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!

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.