", files = NULL, list = FALSE, exdir = ".",
> +       compressed = gzip, extras = NULL, verbose = FALSE,
> +       tar = Sys.getenv("TAR")
> + )
> Error in getOct(block, 100, 8) : invalid octal digit
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_xxx.1252  LC_CTYPE=English_xxx.1252
> [3] LC_MONETARY=English_xxx.1252 LC_NUMERIC=C
> [5] LC_TIME=English_xxx.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] affy_1.32.1     GEOquery_2.20.8 Biobase_2.14.0
>
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