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.
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
-----------------------------------------------------
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