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.
>>
>>