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

From: Hin-Tak Leung <htl10_at_users.sourceforge.net>
Date: Tue, 29 Mar 2011 11:34:52 +0100

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.
> >>
> >>
> ______________________________________________ R-devel_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Received on Tue 29 Mar 2011 - 11:21:03 GMT

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