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

From: Hin-Tak Leung <htl10_at_users.sourceforge.net>
Date: Fri, 08 Apr 2011 22:22:36 +0100 (BST)

> Fantastic.聽 Thanks a lot, Luke!
>
> .... I can close the thread just to say the final聽
> 聽 "it wasn't
> Matrix after all!"
> ;-)

I am glad it is all working out - I have spent way too much time on this, having gone through about 4 different packages to get to the bottom. finger-cross gctorture(TRUE) works - and continue to :-)... until next time.

Cheers,
Hin-Tak

>
>
> On Fri, Apr 8, 2011 at 20:48,聽 <luke-tierney_at_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 <pdalgd_at_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.聽 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 聽--enable-memory-profiling
> --enable-strict-barrier
> >> --enable-byte-compiled-packages
> --with-valgrind-instrumentation=2 聽; make
> >> cd src/library/
> >> cd Recommended/
> >> ../../../bin/R CMD check --use-gct
> Matrix_0.999375-49.tar.gz
> >>
> >> ------------------------------
> >> ...
> >> Running examples in 鈥楳atrix-Ex.R鈥 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) :
> >> 聽unprotected object (0x3be2ba8) encountered (was
> INTSXP)
> >> Error: package/namespace load failed for 'Matrix'
> >> Execution halted
> >> -------------------------
> >>
> >>
> >> ______________________________________________
> >> R-devel_at_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 聽 聽 聽 聽 聽 聽 聽 聽 聽Phone: 聽
> 聽 聽 聽 聽 聽 319-335-3386
> > Department of Statistics and 聽 聽 聽 聽Fax: 聽 聽 聽
> 聽 聽 聽 聽 319-335-3017
> > 聽 Actuarial Science
> > 241 Schaeffer Hall 聽 聽 聽 聽 聽 聽 聽 聽 聽email: 聽
> 聽 聽luke_at_stat.uiowa.edu
> > Iowa City, IA 52242 聽 聽 聽 聽 聽 聽 聽 聽 WWW: 聽http://www.stat.uiowa.edu
>



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