[BioC] update.packages() for bioconductor packages generates bus error in R.app for R-2.6.1 on Mac OS X

[Steven McKinney]

Greetings,

I just installed the latest Mac upgrade version of R
R-2.6.1

When I attempt to update bioconductor packages,
R catches a bus to crashville.

I'm using the recommended approach from 
http://www.bioconductor.org/docs/install-howto.html

i.e.

source("http://bioconductor.org/biocLite.R")
update.packages(repos=biocinstallRepos(), ask=FALSE)


Session info and error report are below.  I'm not
seeing this issue in R news groups yet.  Anyone
else having this problem?

Steve McKinney

Mac info:

System Version:	Mac OS X 10.4.11 (8S165)
  Kernel Version:	Darwin 8.11.0
  Boot Volume:	Macintosh HD

 Machine Name:	Power Mac G5 Quad
  Machine Model:	PowerMac11,2
  CPU Type:	PowerPC G5 (1.1)
  Number Of CPUs:	4
  CPU Speed:	2.5 GHz
  L2 Cache (per CPU):	1 MB
  Memory:	16 GB
  Bus Speed:	1.25 GHz



R info:

R version 2.6.1 (2007-11-26)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Workspace restored from /Users/stevenmckinney/.RData]

> sessionInfo()
R version 2.6.1 (2007-11-26) 
powerpc-apple-darwin8.10.1 

locale:
en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
> help.start()
Making links in per-session dir ...
If '/usr/bin/open' is already running, it is *not* restarted, and you must switch to its window.
Otherwise, be patient ...
> source("http://bioconductor.org/biocLite.R")
> update.packages(repos=biocinstallRepos(), ask=FALSE)
trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/annaffy_1.10.1.tgz'
Content type 'application/x-gzip' length 277396 bytes (270 Kb)
opened URL
==================================================
downloaded 270 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/biomaRt_1.12.2.tgz'
Content type 'application/x-gzip' length 398253 bytes (388 Kb)
opened URL
==================================================
downloaded 388 Kb

trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/cellHTS2_2.2.3.tgz'
Content type 'application/x-gzip' length 4448886 bytes (4.2 Mb)
opened URL
==================================================
downloaded 4.2 Mb

trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/oligo_1.2.2.tgz'
Content type 'application/x-gzip' length 532702 bytes (520 Kb)
opened URL
==================================================
downloaded 520 Kb


 *** caught bus error ***
address 0x20, cause 'invalid alignment'

Traceback:
 1: unlink(instPath, recursive = TRUE)
 2: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers)
 3: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,     method = method, available = available, destdir = destdir,     installWithVers = installWithVers, dependencies = dependencies)
 4: install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,     method = method, available = available, ..., type = type)
 5: update.packages(repos = biocinstallRepos(), ask = FALSE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: