core Matrix package segfaulted on R CMD check --use-gct

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

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.
? ?>> ? ? >>