CRAN/ Bioconductor package installs fail: Error: Line starting '<!DOCTYPE HTML PUBLI ...' is malformed

Asked 21/8, 2015 at 2:24 Answered 21/8, 2015 at 2:45

Solved r http-redirect installation package cran

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??

Cedric answered 21/8, 2015 at 2:24 Comment(1)

This is a generic issue with any package when trying to download from an URL that is a redirect. – Stile 23/2, 2017 at 23:49

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!

Cedric answered 21/8, 2015 at 2:45 Comment(4)

That should still work. And if you do what I suggested in my answer above, you will no longer have to select a mirror as you will already have done so in the Rprofile.site file. – Sagesagebrush 21/8, 2015 at 2:53

Moreover you should read up on https and why you should use it. You may need to set the download.file.method. – Sagesagebrush 21/8, 2015 at 3:0

For me, specifying method="wget" works; but method="libcurl" (the default) doesn't, even though curl should support https. – Komara 15/10, 2015 at 20:42

See capabilities()[["libcurl"]] which is likely false meaning an insufficient curl library was found when R was built. The issue is local to your machine or distro or versions -- whichever is responsible for the binary. – Sagesagebrush 21/11, 2015 at 13:23

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.

Sagesagebrush answered 21/8, 2015 at 2:31 Comment(0)

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