Question: Trying to download VIPER
0
gravatar for rakhatib
26 days ago by
rakhatib0
rakhatib0 wrote:

Hello,

I am trying to download VIPER. I downloaded the most up to date version of R. I inputed this:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

and received this:

Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installation path not writeable, unable to update packages: boot, foreign,
  KernSmooth, mgcv, nlme

I am on a computer that has adminstrative access and abilities. Please let me know if you know how to fix this bug so I can keep going forward.

Thank you!!!

software error viper • 63 views
ADD COMMENTlink modified 26 days ago by Steve Lianoglou12k • written 26 days ago by rakhatib0

Be careful, though. It seems like viper is on "deprecation watch" since the package is (apparently) not being properly updated/maintained(?)

https://support.bioconductor.org/p/123439/

ADD REPLYlink written 26 days ago by Steve Lianoglou12k
Answer: Trying to download VIPER
0
gravatar for James W. MacDonald
26 days ago by
United States
James W. MacDonald51k wrote:

The message you are getting (presumably you are on Windows?) is simply telling you that you don't have privileges to update the packages that come by default with R. Which, generally speaking, isn't an issue for most people because those packages are pretty stable, having been around since like the late 1990's, and more to the point, most people who use Bioconductor probably don't ever use boot or foreign, or KernSmooth, etc.

Anyway, you haven't actually tried to install viper, which is all lower caps (and given that R is case-sensitive, that matters). You need to do

BiocManager::install("viper")
library(viper)

To use that package.

ADD COMMENTlink written 26 days ago by James W. MacDonald51k
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