Unable to reload Rdoc

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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.
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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

Brian D. Ripley,                  ripley at 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
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")
To avoid this problem, the latest version of devtools has show_rd(),
which allows you to preview an Rd file in R without having to
reinstall the package.  This was actually really simple to implement,
and I don't know why I didn't think of it ages ago - it's certainly
made my workflow much smoother.

Hadley
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/
Related: To simplify reloading a help page after restarting R, I do
have the following in my ~/.Rprofile:

# Always only the HTML help on the same port
local({
  port <- sum(c(1e3,10)*as.double(R.Version()[c("major", "minor")]));
  ports <- 10*port + 0:9;
  options(help.ports=ports);
});

# Try to start HTML help server
tryCatch({
  if (interactive()) {
    tools::startDynamicHelp();
  }
}, error = function(ex) {
  print(ex);
})

That way the URL for the help page remain the same (as long as you
only run one R session) and the internal web server is up and running
(no need for help.start()).

My $.02

/Henrik
On Fri, Jan 27, 2012 at 3:47 AM, Mark Cowley <m.cowley at garvan.org.au> 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.

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")
To avoid this problem, the latest version of devtools has show_rd(),
which allows you to preview an Rd file in R without having to
reinstall the package. ?This was actually really simple to implement,
and I don't know why I didn't think of it ages ago - it's certainly
made my workflow much smoother.

Hadley

--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Gentlemen,
Thanks for your insights, all 3 hints are very useful.

Mark

Related: To simplify reloading a help page after restarting R, I do
have the following in my ~/.Rprofile:

# Always only the HTML help on the same port
local({
 port <- sum(c(1e3,10)*as.double(R.Version()[c("major", "minor")]));
 ports <- 10*port + 0:9;
 options(help.ports=ports);
});

# Try to start HTML help server
tryCatch({
 if (interactive()) {
   tools::startDynamicHelp();
 }
}, error = function(ex) {
 print(ex);
})

That way the URL for the help page remain the same (as long as you
only run one R session) and the internal web server is up and running
(no need for help.start()).

My $.02

/Henrik

On Fri, Jan 27, 2012 at 6:15 AM, Hadley Wickham <hadley at rice.edu> wrote:
On Fri, Jan 27, 2012 at 3:47 AM, Mark Cowley <m.cowley at garvan.org.au> 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.

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")
To avoid this problem, the latest version of devtools has show_rd(),
which allows you to preview an Rd file in R without having to
reinstall the package.  This was actually really simple to implement,
and I don't know why I didn't think of it ages ago - it's certainly
made my workflow much smoother.

Hadley

--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel