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

[Ovokeraye Achinike-Oduaran]

Thanks a bunch, Sean.

-Avoks

On Mon, Apr 9, 2012 at 4:47 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> You'll need version 2.23.1.  It is the current release version.
>
> Sean
>
> On Apr 9, 2012 10:39 AM, "Ovokeraye Achinike-Oduaran" <ovokeraye at gmail.com>
> wrote:
>>
>> Hi Sean,
>>
>> I still get thesame errors when I run the code as is. Has the fix gone
>> through the build system?
>>
>> Thanks.
>>
>> Avoks
>>
>> sessionInfo()
>>
>> R version 2.15.0 (2012-03-30)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_.1252  LC_CTYPE=English_.1252
>> [3] LC_MONETARY=English_.1252 LC_NUMERIC=C
>> [5] LC_TIME=English_.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] GEOquery_2.20.8 Biobase_2.14.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1
>>
>> On Sun, Apr 1, 2012 at 3:19 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> > 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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