Dear all,

I have a question regarding installation of package "lumi" that i want to use to analyze Sentrix HumanRef-8 Expression BeadChip data. THis was successful on one machine I have at work which runs on Ubuntu 16.04 LTS. (nevertheless for this i had to install few linux libraries, see bottom if you want to check). But for another station running on 14.04 LTS, i have an error message related to xtable. see the output:

could you tell me where it comes from? Apparently this deals with building vignettes in latex to display the pdfs.

* installing *source* package ‘xtable’ ...
** package ‘xtable’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘OtherPackagesGallery.Rnw’
Error : running Stangle on vignette 'OtherPackagesGallery.Rnw' failed with message:
'arg' should be one of “verbatim”, “tex”, “hide”
ERROR: installing package indices failed
* removing ‘/home/anne/R/x86_64-pc-linux-gnu-library/2.14/xtable’
Warning in install.packages :
  installation of package ‘xtable’ had non-zero exit status

The downloaded packages are in
    ‘/tmp/RtmpIkSf1Z/downloaded_packages’ 

for info, my own installation on Ubuntu 16.04 LTS was successful after installation of the following packages:

sudo apt-get install libx11-dev
sudo apt-get install libglu1-mesa-dev
sudo apt-get install libcurl3-dbg
sudo apt-get install libxml2-dev
sudo apt-get install libssl-dev

A big thank you in advance!

David

I know this isnt exact what you are looking for, but I have dealt with many installations of packages in R that sometimes conflict and lead to errors such as these. What I do in these situations is just wipe everything and do a clean install. Sorry if this answer is too general, but this sorts it out for me and it doesn't actually take very long. I have a text file with the details which also includes a function to automatically install several packages at once with dependences:

# Find the pathways uninstall with rm -R
.libPaths()
#
sudo apt-get remove r-base-core
sudo apt-get remove r-base
sudo apt-get autoremove
#
sudo apt-get update
sudo apt-get -y install r-base
#

ipak <- function(pkg){
  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
  if (length(new.pkg))
    install.packages(new.pkg, dependencies = TRUE)
  sapply(pkg, require, character.only = TRUE)
}

# usage
packages <- c("ggplot2", "plyr", "reshape2", "RColorBrewer", "scales", "grid", 'ranger', 'glmnet', 'ggm', 'caret', 'doMC', 'FSelector', 'varSelRF')
ipak(packages)

Thanks for both answers. Yes, the R library was too old.

I actually upgraded Ubuntu (which was 12.04 contrary to what I thought at first) to 14.04, a new version of R (3.3) and i could install the library with no problem.