[R] "Error: cannot allocate vector of size 1.9 Gb" when loading xtable help

Duncan Murdoch murdoch.duncan at gmail.com
Sat Jun 15 13:18:16 CEST 2013

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)
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> and provide commented, minimal, self-contained, reproducible code.

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