From hintak_leung at yahoo.co.uk  Thu Apr  7 22:11:26 2011
From: hintak_leung at yahoo.co.uk (Hin-Tak Leung)
Date: Thu, 07 Apr 2011 21:11:26 +0100
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <4D9E0307.7070802@users.sourceforge.net>
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Hin-Tak Leung wrote:
> 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.
> 

finished testing trunk r2666 (0.9996875-0). It takes about 3.5 hours (with 
gctorture(TRUE)) to get to:

 > pkgname <- "Matrix"
 > source(file.path(R.home("share"), "R", "examples-header.R"))
 > gctorture(TRUE)
 > options(warn = 1)
 > library('Matrix')
Loading required package: lattice
Error in regexpr("package:", envName, fixed = TRUE) :
   unprotected object (0x3a37878) encountered (was INTSXP)
Error: package/namespace load failed for 'Matrix'
Execution halted



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