Installing R Packages Error in readRDS(file) : error reading from connection

Question

Whenever I try to install any package in R on Ubuntu 14.04, I'm getting the following error:

Error in readRDS(file) : error reading from connection

I already tried the methods given here but could not solve the problem.

Answer 1

I was facing the same error and I restarted R session, it worked for me.

Answer 2

1- Install the latest version of R form the CRAN and try to install a package.

2- If it is possible check it with another user account.

3- Try to install the R package locally.

4- If there is an RDS file created by the old version of R you may have another sort of problem, this is the warning from R help:

Warning

These functions have provided a stable interface since R 2.4.0 (when the storage of serialized objects was changed from character to raw vectors). However, the serialization format may change in future versions of R, so this interface should not be used for long-term storage of R objects.

On 32-bit platforms a raw vector is limited to 2^31 - 1 bytes, but R objects can exceed this and their serializations will normally be larger than the objects.

Ref: help(serialize)

Answer 3

If you have one or more incorrectly installed packages (e.g. because you had to force-reboot during installation) you need to re-install this/these package(s). You can find them using this code:

library(purrr)

.libPaths() %>%
set_names() %>%
map(function(lib) {
    .packages(all.available = TRUE, lib.loc = lib) %>%
    keep(function(pkg) {
        f <- system.file('Meta', 'package.rds', package = pkg, lib.loc = lib)
        tryCatch({readRDS(f); FALSE}, error = function(e) TRUE)
    })
})

This will return a nested list containing the broken packages:

$`/home/yourname/R`
[1] "brokenpkg"

$`/usr/lib64/R/library`
character(0)

$`/usr/share/R/library`
character(0)

You might need to delete the directories 00LOCK-<pkgname> that R created in the library location while trying to install the packages.

Answer 4

I had this error on Windows 10 after installing R 3.4.0 from 3.3.1 (all 64-bit). It was resolved by manually installing an unrelated package from CRAN (I used ggplot2). No idea what the root cause was, but perhaps this will work for you as well.

Output from my code:

> library(pacman)
> p_load(plyr, XLConnect, ggplot2, stringr, magrittr, kirkegaard, lubridate, weights, psych, psychometric, polycor, effsize, readr)
Installing package into ‘C:/Users/Emil/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Error in install.packages : error reading from connection
 Error in loadNamespace(name) : there is no package called ‘BiocInstaller’ 

Then I restarted R, and ran the same code:

> library(pacman)
> p_load(plyr, XLConnect, ggplot2, stringr, magrittr, kirkegaard, lubridate, weights, psych, psychometric, polycor, effsize, readr)
Installing package into ‘C:/Users/Emil/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Error in readRDS(dest) : error reading from connection

I.e. same code, different error. Odd. Then I restarted R again and installed a random package, then reran my code and it worked.

> install.packages("ggplot2")
Warning in install.packages :
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES.rds': HTTP status was '404 Not Found'
Installing package into ‘C:/Users/Emil/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES.rds': HTTP status was '404 Not Found'
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/ggplot2_2.2.1.zip'
Content type 'application/zip' length 2782171 bytes (2.7 MB)
downloaded 2.7 MB

package ‘ggplot2’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Emil\AppData\Local\Temp\RtmpCq4cFX\downloaded_packages
> library(pacman)
> p_load(plyr, XLConnect, ggplot2, stringr, magrittr, kirkegaard, lubridate, weights, psych, psychometric, polycor, effsize, readr)
Installing package into ‘C:/Users/Emil/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/effsize_0.7.1.zip'
Content type 'application/zip' length 36713 bytes (35 KB)
downloaded 35 KB

package ‘effsize’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Emil\AppData\Local\Temp\RtmpCq4cFX\downloaded_packages

effsize installed

So, error seems to have had something to do with pacman trying to install effsize.