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

[Dan Keshet]

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)
>>
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>>
>