Unable to install rmarkdown packages - r

Question

Here's what I got...
** Installing R Package Dependencies for R Markdown: 'rmarkdown', 'stringi'
[1/2] Installing rmarkdown...
trying URL 'http://cran.rstudio.com/src/contrib/rmarkdown_2.9.tar.gz'
Content type 'application/x-gzip' length 3246617 bytes (3.1 MB)
================================================[2/2] Installing stringi...
downloaded 3.0 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'http://cran.rstudio.com/src/contrib/rmarkdown_2.9.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 3152276 != reported length 3246617
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'http://cran.rstudio.com/src/contrib/rmarkdown_2.9.tar.gz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘rmarkdown’ failed
trying URL 'http://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.3.tgz'
Content type 'application/x-gzip' length 14636855 bytes (14.0 MB)
=========
downloaded 2.7 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'http://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.3.tgz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 2835937 != reported length 14636855
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'http://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.3.tgz': Timeout of 60 seconds was reached
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘stringi’ failed

Answer 1

You can stop all of that output after the first mention of Timeout of 60 seconds was reached. It appears you are experiencing network glitches, and R is not adapting to them well.
Three suggestions:
increase R's timeout, per #Phil's answer;
keep trying with install.packages(..) until it finally works, hoping luck will eventually smile on you; or
download externally, verify the files downloaded, then install manually.
Assuming the third, then using firefox/chrome/safari (or whatever you prefer), download the URLs present in your R console manually to a directory. I'll assume the local directory, but you can save them to where-ever you prefer.
AP <- available.packages()
AP[AP[,1] %in% c("rmarkdown", "stringi"),c("Package", "Version", "MD5sum", "Repository")]
# Package Version MD5sum Repository
# rmarkdown "rmarkdown" "2.9" "acd82da6a09f8e6564595dfa9039e032" "https://cran.rstudio.com/src/contrib"
# stringi "stringi" "1.7.3" "94c37221840cd9f5b7545c585d0c6b07" "https://cran.rstudio.com/src/contrib"
system("md5sum rmarkdown_2.9.tar.gz")
# acd82da6a09f8e6564595dfa9039e032 *rmarkdown_2.9.tar.gz
# [1] 0
(and repeat for stringi).
Assuming that the checksums match, then you can do
install.packages(c("rmarkdown_2.9.tar.gz", "stringi_1.7.3.tgz"), repos = NULL)
to install the downloaded files.

Answer 2

The error is that the timeout of 60 seconds is reached (i.e. it's taking too long to download). A workaround is to increase the timeout time:
options(timeout=120)
Or maybe longer if you need it