installing jackstraw from CRAN fails due to missing packages

[idc9]

problem

When I install jackstraw from CRAN it does not work because it fails to install two packages: qvalue and lfa e.g.

install.packages('jackstraw')
> library(jackstraw)
Error: package or namespace load failed for ‘jackstraw’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘lfa’

solution

After installing these two packages I can load jackstraw

# install.packages("devtools")
library("devtools")
install_github("Storeylab/lfa")   # see note for OS X users on lfa's github page
install_github("jdstorey/qvalue")

You might consider having these installed automatically or making them optional. Adding this as a note on the readme would also be helpful.

system details

> R.Version() 
$platform
[1] "x86_64-apple-darwin15.6.0"

$arch
[1] "x86_64"

$os
[1] "darwin15.6.0"

$system
[1] "x86_64, darwin15.6.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "4.3"

$year
[1] "2017"

$month
[1] "11"

$day
[1] "30"

$`svn rev`
[1] "73796"

$language
[1] "R"

$version.string
[1] "R version 3.4.3 (2017-11-30)"

$nickname
[1] "Kite-Eating Tree"

[ncchung]

Thanks for raising this issue. I've updated the README file to reflect your suggestion.

FYI, I had included biocViews: in the description file to automatically search and install the bioconductor packages (r-lib/devtools#700 (comment)). But it seems that trick doesn't work always.