[Bioc-devel] Need help on biomaRt

Sean Davis seandavi at gmail.com
Tue Jun 2 17:16:45 CEST 2009


On Tue, Jun 2, 2009 at 11:06 AM, Zhu, Julie <Julie.Zhu at umassmed.edu> wrote:
> Hi Florian,
>
> The following error occurred when I tried to perform R CMD check RCurl for the version 0.97-3. Do you have any suggestion to get Rcompression? Thanks!
>
> new-host-3:~/Documents/download _lzh217$  R CMD check RCurl
> * checking for working pdflatex ... OK
> * using log directory '/Users/_lzh217/Documents/download/RCurl.Rcheck'
> * using R version 2.10.0 Under development (unstable) (2009-05-20 r48588)
> * using session charset: ASCII
> * checking for file 'RCurl/DESCRIPTION' ... OK
> * this is package 'RCurl' version '0.97-3'
> * checking package name space information ... OK
> * checking package dependencies ... ERROR
> Packages required but not available:
>  Rcompression

Just a quick check--looks like Rcompression is here:

http://www.omegahat.org/Rcompression/index.html

It also appears that it is not yet mirrored by CRAN.

Sean

>> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-05-20 r48588)
> i386-apple-darwin8.11.1
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] multtest_2.1.0     Biobase_2.5.2      biomaRt_2.1.0
>
> -----Original Message-----
> From: bioc-devel-bounces at stat.math.ethz.ch on behalf of Julie Zhu
> Sent: Fri 5/29/2009 11:42 AM
> To: Florian Hahne
> Cc: bioc-devel at stat.math.ethz.ch
> Subject: Re: [Bioc-devel] Need help on biomaRt
>
> Florian,
>
> Thank you very much for the great news!
>
> Best regards,
>
> Julie
>
> On 5/29/09 11:33 AM, "Florian Hahne" <fhahne at fhcrc.org> wrote:
>
>> The problem was fixed by Duncan Temple Lang in the latest RCurl
>> version 0.97-3 which is available from Omegahat
>> (http://www.omegahat.org/RCurl/
>> )
>> The automatic updates on our build systems should pick this up any
>> time now, so all you need is patience for one or two more days :)
>> Florian
>>
>>
>> On 28.05.2009, at 11:32, Julie Zhu wrote:
>>
>>> Hi,
>>>
>>> With the help from Herve, we found out that the devel version of
>>> biomaRt is
>>> broken with the new Rcurl version 095-1. This is confirmed by the
>>> build
>>> system:
>>>
>>> http://bioconductor.org/checkResults/2.5/bioc-LATEST/biomaRt/wilson2-buildsr
>>> c.html
>>>
>>> As you can see, it's broken on Linux and Mac OS. It looks OK
>>> on the Window build machine because this machine is using an
>>> older version of RCurl (0.94-1).
>>>
>>> I am in the process of submitting a contributed package that relies on
>>> biomaRt and my package won't be passed to the reviewers until
>>> biomaRt is
>>> fixed. Could someone please fix the devel version of biomaRt? Thanks
>>> a lot
>>> for your kind help!
>>>
>>> Best regards,
>>>
>>> Julie
>>>
>>>
>>> *******************************************
>>> Julie Zhu, Ph.D
>>> Research Assistant Professor
>>> Program Gene Function and Expression
>>> University of Massachusetts Medical School
>>> 364 Plantation Street, Room 613
>>> Worcester, MA 01605
>>> http://www.umassmed.edu/pgfe/faculty/zhu.cfm
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>
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