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

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Thu, 07 Apr 2011 19:45:24 +0200

>>>>> 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 ???

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 ?

Martin



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