From ripley at stats.ox.ac.uk  Fri Apr  8 13:14:40 2011
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Fri, 8 Apr 2011 12:14:40 +0100 (BST)
Subject: [Rd] core Matrix package segfaulted on R CMD check --use-gct
In-Reply-To: <3DEDAFF8-5C66-425D-AF4E-256A4BBB3382@gmail.com>
References: <191025.59368.qm@web29508.mail.ird.yahoo.com>
	<3DEDAFF8-5C66-425D-AF4E-256A4BBB3382@gmail.com>
Message-ID: <alpine.LFD.2.02.1104080834290.5199@gannet.stats.ox.ac.uk>

On Fri, 8 Apr 2011, peter dalgaard wrote:

> (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.

And despite claims to the contrary earlier in this thread, we 
certainly did.  (One example was in regexpr, although not AFAICS in a 
code branch used in this issue.)  Once 2.x.0 branches, the trunk 
becomes a playpen for ideas considered too radical/experimental for a 
release a month or two off.

>> 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

Note that the first define does nothing and the second just repeats 
what --enable-memory-profiling does.  Neither are documented in 
current R AFAICS.

> 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.

But --enable-byte-compiled-packages does nothing, as configure --help 
says in 2.13.0 RC (and AFAICS it is documented nowhere else).

You really can't asumme that things not described in the R-admin 
manual are actually relevant to R (or current R).  autoconf puts 
things in configure that are boilerplate code we do not use (and I've 
tried to indicate which ones come from libtool or libintl).

>> --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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595


[Rd] core Matrix package segfaulted on R CMD check --use-gct
Prof Brian Ripley