[Rd] Unable to reload Rdoc

From: Mark Cowley <m.cowley_at_garvan.org.au>
Date: Fri, 27 Jan 2012 20:47:35 +1100

Dear list,
I'm hoping the R guru's can help with an error i've been getting for at least a year during active package development.

I have a package loaded & spot a documentation bug, so I: edit the Rd file (or in the roxygen header + roxygenize); then R CMD BUILD,
then in the same R session, reload the library & lookup a man page, I always get this error: Error in fetch(key) : internal error -3 in R_decompress1

I've tried all ways of reloading the package that i'm aware of: detach then library
unloadNamespace then library

all lead to the error.

I see from ?detach:
... So detaching and re-attaching a package may not refresh some or all components of the package, and is inadvisable.

restarting the R session results in loading the updated man file, but do you have any ideas how to word around this & continue within the same R session?


# 1) using Hadley's devtools
> library(devtools)
> library(updateR) # my package under development
> install("~/src/R/updateR")
> install("~/src/R/updateR")

Installing updateR

* checking for file ‘/Users/marcow/src/R/updateR/DESCRIPTION’ ... OK
* preparing ‘updateR’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘updateR_1.0.4.tar.gz’

Warning in normalizePath(c(new, .Library.site, .Library), "/") :   path[3]="": No such file or directory

* installing *source* package ‘updateR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

> sessionInfo()

R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:

[1] tools     stats     graphics  grDevices datasets  utils     methods  
[8] base     

other attached packages:
[1] updateR_1.0.4 codetools_0.2-8 devtools_0.4

loaded via a namespace (and not attached): [1] RCurl_1.6-7

Mark Cowley, PhD

Pancreatic Cancer Program | Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia

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