Fantastic. Thanks a lot, Luke! .... I can close the thread just to say the final "it wasn't Matrix after all!" ;-)
On Fri, Apr 8, 2011 at 20:48, <luke-tier...@uiowa.edu> wrote: > Fixed in R-devel by 55385 and R-2-113-branch by 55386. > > The problem was a call to install() in the C srouce code without > protecting another value before the install call. This particular > issue was very unlikely to cause a problem outside of a gctorture > context, but in that context with the memory checking enabled by the > strict barrier it will get caught. > > Quick notes in case someone else needs to track this sort of thing > down: When gctorture is used in conjuction with the memory checks > enabled by the strict barrier it is very likely that an error will be > detected and signaled very close to where the problem in the C code > actually is, which is why I tried an example using only regexpr when > the error was being signaled there. Once a reproducable example is > found, setting a breakpoint in memory.c:CHK on the line that signals > the error gives a stack trace of the C calls involved, and in this > case the culprit was pretty easy to find at that point. > > luke > > On Fri, 8 Apr 2011, Hin-Tak Leung wrote: > >> --- On Fri, 8/4/11, peter dalgaard <pda...@gmail.com> wrote: >> >>> On Apr 7, 2011, at 23:57 , Hin-Tak Leung wrote: >>> >>> > > Oh, I am tracking both R and Matrix via git-svn and >>> retrieves all revisions to all branches daily (or at least, >>> regularly). I.e. R svn head. 2.13.0 only forked off >>> recently and most of the trunk<->2.13.0rc differences >>> are so far mostly documentation-related. I could switch to >>> track R 2.13.x branch if you insist. >>> > >>> Please do. It's the branch that is supposed to stabilize >>> during prerelease times. >>> >>> Also, please check the prerelease tarballs, errors in "make >>> dist" are not caught when building from svn. >> >> Just so that there is no doubt, here is the recipe with the latest rc tar >> ball, cutting-and-pasting from my command history: >> >> wget -m >> http://cran.r-project.org/src/base-prerelease/R-rc_2011-04-07_r55373.tar.gz >> cd /tmp >> tar -zxpvf >> ~/cran.r-project.org/src/base-prerelease/R-rc_2011-04-07_r55373.tar.gz >> cd R-rc/ >> export DEFS='-DUSE_TYPE_CHECKING_STRICT -DR_MEMORY_PROFILING' ; >> ./configure --enable-memory-profiling --enable-strict-barrier >> --enable-byte-compiled-packages --with-valgrind-instrumentation=2 ; make >> cd src/library/ >> cd Recommended/ >> ../../../bin/R CMD check --use-gct Matrix_0.999375-49.tar.gz >> >> ------------------------------ >> ... >> Running examples in ‘Matrix-Ex.R’ failed >> The error occurred in: >> >> >> R version 2.13.0 RC (2011-04-07 r55373) >> Copyright (C) 2011 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> Platform: x86_64-unknown-linux-gnu (64-bit) >> ... >>> >>> pkgname <- "Matrix" >>> source(file.path(R.home("share"), "R", "examples-header.R")) >>> gctorture(TRUE) >>> options(warn = 1) >>> library('Matrix') >> >> Loading required package: lattice >> Error in regexpr("package:", envName, fixed = TRUE) : >> unprotected object (0x3be2ba8) encountered (was INTSXP) >> Error: package/namespace load failed for 'Matrix' >> Execution halted >> ------------------------- >> >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel > > -- > Luke Tierney > Statistics and Actuarial Science > Ralph E. Wareham Professor of Mathematical Sciences > University of Iowa Phone: 319-335-3386 > Department of Statistics and Fax: 319-335-3017 > Actuarial Science > 241 Schaeffer Hall email: l...@stat.uiowa.edu > Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel