Recently, i was trying to using trinity to do Differential Expression Analysis, which need to install the edgeR first.

After installing the package with two steps:

 > source("http://bioconductor.org/biocLite.R")
 > biocLite('edgeR')

i got some error messages as following:

BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.0 (2015-04-16).
Installing package(s) 'edgeR'
also installing the dependency 'limma'

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/limma_3.26.9.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/limma_3.26.9.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '405 Not Allowed'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'limma' failed
trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/edgeR_3.12.1.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/edgeR_3.12.1.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open: HTTP status was '405 Not Allowed'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'edgeR' failed

When i try to download the source package of limma from http://bioconductor.org/packages/3.2/bioc/html/limma.html

, it reports "405" not found.

Any help will be appreciate.

The error messages show that there is a problem with your internet connection or with your browser. We can't help you with that. The code you give will work fine if you have a fully working internet connection.

Of course, as Yunshen has mentioned, you should use the current version of R, which is R 3.3.1.

The current Bioconductor release version is 3.3, compatible with R 3.3. It seems you are not using an old version of R. Please update your R to the latest version before you try it again.