[BioC] Problem installing \'survival\' package/ Fix request + other options?

[James W. MacDonald]

Hi Ranjani,

On 7/12/2013 5:02 PM, Ranjani R [guest] wrote:
> Hi,
> I have to generate Kaplan-Meier curves and do some survival analysis. From what I understand the 'Survival' package in R is the best bet (please give me other options if you think otherwise).
> I've seldom had trouble installing any packages in R - but this one is having me puzzled. I do not have any 'older' versions of the package installed:
>
> install.packages("survival")
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'http://cran.cs.wwu.edu/bin/windows/contrib/2.15/survival_2.37-4.zip'
> Content type 'application/zip' length 3040152 bytes (2.9 Mb)
> opened URL
> downloaded 2.9 Mb
>
> package ‘survival’ successfully unpacked and MD5 sums checked
> Warning: cannot remove prior installation of package ‘survival’
>
> The downloaded binary packages are in<...edited>
>
> library(survival)
> Error in library(survival) : there is no package called ‘survival’
>
> What am I doing incorrectly?

First, you are sending this question to the wrong list. The survival 
package isn't part of BioC, so you should be asking on R-help.

Second, the survival package is part of the set of recommended packages, 
and comes by default with all binary installations of R. 
(http://cran.r-project.org/doc/FAQ/R-FAQ.html#Add_002don-packages-from-CRAN)

Oh wait, there are three!

Third, using an outdated version of R.

Upgrade R to 3.0.1, and you will have a functioning survival package 
already installed.

Best,

Jim

>
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099