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.pathError 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]]
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 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
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/
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