From htl10 at users.sourceforge.net  Tue Mar 29 12:34:52 2011
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Tue, 29 Mar 2011 11:34:52 +0100
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <19856.40809.236979.731769@stat.math.ethz.ch>
References: <255683.81856.qm@web29515.mail.ird.yahoo.com>	<AANLkTimDJbJ-u3wXOyvPB0EePf98AZ-R5duKVr+Guh-v@mail.gmail.com>
	<19856.40809.236979.731769@stat.math.ethz.ch>
Message-ID: <4D91B5CC.1040500@users.sourceforge.net>

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.
>     >> 
>     >> 
>



[Rd] core Matrix package segfaulted on R CMD check --use-gct
Hin-Tak Leung