In Linux bash, I can use something like
history | egrep "df"
and it will list all instances of my history that have the pattern "df" in them.
I am trying to find a similar syntax for R software. I found something similar here (history search backward in R), however, the suggestion in the first answer did not seem to work.
Based off that answer, I tried the following in R:
> history(pattern="df\\(")
> history(pattern="df(")
> history(pattern="df")
But got no history commands with pattern "df" outputted to console (or outputted to anywhere else I could see).
Thank you...
This alternate version works for me:
grep("df", readLines(".Rhistory"), value=T)
The history version also did not work for me. The docs mention that the history functions are somewhat implementation dependent. For example, in Rstudio, history() returns nothing.
Also, you may need to run savehistory() before the grep because your console may buffer the history for a while before actually writing it to file.
Related
Is there a comprehensive list somewhere of what you can pass to R CMD CHECK? I don't see anything in the manual but it's brutal to read. It'd be great if every line of this output could be run independently or if I could at least skip some things but I don't see a comprehensive list describing how to do this.
Even better would be something I could use like
check_dependencies()
check_executable_files()
check_hidden_files()
For context, I had a note about large file sizes that was hard to debug (it was plotly using it's full JS library in my vignettes) and devtools::check() took 3 minutes each time I ran it.
As rawr# points out, the "official" answer is to run R CMD check --help, which will give the most accurate results for the version of R you are running.
Still, it is surprisingly difficult to find this info online. It would be nice not to need the terminal to look this up... so I'm filing this answer with some pointers in the right direction for anyone else that manages to Google their way to this Q&A:
This permalink highlights the documentation as of this writing, but that will stale as the function evolves.
tools/R/check.R is the correct file at HEAD; search for "Usage <- function", where the contents of R CMD check --help are maintained. (in principle, this could also change, but this anchor has remained accurate for the entire 12-year history of the R implementation of R CMD check)
Is there an easy way to have R record all input and output from your R session to disk while you are working with R interactively?
In R.app on Mac OS X I can do a File->Save..., but it isn't much help in recovering the commands I had entered when R crashes.
I have tried using sink(...,split=T), but it doesn't seem to do exactly what I am looking for.
Many of us use ESS / Emacs for this very reason. Saving old sessions with extension '.Rt' even gives you mode-specific commands for re-running parts of your session.
Greg Snow wrote recently on the R-help list (a very valuable resource, SO R people!):
"You may also want to look at ?TeachingDemos::txtStart as an alternative to sink, one advantage is that the commands as well as the output can be included. With a little more work you can also include graphical output into a transcript file."
r-help
Check out the savehistory() command
I'm not sure yet how to answer an answer, but there is an updated version of Ranke's vim r-plugin called r-plugin2 available here. It seems more user-friendly and robust than the original.
Emacs is good, but for those of us with a vi preference there's the vim-r plugin at:
http://www.uft.uni-bremen.de/chemie/ranke/index.php?page=vim_R_linux
It works brilliantly and has a tiny memory footprint.
Is there something like the Common Lisp function DRIBBLE or Unix command tee in R?
Specifically, I want everything I type and everything R prints back to me to be appended to a file (tee only captures stdout; I want everyting: errors, warnings, print, cat, my input).
I found a 10 year old message on the subject which offers a weak version of that (it does not capture the output from cat/print).
The standard function sink only captures (not duplicates) the R's output; and it does not capture my input.
Is there a better way?
Look at the txtStart function (and related functions) in the TeachingDemos package. I think that it does everything you want except capturing errors (and the TaskCallback system in the R guts needs to be updated for that to happen).
The other option is to run R inside of another environment such as ESS (inside of Emacs) (there are others, but I am less familiar with them). Then everything is captured in the editor/buffer and can be saved to a file.
Note that the sink function does have a split argument that works like tee to show the output on screen as well as duplicate it to the file, but it still only does the output, not the input commands.
You probably want sink() -- see help(sink) for examples.
Has anyone managed to get color syntax-highlighting working in the output of Sweave documents? I've been able to customize the output style by adding boxes, etc. in the Sweave.sty file as follows:
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontseries=bc,frame=single}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{frame=leftline}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontseries=bc}
And I can get the minted package to do syntax highlighting of verbatim-code blocks in my document like so:
\begin{minted}{perl}
use Foo::Bar;
...
\end{minted}
but I'm not sure how to combine the two for R input sections. I tried the following:
\DefineVerbatimEnvironment{Sinput}{minted}{r}
\DefineVerbatimEnvironment{Scode}{minted}{r}
Any suggestions?
Yes, look at some of the vignettes for Rcpp as for example (to pick just one) the Rcpp-FAQ pdf.
We use the highlight by Romain which itself can farm out to the hightlight binary by Andre Simon. It makes everything a little more involved---Makefiles for the vignettes etc pp---but we get colourful output from R and C/C++ code. Which makes it worth it.
I have a solution that has worked for me, I have not tried it on any other systems though so things may not work out of the box for you. I've posted some code at https://gist.github.com/797478 that is a set of modified Rweave driver functions that make use of minted blocks instead of verbatim blocks.
To use this driver just specify it when calling the Sweave function with the driver=RweaveLatexMinted() option.
Here's how I've ended up solving it, starting from #daroczig's suggestion.
\usepackage{minted}
\renewenvironment{Sinput}{\minted[frame=single]{r}}{\endminted}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{frame=leftline}
\DefineVerbatimEnvironment{Scode}{Verbatim}{}
While I was at it, I needed to get caching working because I'm using large data sets and one chunk was taking around 3 minutes to complete. So I wrote this zsh shell function to process an .Rnw file with caching:
function sweaveCache() {
Rscript -e "library(cacheSweave); setCacheDir(getwd()); Sweave('$1.Rnw', driver = cacheSweaveDriver)" &&
pdflatex --shell-escape $1.tex &&
open $1.pdf
}
Now I just do sweaveCache myFile and I get the result opened in Preview (on OS X).
This topic on tex.StackExchange might be interesting for you, as it suggest loading the SweaveListingUtils package in R for easy solution.
Is there an easy way to have R record all input and output from your R session to disk while you are working with R interactively?
In R.app on Mac OS X I can do a File->Save..., but it isn't much help in recovering the commands I had entered when R crashes.
I have tried using sink(...,split=T), but it doesn't seem to do exactly what I am looking for.
Many of us use ESS / Emacs for this very reason. Saving old sessions with extension '.Rt' even gives you mode-specific commands for re-running parts of your session.
Greg Snow wrote recently on the R-help list (a very valuable resource, SO R people!):
"You may also want to look at ?TeachingDemos::txtStart as an alternative to sink, one advantage is that the commands as well as the output can be included. With a little more work you can also include graphical output into a transcript file."
r-help
Check out the savehistory() command
I'm not sure yet how to answer an answer, but there is an updated version of Ranke's vim r-plugin called r-plugin2 available here. It seems more user-friendly and robust than the original.
Emacs is good, but for those of us with a vi preference there's the vim-r plugin at:
http://www.uft.uni-bremen.de/chemie/ranke/index.php?page=vim_R_linux
It works brilliantly and has a tiny memory footprint.