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I have just made a fresh Ubuntu 14.04 installation and installed R following the instructions at this link and this other one, selecting the Berkeley mirror as I always do.
On emacs (+ess), I am unable to install any CRAN or Bioconductor package at all, for example:
install.packages("ggplot2")
Or:
source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
I constantly get the following error:
Error: Line starting '<!DOCTYPE HTML PUBLI ...' is malformed!
Following on this other thread, I have just waited to see if the problem solved by itself, but after 2 days I keep getting the same error. Any suggestion??
522
Alright I already solved the problem, turns out when prompting to select a CRAN mirror, I was selecting
USA (CA1) [https]
Instead of
(HTTP mirrors)
This is a feature I had never seen...
Selecting HTTP mirrors brings me to the list of mirrors I was expecting, and selecting now
USA (CA1)
Makes the installation process work perfectly. Thanks!
167
Please show what
Rscript -e 'print(options("repos"))'
contains. For what it is worth, I set CRAN as well as two more drat this way and never have an issue:
## Example of Rprofile.site snippet
local({
r <- getOption("repos")
r["CRAN"] <- "http://cran.rstudio.com"
r["eddelbuettel"] <- "http://eddelbuettel.github.io/drat"
r["ghrr"] <- "http://ghrr.github.io/drat"
options(repos = r)
})
You can set CRAN, BioC and any other number of repositories this way.
23
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