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
How are you trying to install xtable? It looks like you're building it from source, rather than installing the built tarball. Try
Or provide more details on what you are doing.
Also, it looks like (from the library path) you are using an old version of R (2.14, February, 2012; the current version is 3.3.0, May, 2016). I guess you are trying to install a brand-new version of xtable on an ancient version of R, so I'd really recommend updating your R as a first step.