[BioC] failure trying to install GO

Jenny Bryan jenny at stat.ubc.ca
Wed Nov 24 01:36:56 CET 2004

I have just upgraded to 2.0.1 (patched) and am in the process of
updating my Bioconductor installation (BTW, OS is RedHat 9).

I had some problems using getBioC(), which I now believe were due to
being incredibly unlucky in my timing (was the main repository
off-line or in flux in some way today?).  Thus, I tried to use
install.packages2() on some individual packages.  When I try to
install GO, a secondary R process eventually takes up all my available
RAM (a paltry 400M on this machine) and the machine just thrashes.
When I kill that R process, I get the errors below and my command
prompt back.  Any ideas?  Lots of other packages seem to require GO,
so this is a real roadblock for me.

Thanks in advance, Jenny

################ my session #################

R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.1 Patched (2004-11-22), ISBN 3-900051-07-0

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Type 'license()' or 'licence()' for distribution details.

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

WARNING: UTF-8 locales are not currently supported

> options(STERM='iESS', editor='emacsclient')
> library(reposTools)
Loading required package: tools 
> install.packages2("GO", develOK=TRUE)

Note: You did not specify a download type.  Using a default value of: Source 
This will be fine for almost all users
[1] "Attempting to download GO from http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing GO"
* Installing *source* package 'GO' ...
** R
** data
** preparing package for lazy loading

** help
 >>> Building/Updating help pages for package 'GO'
     Formats: text html latex example 
  GO                                text    html    latex
  GOALLLOCUSID                      text    html    latex   example
  GOBPANCESTOR                      text    html    latex   example
  GOBPCHILDREN                      text    html    latex   example
  GOBPOFFSPRING                     text    html    latex   example
  GOBPPARENTS                       text    html    latex   example
  GOCCANCESTOR                      text    html    latex   example
  GOCCCHILDREN                      text    html    latex   example
  GOCCOFFSPRING                     text    html    latex   example
  GOCCPARENTS                       text    html    latex   example
  GOLOCUSID                         text    html    latex   example
  GOLOCUSID2ALLGO                   text    html    latex   example
  GOLOCUSID2GO                      text    html    latex   example
  GOMFANCESTOR                      text    html    latex   example
  GOMFCHILDREN                      text    html    latex   example
  GOMFOFFSPRING                     text    html    latex   example
  GOMFPARENTS                       text    html    latex   example
  GOQC                              text    html    latex
  GOTERM                            text    html    latex   example
/usr/local/lib/R/bin/INSTALL: line 1: 19406 Done                    echo "invisible(.libPaths(c(\"${lib}\", .libPaths()))); tools:::.install_package_indices(\".\", \"${R_PACKAGE_DIR}\")"
     19407 Terminated              | R_DEFAULT_PACKAGES=NULL LANG=C "${R_EXE}" --vanilla >/dev/null
ERROR: installing package indices failed
** Removing '/usr/local/lib/R/library/GO'
** Restoring previous '/usr/local/lib/R/library/GO'
>From URL:  http://www.bioconductor.org/data/metaData-devel/
	GO version 1.6.6

Warning message: 
Installation of package GO had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
> > q()
Save workspace image? [y/n/c]: n

Process R finished at Tue Nov 23 16:25:03 2004

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