From pdalgd at gmail.com  Fri Apr  8 08:50:02 2011
From: pdalgd at gmail.com (peter dalgaard)
Date: Fri, 8 Apr 2011 08:50:02 +0200
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
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References: <191025.59368.qm@web29508.mail.ird.yahoo.com>
Message-ID: <3DEDAFF8-5C66-425D-AF4E-256A4BBB3382@gmail.com>

(Resending with fewer recipients...)

On Apr 8, 2011, at 07:09 , 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:

Thanks. I wasn't expecting things to be different, just making a point about checking the right object. In principle, we could be putting in unstable development code in the trunk as soon as the branch was made.

> 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

Aha... Does it happen without --enable-byte-compiled-packages? To quote NEWS:

"by default the compiler is not used in this release"

so bugs in the compiler are interesting, but not release-critical.

> --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
> -------------------------
> 

-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com



[Rd] core Matrix package segfaulted on R CMD check --use-gct
peter dalgaard