From bates at stat.wisc.edu  Tue Mar 29 21:17:54 2011
From: bates at stat.wisc.edu (Douglas Bates)
Date: Tue, 29 Mar 2011 14:17:54 -0500
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
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On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung
<htl10 at users.sourceforge.net> wrote:
> Martin Maechler wrote:
>>>>>>>
>>>>>>> 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
>
> 64-bit fedora 14. For building R svn (and checking soon-to-be-released R
> packages, rather than daily R-related work), I also have these, and indeed
> have "--enable-strict-barrier":
>
> export DEFS='-DUSE_TYPE_CHECKING_STRICT -DR_MEMORY_PROFILING' \
> ./configure --enable-memory-profiling --enable-strict-barrier
> --enable-byte-compiled-packages --with-valgrind-instrumentation=2
>
>> sessionInfo()
> R version 2.14.0 Under development (unstable) (--)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> ?[1] LC_CTYPE=en_GB.UTF-8 ? ? ? LC_NUMERIC=C
> ?[3] LC_TIME=en_GB.UTF-8 ? ? ? ?LC_COLLATE=en_GB.UTF-8
> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_GB.UTF-8
> ?[7] LC_PAPER=en_GB.UTF-8 ? ? ? LC_NAME=C
> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

Thanks for the information.  I can replicate the problem on a Red Hat
EL 5 64-bit system and will start to debug now.

>>>>>>> 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
Douglas Bates