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

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Mon, 28 Mar 2011 16:47:05 +0200

>>>>> 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@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.
    >> 
    >>

______________________________________________
R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Mon 28 Mar 2011 - 14:54:35 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 29 Mar 2011 - 13:00:37 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive