gmbecker

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

gmbecker

```{r}
fancystopifnot = function(obj, condfun) {
    x = capture.output(str(obj))
    if(!condfun(obj))  stop(paste(c("Condition not met, got", x),
                                  collapse = "\n\t"))}

fancystopifnot(data.frame(x = sample(1:100, 10), 
                          y = sample(c("a", "b"), 10, replace=TRUE)),
               is.integer)
```

gmbecker

library(devtools) # someday this will be switchr ;-)
install_github("duncantl/CodeDepends")
library(knitr)
library(CodeDepends)

## package you're dealing with (pkgname) MUST be loaded before calling this
vignetteCoverage = function(pkgdir, pkgname = basename(pkgdir), vignexts = c(".Rmd", ".Rnw")) {
    vigns = list.files(file.path(pkgdir, "vignettes"), pattern = paste0("(", paste(vignexts, collapse="|"), ")"), full.names=TRUE)
    tmpfils = sapply(seq(along=vigns), function(x) tempfile( fileext=".R"))
    rfils = mapply(function(inp, out) knit(inp, out, tangle=TRUE), inp = vigns, out = tmpfils)

gmbecker

col1 <- runif (12^6, 0, 2)
col2 <- rnorm (12^6, 0, 2)
col3 <- rpois (12^6, 3)
col4 <- rchisq (12^6, 2)
df <- data.frame (col1, col2, col3, col4)

## process the rows

## slightly less than  3 times slower than Rcpp example here http://rstatistics.net/strategies-to-speed-up-r-code/  (on my machine)
## but written only in R

gmbecker

test gist contents

gmbecker

# R manifest
# Manifest type: package
# Dependency repositories: 5
# repo: http://bioconductor.org/packages/3.1/bioc
# repo: http://bioconductor.org/packages/3.1/data/annotation
# repo: http://bioconductor.org/packages/3.1/data/experiment
# repo: http://bioconductor.org/packages/3.1/extra
# repo: http://cran.fhcrc.org
"name","url","type","branch","subdir","extra"
"http://github.com/gmbecker/fastdigest","fastdigest","http://github.com/gmbecker/fastdigest","git","master",".",NA

gmbecker

happyfun = function(pat, txt) {
    m = gregexpr(pat, txt, perl=TRUE)[[1]];
    t = attr(m, "capture.start");
    mapply(function(st, end) substr(txt, st, end),
           st =  t,
           end =  t+attr(m, "capture.length")-1)
}

gmbecker

We set up knitr so it doesn't catch errors, then set
`options(error=recover)` to set up R's debug-on-error machinery.

We have to do one additional thing, before the options call though: 
trace the recover function with`sink(NULL)` to turn off the output 
capturing so the R console is useful when the debugging framework 
dumps us back into it. This has to happen before the options call
because that call grabs the `recover` object and stores it somewhere
so setting a trace on recover after the call won't affect the cached
version that gets called upon an error.

gmbecker

## this worked for me
df = data.frame("omg" = factor(sample(1:2, 100, replace=TRUE)), x = rnorm(100), y = rnorm(100))
ggplot(data=df) + aes(x = x, y = y, color = omg) + geom_point() + scale_colour_discrete(guide_legend(title="whaaat?\nok!"))

gmbecker

# R manifest
# Manifest type: session
# Dependency repositories: 5
# repo: https://bioconductor.org/packages/3.5/bioc
# repo: https://bioconductor.org/packages/3.5/data/annotation
# repo: https://bioconductor.org/packages/3.5/data/experiment
# repo: https://bioconductor.org/packages/3.5/extra
# repo: https://cran.rstudio.com
"name","url","type","branch","subdir","extra","version"
"switchrGist","https://cran.rstudio.com/src/contrib","CRAN","trunk",".",NA,"0.2.1"