From maechler at stat.math.ethz.ch  Mon Mar 28 16:47:05 2011
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Mon, 28 Mar 2011 16:47:05 +0200
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <AANLkTimDJbJ-u3wXOyvPB0EePf98AZ-R5duKVr+Guh-v@mail.gmail.com>
References: <255683.81856.qm@web29515.mail.ird.yahoo.com>
	<AANLkTimDJbJ-u3wXOyvPB0EePf98AZ-R5duKVr+Guh-v@mail.gmail.com>
Message-ID: <19856.40809.236979.731769@stat.math.ethz.ch>

>>>>> Douglas Bates <bates at stat.wisc.edu>
>>>>>     on Mon, 28 Mar 2011 09:24:39 -0500 writes:

    > Can you provide the output from sessionInfo()

    > so we can know the platform?  Also, did you configure R
    > with --enable-strict-barrier or set the C compilation flag
    > -DTESTING_WRITE_BARRIER?  I think that run-time error
    > message can only be thrown under those circumstances (not
    > that it isn't an error, it's just not checked for in other
    > circumstances).

interesting.

In the mean time, I *did* run --- for several hours! ---
your code example below,
and it did *not* segfault for me (64-bit, Linux Fedora 13).

Martin

>>>>> Douglas Bates <bates at stat.wisc.edu>
>>>>>     on Mon, 28 Mar 2011 09:24:39 -0500 writes:

    > Can you provide the output from
    > sessionInfo()

    > so we can know the platform?  Also, did you configure R with
    > --enable-strict-barrier or set the C compilation flag
    > -DTESTING_WRITE_BARRIER?  I think that run-time error message can only
    > be thrown under those circumstances (not that it isn't an error, it's
    > just not checked for in other circumstances).

    > On Sat, Mar 26, 2011 at 5:21 PM, Hin-Tak Leung <hintak_leung at yahoo.co.uk> wrote:
    >> Current core/Recommended Matrix package (0.999375-48) has been segfaulting against R 2.13-alpha/2.14-trunk for the last week or so (since R-2.13 was branched, when I started trying) when "run with R CMD check --use-gct":
    >> 
    >> --------------
    >>> pkgname <- "Matrix"
    >>> source(file.path(R.home("share"), "R", "examples-header.R"))
    >>> gctorture(TRUE)
    >>> options(warn = 1)
    >>> library('Matrix')
    >> Loading required package: lattice
    >> Error : .onLoad failed in loadNamespace() for 'Matrix', details:
    >> ?call: fun(...)
    >> ?error: unprotected object (0x2768b18) encountered (was REALSXP)
    >> Error: package/namespace load failed for 'Matrix'
    >> Execution halted
    >> ---------------
    >> 
    >> I traced to this because "R CMD check --use-gct snpStats" (both 1.1.13 and 1.1.12) segfaults with the same message, and before that, the snpMatrix 1.15.8.4 which includes some of David's newly written ld() ( which depends on Matrix.)
    >> 
    >> If the Matrix package segfaults, David's new ld() isn't useable.
    >> 
    >>



[Rd] core Matrix package segfaulted on R CMD check --use-gct
Martin Maechler