From htl10 at users.sourceforge.net  Thu Apr  7 20:31:35 2011
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Thu, 07 Apr 2011 19:31:35 +0100
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <19869.63540.370576.208443@stat.math.ethz.ch>
References: <255683.81856.qm@web29515.mail.ird.yahoo.com>	<AANLkTimDJbJ-u3wXOyvPB0EePf98AZ-R5duKVr+Guh-v@mail.gmail.com>	<19856.40809.236979.731769@stat.math.ethz.ch>	<4D91B5CC.1040500@users.sourceforge.net>	<AANLkTimuxb199-32D+043u9fNp7VsDjf5QD2qX3_Zjof@mail.gmail.com>	<AANLkTi=Tjjq9JtuzYp8x4Pp=gtg2eGT7C6RoaXehmX_W@mail.gmail.com>	<4D9D5F00.9040200@users.sourceforge.net>	<19869.37088.323145.396106@stat.math.ethz.ch>
	<19869.63540.370576.208443@stat.math.ethz.ch>
Message-ID: <4D9E0307.7070802@users.sourceforge.net>

Martin Maechler wrote:
>>>>>> Martin Maechler <maechler at stat.math.ethz.ch>
>>>>>>     on Thu, 7 Apr 2011 12:24:32 +0200 writes:
> 
>>>>>> "HL" == Hin-Tak Leung <htl10 at users.sourceforge.net>
>>>>>>     on Thu, 7 Apr 2011 07:51:44 +0100 writes:
> 
>     HL> Douglas Bates wrote:
>     >>> I isolated the problem and tested then committed a fix. I am
>     >>> going to ask Martin to upload the new release as I have gotten
>     >>> out of sync with some of his recent changes and he will, I
>     >>> hope, reconcile the branches and trunk.  If you need the fixed
>     >>> version immediately, say for testing, the changes are in the
>     >>> file Matrix/src/chm_common.c You can visit the SVN archive for
>     >>> the project, https://r-forge.r-project.org/scm/?group_id=61,
>     >>> click on the link to Browse Subversion Repository and go to
>     >>> pkg/Matrix/src/chm_common.c
>     >>> 
>     >>> I made the mistake that I chastised others for making,
>     >>> performing an operation on the result of a call to install and
>     >>> another value that may have required allocation of memory.
>     >>> The first time install is called on a particular string it
>     >>> allocates and SEXPREC, which may cause a garbage collection.
> 
>     HL> Matrix-for-R-2.13 at 2659 (0.999375-49) has the problem at a different place:
> 
> Are you sure that you really took  0.999375-49  and not its
> predecessor ???

The two errors look similiar but different (the previous one was about a 
REALSXP), and both are fairly reproducible.

As much as I can be sure, I guess. I overwrote src/library/Recommended and
library/Matrix to be sure.

> I haven't been able to reproduce the problem (on 32-bit Linux,
> R-2.13.0 RC, after running your code snippet below for a couple
>  of hours, I got the prompt back, and things continued working..)
> and Doug Bates has had a strong suspicion that the error message
> below looks like the problem that he fixed just between *-48 and *-49.
> 
>     >>> pkgname <- "Matrix"
>     >>> source(file.path(R.home("share"), "R", "examples-header.R"))
>     >>> gctorture(TRUE)
>     >>> options(warn = 1)
>     >>> options(error=dump.frames)
>     >>> library('Matrix')
> 
>     HL> Loading required package: lattice
>     HL> Error in regexpr("package:", envName, fixed = TRUE) :
>     HL> unprotected object (0x2fe5818) encountered (was INTSXP)
>     HL> Error: package/namespace load failed for 'Matrix'
> 
> Can you give more exact info about the platform ?

fedora 14 x86_64.

export DEFS='-DUSE_TYPE_CHECKING_STRICT -DR_MEMORY_PROFILING'
  ./configure  --enable-memory-profiling --enable-strict-barrier \ 
--enable-byte-compiled-packages --with-valgrind-instrumentation=2

Matrix-for-R-2.13 at 2659 was the one I was playing with.
I am currently testing Matrix trunk at 2666, since you seems to have put something 
relevant in r2661.



[Rd] core Matrix package segfaulted on R CMD check --use-gct
Hin-Tak Leung