[BioC] alternate /tmp for Bioconductor install

[Marcus Davy]

You should also be able to install core parts of bioconductor you require providing the appropriate arguement for a subset of packages which hopefully wont fill up your assigned temp directory. e.g.
getBioC("affy")  
## - packages "affy", "affydata",
##  "affyPLM", "annaffy", "matchprobes",
##   "gcrma", "makecdfenv", plus exprs.

see http://www.bioconductor.org/faq.html#getBioC, and the first few lines of getBioC.

You can also download packages separately (e.g. development versions of packages) and install them from the command line, R CMD INSTALL [package].tar.gz, many packages have dependancies (usual installation path on linux is something like /usr/local/lib/R/library/[package]).

Marcus


>>> Robert Citek <rwcitek at alum.calberkeley.org> 20/05/2005 8:47:40 a.m. >>>

On May 20, 2005, at 12:13 AM, Seth Falcon wrote:
> Sorry for the delay in response.  We've been busy preparing the
> Bioconductor 1.6 release.

No worries.  Thanks for the reply.  And thanks to you and everyone  
else involved in making 1.6.

> Robert Citek <rwcitek at alum.calberkeley.org> writes:
>
>> I'm attempting to install Bioconductor under Debian following the
>> instructions here:
>>
>>   http://www.bioconductor.org/faq.html#getBioC 
>>
>> Apparently, I don't have enough room in /tmp to untar the tar files.
>> What is the "R way" to specify an alternate /tmp folder to use while
>> installing Bioconductor?  "export TMPDIR=" comes to mind.
>>
>
> Yes, exporting TMPDIR should result in files downloaded by getBioC
> being placed in TMPDIR.

Great.  I'll give that a shot in the morning.

Since I last posted, my short-term work around was to create a soft- 
link, pointing /tmp to a partition with more room.  Once I did that  
BioC seemed to hum along nicely.  Since I did this on Thursday night,  
I suspect that I've already installed BioC 1.6.

Regards,
- Robert

_______________________________________________
Bioconductor mailing list
Bioconductor at stat.math.ethz.ch 
https://stat.ethz.ch/mailman/listinfo/bioconductor

______________________________________________________

The contents of this e-mail are privileged and/or confidenti...{{dropped}}