[Bioc-devel] Need help on biomaRt

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

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