This is simply not supported. Lazy-load databases are cached, and you
cannot expect to change them during the R session once they have been used.
Spend the few milliseconds needed to start a new session.
And R CMD Rdconv is a much simpler way to check a changed .Rd file.
On 27/01/2012 09:47, Mark Cowley wrote:
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,
R CMD INSTALL
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
devtools::install
devtools::reload
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.
You were warned ....
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?
cheers,
Mark
# 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
* DONE (updateR)
Reloading installed updateR
?get.full.path
Error in fetch(key) : internal error -3 in R_decompress1
2) using detach + library
$ R --vanilla
library(updateR)
# ?list.my.packages
detach(pos=2, unload=TRUE, force=TRUE)
#<<make a change to an Rd file>>
system("cd ~/src/R&& R CMD BUILD updateR&& R CMD INSTALL updateR")
library("updateR")
?list.my.packages
Error in fetch(key) : internal error -3 in R_decompress1
3) using unloadNamespace
$ R --vanilla
library(updateR)
# ?list.my.packages
unloadNamespace("updateR")
#<<make a change to an Rd file>>
system("cd ~/src/R&& R CMD BUILD updateR&& R CMD INSTALL updateR")
library("updateR")
?list.my.packages
Error in fetch(key) : internal error -3 in R_decompress1
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[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
-----------------------------------------------------
[[alternative HTML version deleted]]
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
