From luke-tierney at uiowa.edu  Fri Apr  8 19:42:35 2011
From: luke-tierney at uiowa.edu (luke-tierney at uiowa.edu)
Date: Fri, 8 Apr 2011 12:42:35 -0500
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <191025.59368.qm@web29508.mail.ird.yahoo.com>
References: <191025.59368.qm@web29508.mail.ird.yahoo.com>
Message-ID: <alpine.DEB.2.00.1104081240160.1770@luke-inspiron>

Given the configure settings this looks like its probably an issue in
regexpr's internals rather than in Matrix per se. I can confirm that
with

> gctorture()
> for (i in 1:100) regexpr("package:", "package:lattice", fixed = TRUE)
Error in regexpr("package:", "package:lattice", fixed = TRUE) :
   unprotected object (0x26b30a8) encountered (was INTSXP)

run in r55347 with --enable-strict-barrier.  I'll see if I can spot anyting.

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
luke-tierney at uiowa.edu