From Mark.Bravington at csiro.au  Sun Nov  1 03:18:24 2009
From: Mark.Bravington at csiro.au (Mark.Bravington at csiro.au)
Date: Sun, 1 Nov 2009 13:18:24 +1100
Subject: [Rd] parse_Rd and/or lazyload problem
In-Reply-To: <4AEC4954.9070400@stats.uwo.ca>
References: <62C82B39B8A85E4B95A18F7F7B852F87055595B001@exvic-mbx03.nexus.csiro.au>,
	<4AEB61C4.4050300@stats.uwo.ca>
	<62C82B39B8A85E4B95A18F7F7B852F87055595B002@exvic-mbx03.nexus.csiro.au>,
	<4AEC4954.9070400@stats.uwo.ca>
Message-ID: <62C82B39B8A85E4B95A18F7F7B852F87055595B003@exvic-mbx03.nexus.csiro.au>

> Does this happen in R-patched?  I've seen similar errors in 2.10.0, but
> not in a current build.

Yes, still there in R-patched.

(Still haven't got to your code, this was in
> mine.  I'm reluctant to spend time on code that is messing with
> internals, because you might be using things in a way not intended by
> the author.  Now, if you can show me some code that demonstrates the
> problem without using internals directly, I'll follow up.)

I did try, but it's not completely possible, because 'makeLazyLoadDB' is internal and there is no public alternative (a pity-- it's useful). However, the problem(s) can be demonstrated without directly calling 'parse_Rd', and with 'lazyLoad' (public) instead of 'fetchRdDB' (private), as per "pointer 1" below. If you have a look at 'tools:::.install_package_Rd_objects', you'll see that my use of 'makeLazyLoadDB' is quite standard.

The problem is not easy to reproduce. It took 4-5 hours work to get the 3-line reproducible example that I posted, plus another couple since, so I'm also reluctant to spend more time...

The examples in my previous post still apply-- the first one involves just 3 statements-- but here are some more pointers I've unearthed since:


1. Sometimes 'fetchRdDB' or 'lazyLoad' called directly from the prompt doesn't work, but public 'Rd_db' (which directly calls 'fetchRdDB') does. I've experimented with copying the installed 'tools' package into a new library "d:/temp/fakelib", then stuff like this:

test> e <- new.env()
test> lazyLoad( 'd:/temp/fakelib/tools/help/tools', e) # original files tools.rdx, tools.rdb
test> e <- as.list( e) # force evaluation
test> tools:::makeLazyLoadDB( e, 'd:/temp/fakelib/tools/help/tools') # modify tools.rd*
test> e1 <- new.env()
test> lazyLoad( 'd:/temp/fakelib/tools/help/tools', e1)
test> as.list( e1) # try to force evaluation...
Error in as.list.environment(e1) : 
  cannot allocate memory block of size 2.7 Gb
test> 
test> Rd_db( 'tools', 'd:/temp/fakelib') # no probs !?


2. Sometimes 'fetchRdDB' or 'lazyLoad' will fail in one R session, but will work in a fresh session on exactly the same files. For example, after restarting R, the previous commands involving 'e1' work fine.

Mark

> 
> Duncan Murdoch
> 

>
>>> I'm encountering problems when making lazy-loadable databases of the output from 'parse_Rd'. The lazy-
>>> load database is of seemingly limitless size when I try to reload it... Admittedly I am using functions
>>> that I'm not really supposed to use, which is why this isn't a bug report, but there does seem to be
>>> something strange going on; my code is very similar to code that lives inside
>>> 'tools:::.install_package_Rd_objects'. The problems occur with just-released R2.10.0 on Windows.
>> object.size() has problems when working on Rd objects, because it counts
>> every environment separately, even though they may all be references to
>> the same one. I haven't looked at your code, but that could be a problem.
>>
>>
>
> Mark
>
> ________________________________________
> From: Duncan Murdoch [murdoch at stats.uwo.ca]
> Sent: 31 October 2009 08:59
> To: Bravington, Mark (CMIS, Hobart)
> Cc: r-devel at r-project.org
> Subject: Re: [Rd] parse_Rd and/or lazyload problem
>
> On 30/10/2009 12:50 AM, Mark.Bravington at csiro.au wrote:
>> I'm encountering problems when making lazy-loadable databases of the output from 'parse_Rd'. The lazy-load database is of seemingly limitless size when I try to reload it... Admittedly I am using functions that I'm not really supposed to use, which is why this isn't a bug report, but there does seem to be something strange going on; my code is very similar to code that lives inside 'tools:::.install_package_Rd_objects'. The problems occur with just-released R2.10.0 on Windows.
>
> object.size() has problems when working on Rd objects, because it counts
> every environment separately, even though they may all be references to
> the same one. I haven't looked at your code, but that could be a problem.
>
> Duncan Murdoch
>
>> The examples below use files which can be found at ftp://ftp.csiro.au/MarkBravington, but you'll obviously need to modify the paths. The file "scrunge.Rd" is just "Rdiff.Rd" from the 'tools' package. The file "fakepack.7z" should unzip to create a fake package with a DESCRIPTION file and a "man" directory that contains two Rd files.
>>
>> Transcript of first example:
>> eglist <- list( scrunge=tools:::prepare_Rd(  'd:/temp/scrunge.Rd',
>>     defines=.Platform$OS.type, stages='install', warningCalls=FALSE))
>> tools:::makeLazyLoadDB( eglist, 'd:/temp/ll', compress=FALSE)
>> tools:::fetchRdDB( 'd:/temp/ll')
>> # Error: cannot allocate vector of size 1.4 Gb
>>
>> The second example triggers an error with 'tools:::.install_package_Rd_objects' itself. It doesn't happen the first time, but frequently does after the Rd files have been changed. Transcript:
>>
>> # Make sure d:/temp/help/ is empty, then
>> test> tools:::.install_package_Rd_objects( 'd:/temp/fakepack', 'd:/temp')
>> test> tools:::fetchRdDB( 'd:/temp/help/temp')
>> # All good. Next, I *removed* one of the two Rd files in "d:/temp/fakepack/man", ...
>> # ...deleted "d:/temp/help/temp*", and tried again
>> test> tools:::.install_package_Rd_objects( 'd:/temp/fakepack', 'd:/temp')
>> test> tools:::fetchRdDB( 'd:/temp/help/temp')
>> Warning: Reached total allocation of 1535Mb: see help(memory.size)
>> Warning: Reached total allocation of 1535Mb: see help(memory.size)
>> Warning: Reached total allocation of 1535Mb: see help(memory.size)
>> Warning: Reached total allocation of 1535Mb: see help(memory.size)
>> Error: cannot allocate vector of size 1.9 Gb
>> # Or on other occasions I get
>> Error: internal error -3 in R_decompress1
>>
>> Mark Bravington
>> CSIRO CMIS
>> Hobart
>> Australia
>>
>> --please do not edit the information below--
>> Version:
>>  platform = i386-pc-mingw32
>>  arch = i386
>>  os = mingw32
>>  system = i386, mingw32
>>  status =
>>  major = 2
>>  minor = 10.0
>>  year = 2009
>>  month = 10
>>  day = 26
>>  svn rev = 50208
>>  language = R
>>  version.string = R version 2.10.0 (2009-10-26)
>> Windows XP (build 2600) Service Pack 2
>> Locale:
>> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>> Search Path:
>>  .GlobalEnv, ROOT, package:grDevices, package:ad, package:chstuff, package:handy2, package:tweedie, package:statmod, package:handy, package:debug, package:mvbutils, mvb.session.info, package:tools, package:tcltk, package:stats, package:graphics, package:utils, package:methods, Autoloads, package:base
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel



[Rd] parse_Rd and/or lazyload problem
Mark.Bravington at csiro.au