Entering edit mode
Just FYI, I've been able to reproduce this, and the maintainer of
RCurl is
looking into the issue.
Michael
On Fri, Apr 30, 2010 at 4:28 AM, Li, Xuejun <xueli@coh.org> wrote:
> Michael,
> Thanks for your reply. Actually I didn't notice the change. I will
take a
> look next Monday.
>
> Best,
> Arthur
>
> ------------------------------
> *From:* Michael Lawrence [mailto:lawrence.michael@gene.com]
> *Sent:* Fri 4/30/2010 4:26 AM
> *To:* Li, Xuejun
> *Cc:* bioconductor@stat.math.ethz.ch
> *Subject:* Re: [BioC] rtracklayer - getTable
>
>
>
> On Thu, Apr 29, 2010 at 3:08 PM, Li, Xuejun <xueli@coh.org> wrote:
>
>> Hello everything,
>>
>> I have a question regarding the getTable function in the
rtracklayer
>> package. The code below used to work in previous R version, but it
>> doesn't for the current release. I can't figure out what the
problem is.
>> Can anyone give some hint? Thanks for your help!
>>
>>
>>
>> Best,
>>
>>
>>
>> Arthur Xuejun Li
>>
>> City of Hope Comprehensive Cancer Center
>>
>> Department of Information Science
>>
>> 1500 East Duarte Road
>>
>> Duarte, CA 91010 - 3000
>>
>> Ph: (626) 256-4673 ext. 65121
>>
>> Fax: (626) 471-7106
>>
>>
>>
>>
>>
>>
>>
>> > session <- browserSession()
>>
>> > genome(session) <- "mm9"
>>
>> > foo <- trackNames(session)[trackNames(session) =="rmsk"]
>>
>>
> Why not just set foo to "rmsk"?
>
>
>> > bar<- ucscTableQuery(session, foo)
>>
>> > bar1 <- getTable(bar)
>>
>> Error in if (st[["status"]] == 100) { :
>>
>> missing value where TRUE/FALSE needed
>>
>>
> This look something is happening in RCurl. I won't be able to look
into
> this for a couple of days, but do you know if your RCurl version
changed
> along with rtracklayer?
>
> Thanks,
> Michael
>
>
>> >
>>
>> >
>>
>> > sessionInfo()
>>
>> R version 2.11.0 (2010-04-22)
>>
>> x86_64-unknown-linux-gnu
>>
>>
>>
>> locale:
>>
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>>
>>
>> attached base packages:
>>
>> [1] stats graphics grDevices utils datasets methods
base
>>
>>
>>
>>
>> other attached packages:
>>
>> [1] rtracklayer_1.8.1 RCurl_1.4-1 bitops_1.0-4.1
>>
>> [4] ShortRead_1.6.0 Rsamtools_1.0.0 lattice_0.18-5
>>
>> [7] Biostrings_2.16.0 GenomicRanges_1.0.1 IRanges_1.6.0
>>
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] Biobase_2.8.0 BSgenome_1.16.0 grid_2.11.0 hwriter_1.2
>>
>> [5] tools_2.11.0 XML_2.8-1
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>
>
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