From htl10 at users.sourceforge.net  Fri Apr  8 23:22:36 2011
From: htl10 at users.sourceforge.net (Hin-Tak Leung)
Date: Fri, 8 Apr 2011 22:22:36 +0100 (BST)
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <BANLkTim_X4xuNkttJ=nxxQ6iSFLAQi8r7w@mail.gmail.com>
Message-ID: <456228.47846.qm@web29517.mail.ird.yahoo.com>

--- On Fri, 8/4/11, Martin Maechler <maechler at stat.math.ethz.ch> wrote:

> Fantastic.? Thanks a lot, Luke!
> 
>  .... I can close the thread just to say the final?
> ? "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,? <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.? 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 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 ? ? ? ? ? ? ? ? ?Phone: ?
> ? ? ? ? ? 319-335-3386
> > Department of Statistics and ? ? ? ?Fax: ? ? ?
> ? ? ? ? 319-335-3017
> > ? Actuarial Science
> > 241 Schaeffer Hall ? ? ? ? ? ? ? ? ?email: ?
> ? ?luke at stat.uiowa.edu
> > Iowa City, IA 52242 ? ? ? ? ? ? ? ? WWW: ?http://www.stat.uiowa.edu
>



[Rd] core Matrix package segfaulted on R CMD check --use-gct
Hin-Tak Leung