The I key on the keyboard of my 12 year old Dell laptop has become very difficult to use (need to press VERY HARD to produce an I), so I am considering upgrading to my 10 year old Macbook Pro. I had installed dual boot Ubuntu 14.04 on it several years ago, so I fired that up, then ran update-manager, clicked to upgrade to ubuntu 16.04, did that, restart, click to upgrade to ubuntu 18.04, restart, then I have my fresh Ubuntu LTS system. Now what? Let’s get emacs + ess + R working.

First some APT packages:

sudo aptitude install emacs ess aptitude \ #basics
     r-recommended libcairo-dev libtiff-dev \ #R
     default-jre default-jdk \ #for java
     libbz2-dev liblzma-dev zlib1g-dev libcurl4-gnutls-dev xorg-dev \ #r
     texlive ghostscript texlive-fonts-extra texinfo \ #r manuals
     libxml2-dev libssl-dev \ #some packages
     texlive-science \ #for algorithm.sty
     r-cran-rgl \ #for 3dviz
     tcl-dev tk-dev #for library(tcltk), library(loon)

Then I downloaded the R-3.6.2 source code and compiled it, similar to install-r-devel.sh. Also installed parts of those startup files (.emacs, .Rprofile, .bashrc).

I had some troubles redoing the tikz figures in https://github.com/tdhock/PeakSegFPOP-paper with the most recent version of the tikzDevice R package. It seems that the tikzDevice package now calculates font metrics (width/height) using a file in a temporary directory (rather than the current directory). This is an issue in this project because I told tikzDevice to calculate metrics using the same jss document class as the final latex file:

options(tikzDocumentDeclaration="\\documentclass{jss}")

but I put the jss.cls file in the project directory. So when tikzDevice tries to compute font metrics (from a temporary directory) it stops me with an error, can’t find jsslogo.jpg:

``` tdhock@maude-MacBookPro:~/projects/PeakSegFPOP-paper$ R –vanilla -e ‘options(tikzDocumentDeclaration=”\documentclass{jss}”);tikzDevice::tikzTest()’ … TeX was unable to calculate metrics for:

A ... (/tmp/Rtmp12xHO8/tikzDevice25013d1aafd5/tikzStringWidthCalc.tex ... (/usr/share/texmf/tex/latex/R/tex/latex/jss.cls ...  ! LaTeX Error: File `jsslogo' not found.  ``` The output above shows that (1) the test tried to compute font metrics for A via a temporary file then (2) found jss.cls under /usr but (3) could not find jsslogo graphics file.

There are a number of fixes for this issue:

  • put jsslogo.jpg in ~/texmf/tex which is the user-specific directory which pdflatex searches for input tex and image files (see kpsewhich, kpsepath, kpsewhere).
  • use \documentclass{article} or \documentclass[nojss]{jss} which does not require the jsslogo.jpg image.
  • set TEXINPUTS environment variable to add project directory containing the jsslogo.jpg image.
  • add jsslogo.jpg under the /usr/share/texmf/tex/latex/R directory which the debian pacakge copies from the R-src/share/texmf directory. R-core doesn’t want to include jsslogo.jpg though, so this won’t be a general solution any time soon. You can do it on your own system using e.g. sudo cp jsslogo.jpg /usr/share/texmf/tex/latex/R/tex/latex but you need to run sudo mktexlsr after in order to rebuild the tex path search data files.