Henrik Bengtsson HenrikBengtsson

R package statuses

Package

RSP: Including file into Markdown

This can be done using the <%@include file="..."%> RSP preprocessing construct.

From R:

> R.rsp::rfile('main.md.rsp', postprocess=FALSE)
RspFileProduct:
Pathname: C:/Users/hb/braju.com.R/R.rsp/main.md
File size: 66 bytes

Agilent adds random TABs to end of data rows?!?

Below are the first few lines(*) of two files exported from the Agilent CytoGenomics Software. These files are plain text files with a few "metadata" rows before the actual tab-delimited data begins. The tab-delimited data appears to have a header row with tab-delimited column names followed by corresponding tab-delimited data rows. But it also appears as if there are "random" TABs (ASCII 0x09 = '\t') added to the end of either to header row or the data rows. What's up with that?

PS. (*) I cut out the top few lines by reading the files as a binary file in order to remove the risk of it being me/my editor introducing these TAB outliers. Also, I've verified using binary diff that these example files are identicial to the top of the full files.

Function to count TABs in a string

> countTABs <- function(x) sum(charToRaw(x) == cha

The overhead of method dispatching can be noticable, particularly if done on small objects and it adds up if doing many many times. For instance,

> add <- function(a,b) UseMethod("add")
> add.integer <- function(a,b) a+b

gives with method dispatching:

> system.time({ for (kk in 1:10e6) add(1L, 2L) })
  user  system elapsed
35.43 0.05 35.70

	<html>
	<style>
	body {
	font-size: 80%;
	}
	</style>
	<body>
	<head>
	<title>Speedtest benchmarks (2014-02-23 -- 2014-04-19)</title>
	</head>

	<%--------------------------------------------------------------
	Usage:
	md <- R.rsp::rfile('table-pandoc.md.rsp', postprocess=FALSE)
	pdf <- gsub("md$", "pdf", md)
	system2("pandoc", args=c(normalizePath(md), "-o", pdf))
	!pdf # Opens PDF in viewer

	Requires Pandoc [http://johnmacfarlane.net/pandoc/] and
	LaTeX, because Pandoc uses LaTeX to generate PDFs.
	--------------------------------------------------------------%>

	source("mixedsortRoman.R")

	# Basics
	yi <- c(1, 5, 10, 50, 100)
	print(yi)
	## [1] 1 5 10 50 100

	yr <- as.character(as.roman(yi))
	print(yr)
	## [1] "I" "V" "X" "L" "C"

	#######################################################################
	# rforge2git.R by Henrik Bengtsson
	#
	# USAGE:
	#
	# Rscript rpkg_svn2git.R <pkg>
	#
	# EXAMPLE:
	# Rscript rpkg_svn2git.R r-forge:r-dots/R.menu
	# Rscript rpkg_svn2git.R bioc-devel:illuminaio

	source("https://gist.githubusercontent.com/HenrikBengtsson/ed1eeb41a1b4d6c43b47/raw/ebe58f76e518dd014423bea466a5c93d2efd3c99/readtable-fix.R")

	kkk <- c("a\tb",
	"3.14\tx")

	colClasses <- c(a="numeric", b="character")
	data <- read.table(textConnection(kkk),
	sep="\t",
	header = TRUE,
	colClasses = colClasses)

	## Identify installed packages that fail to load
	rscript <- function(...) {
	system2(file.path(R.home("bin"), "Rscript"), ...)
	}

	works <- function(pkg) {
	## Need to call in separate R session to not use up all DLLs
	rcmd <- sprintf("cat(isTRUE(requireNamespace('%s')))", pkg)
	as.logical(rscript(args=c("-e", dQuote(rcmd)), stdout=TRUE))
	}