From bates at stat.wisc.edu  Mon Mar 28 16:24:39 2011
From: bates at stat.wisc.edu (Douglas Bates)
Date: Mon, 28 Mar 2011 09:24:39 -0500
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <255683.81856.qm@web29515.mail.ird.yahoo.com>
References: <255683.81856.qm@web29515.mail.ird.yahoo.com>
Message-ID: <AANLkTimDJbJ-u3wXOyvPB0EePf98AZ-R5duKVr+Guh-v@mail.gmail.com>

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
Douglas Bates