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

From: Douglas Bates <>
Date: Mon, 28 Mar 2011 09:24:39 -0500

Can you provide the output from


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 <> 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 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.
> mailing list Received on Mon 28 Mar 2011 - 14:30:17 GMT

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