[R] [SOLVED] Re: "Error: cannot allocate vector of size 1.9 Gb" when loading xtable help
dkesh at qcue.com
Thu Jun 20 20:46:04 CEST 2013
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.
>> 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
> Duncan Murdoch
>> Enter a frame number, or 0 to exit
>> 1: print("/usr/local/analytics/rlibs/xtable/help/xtable")
>> 3: tools::Rd2txt(.getHelpFile(file), out = tempfile("Rtxt"), package =
>> 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
>> PLEASE do read the posting guide
>> and provide commented, minimal, self-contained, reproducible code.
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