[BioC] Problems installing sva and bladderbatch

James Wagner jamesrwagner at gmail.com
Fri Nov 11 16:09:56 CET 2011

OK, my apologies, I did look at the "Before you post" page but must
have skipped the point about sessionInfo(). It is an old version of R
and I will ask admins to upgrade to latest version of R. Thank you

On Fri, Nov 11, 2011 at 9:54 AM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> On Fri, Nov 11, 2011 at 9:44 AM, James Wagner <jamesrwagner at gmail.com> wrote:
>> Hello, when trying to install these packages using biocLite, I get the
>> messages  package "sva" is not available and likewise package
>> "bladderbatch" is not available. With sva I was able to download the tar.gz
>> file and install it using install.packages(), however with bladderbatch I
>> got the message
> A fundamental requirement for getting help through this mailing list is submission of the
> result of sessionInfo() for your R session where you are running into trouble.  I believe
> you have an outdated R, and that you must install R 2.14 and clean out any old biocLite images
> in your workspace, and start again.
>> Error : Invalid DESCRIPTION file
>> Package name and namespace differ.
>> The DESCRIPTION file contained the line "namespace auto", which when I
>> removed gave no further errors with the "install.packages()" command,
>> however then when I run library(bladderbatch) I get the warning message:
>> Warning message:
>> In loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
>> keep.source) :
>>  package 'bladderbatch' contains no R code and then with
>> data(bladderbatch) I get that data set 'bladderbatch' not found.
>> What is the best way to hack the DESCRIPTION file to get bladderbatch
>> actually working?
> If you have to ask you should never do it.  Do not modify DESCRIPTION.  If you do,
> no one will be able to help you reliably.
>> Thank-you
>>        [[alternative HTML version deleted]]
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