Re: [Rd] core Matrix package segfaulted on R CMD check --use-gct

From: Hin-Tak Leung <htl10_at_users.sourceforge.net>
Date: Thu, 07 Apr 2011 19:31:35 +0100

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.



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