On Tue, Mar 29, 2011 at 5:34 AM, Hin-Tak Leung
<ht...@users.sourceforge.net> wrote:
> Martin Maechler wrote:
>>>>>>>
>>>>>>> Douglas Bates <ba...@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 <ba...@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_le...@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.
>> >> >>
>
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