[BioC] rpy save session and package downloads

[Hervé Pagès]

Hi Pete,

On 02/28/2011 03:34 PM, rna seq wrote:
> Hi Sean,
>
> Thanks for getting back. There are two questions, the first I will direct
> towards the rpy list as you suggest. But the second is that as you say these
> packages are loaded using "library", but once I log off a session, the
> packages that are loaded are lost once a session is over. I am trying to
> save these packages because some such as "BSgenome.Hsapiens.UCSC.hg19" are
> rather large.

What do you mean by "saving" a package? As Sean already explained,
packages are "installed" into R and then loaded in a session
using "library". When you quit the session, the loaded packages
are not "lost" (did you mean "deleted from the disk"?) and you
will of course be able to load them again next time you start a
session without having to re-install them. So you don't need to "save"
any package before you quit the session. There is no such mechanism
because it's not needed.

Cheers,
H.

>
> Pete
>
> On Mon, Feb 28, 2011 at 2:41 PM, Sean Davis<sdavis2 at mail.nih.gov>  wrote:
>
>>
>>
>> On Mon, Feb 28, 2011 at 3:48 PM, rna seq<rna.seeker at gmail.com>  wrote:
>>
>>> Dear R,
>>>
>>> Using Ubuntu 10.04 OS and R 2.10, I am running R through python using
>>> "rpy".
>>>
>>
>> Hi, Peter.
>>
>> This isn't really on-topic for the bioconductor list.  I would encourage
>> you to use the rpy support mechanisms for further details.
>>
>>
>>> I have noticed thatmy sessions are not saved and I am wondering if there
>>> is
>>> a way to do this.
>>
>>
>> You would need to save them.  See save().
>>
>>
>>> Also and more importantly. Is there a way to direct R to
>>> save downloaded packages in a specific file that will be recognized when
>>> the
>>> "saved" session is restored?
>>>
>>
>> I'm not sure what you mean here.  Packages are "installed" into R and then
>> loaded using "library".  Simply having a downloaded package in a file will
>> not allow you to use it in R--it must be installed.
>>
>> Sean
>>
>>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319