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Question: R 3.1.1 - Update error
0
gravatar for AJC
3.0 years ago by
AJC0
United States
AJC0 wrote:

Hello R users,

I'm relatively new to advanced R analysis and I'm updating a bunch of packages. I received some warning messages while I was installing it. Is it okay for me to leave it like this? My warning messages are copied and pasted below:

> update.packages(ask='graphics',checkBuilt=TRUE)
Warning: package 'boot' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'class' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'cluster' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'codetools' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'KernSmooth' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'MASS' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'mgcv' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated
Warning: package 'nlme' in library 'C:/Users/voicelab/R/R-3.1.1/library' will not be updated

 

Thank you!

 

ADD COMMENTlink modified 3.0 years ago by James W. MacDonald45k • written 3.0 years ago by AJC0
2
gravatar for James W. MacDonald
3.0 years ago by
United States
James W. MacDonald45k wrote:

This isn't really the place for your question, as it isn't Bioconductor oriented. In addition, if you are trying to update Bioconductor packages, that's not how you do it. Instead you want to do

source("http://www.bioconductor.org/biocLite")

## or if you have already done that before, then just

library(BiocInstaller)

biocLite()

I should also note (pedantically, I know) that you have not got an error, but a warning. This warning usually arises when you have packages installed in a place that you don't have write access (e.g., usually if you install R as an administrator, then run it as a regular user, which is pretty much how you should do it). As an example, if I run your code, I get

Warning: package 'boot' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'class' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'cluster' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'codetools' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'KernSmooth' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'MASS' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'Matrix' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'mgcv' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated
Warning: package 'nlme' in library 'C:/Program Files/R/R-3.1.0/library' will not be updated

Because I don't have write access to that directory as a regular user. If I had used biocLite(), I would get

Warning messages:
1: package ‘BiocInstaller’ was built under R version 3.1.2
2: installed directory not writable, cannot update packages 'BiocStyle', 'boot',
  'class', 'cluster', 'codetools', 'KernSmooth', 'MASS', 'Matrix', 'mgcv',
  'nlme'

Which is obviously a bit more informative.

ADD COMMENTlink written 3.0 years ago by James W. MacDonald45k

Thank you for your assistance. Actually your way worked. I used biocLite() and I didn't get any warning messages. :-)

ADD REPLYlink written 3.0 years ago by AJC0
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