Dan Keshet
2013-Jun-20 18:46 UTC
[R] [SOLVED] Re: "Error: cannot allocate vector of size 1.9 Gb" when loading xtable help
Solved on my end. Turned out to be caused by cyclic dependencies in our (internal) packages. Attempts to install/load them all caused wonky things to happen later on. On Sat, Jun 15, 2013 at 6:18 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:> On 13-06-14 7:02 PM, Dan Keshet wrote: >> >> I am using xtable version 1.7-1 built for R 3.0.1 on: >> >> R version 3.0.1 (2013-05-16) >> Platform: i686-pc-linux-gnu (32-bit) >> >> Sometimes, not every time, when I load xtable or attempt to load the >> help, I get an error such as this "Error: cannot allocate vector of >> size 1.9 Gb" (Stacktrace from recover() below). >> >> Other times, when loading packages that depend on xtable, I get an >> error such as this: >> >> Loading required namespace: xtable >> Error in assign(identifier, list(name, description, identifier, help, : >> lazy-load database 'P' is corrupt >> >> I have attempted to reinstall the package using >> install.packages("xtable", type="source"), but the error persists (and >> the xtable.rdb file is identical). >> >> I have also tried this on macs and gotten the same error. >> >> Thank you for any help. >> >> ------------- >>> >>> ?xtable >> >> Error: cannot allocate vector of size 1.9 Gb > > > I would guess this is not related to the xtable help page, but is a sign of > something being corrupted (e.g. an out of range write in memory), and this > is just a symptom of the corruption. > > If we could make this reliably reproducible, we could track it down, but > without that, it is nearly impossible. > > Could try starting an empty R session (nothing reloaded from .Rdata), > run until you trigger the error, then save the session history? See if > replaying that history triggers the error again in the same place. If so, > see if you can shrink it to a minimal script that others can try, and post > that. > > Duncan Murdoch > >> >> Enter a frame number, or 0 to exit >> >> 1: print("/usr/local/analytics/rlibs/xtable/help/xtable") >> 2: >> print.help_files_with_topic("/usr/local/analytics/rlibs/xtable/help/xtable" >> 3: tools::Rd2txt(.getHelpFile(file), out = tempfile("Rtxt"), package >> pkgname >> 4: prepare_Rd(Rd, defines = defines, stages = stages, fragment = fragment, >> ... >> 5: .getHelpFile(file) >> 6: tools:::fetchRdDB(RdDB, basename(file)) >> 7: lazyLoadDBexec(filebase, fun) >> 8: fun(environment()) >> 9: fetch(key) >> >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >