[BioC] problems with Greg's installer script

Kimpel, Mark W mkimpel at iupui.edu
Wed Apr 14 19:16:24 CEST 2004

When I try to run Greg's installer script I immediately get a syntax error for the command "RCMD ?= R-1.9.0". I am running 1.9.0 on Windows XP.

Am I doing something wrong?


Mark W. Kimpel MD
Department of Psychiatry
Indiana University School of Medicine
Biotechnology, Research, & Training Center
1345 W. 16th Street
Indianapolis, IN  46202
Message: 8
Date: Tue, 13 Apr 2004 22:42:08 -0400
From: "Warnes, Gregory R" <gregory_r_warnes at groton.pfizer.com>
Subject: [BioC] Makefile for installing all available packages
To: "R-Help (E-mail)" <r-help at stat.math.ethz.ch>,	"BioConductor
	(E-mail)" <bioconductor at stat.math.ethz.ch>
Cc: "Lawrence, JC" <JC_Lawrence at groton.pfizer.com>
	<D7A3CFD7825BD6119B880002A58F06C20680B29E at groexmb02.pfizer.com>
Content-Type: text/plain; charset="iso-8859-1"

Below is a makefile I wrote to download and install all available R packages
from the CRAN and BioConductor package repositories.  

The primary advantage of using this makefile instead of R's built-in
install.package() and update.packages() is the creation of a separate
installation log for every package.   Further, if make is invoked with '-k',
failure to install a single package will not derail the installation of
other packages.

I hope that this script may be useful to other folks.  


# Download and install all available R packages from the CRAN and
# package repositories
RCMD ?= R-1.9.0
WGET ?= wget -N -nd -r -A gz -r -l 1 -nv

PACKAGE_FILES = $(wildcard *.gz ) 
PACKAGE_LOGS  = $(addsuffix .log, $(basename $(basename $(PACKAGE_FILES))))

default: cran bioconductor install

	$(WGET) "http://cran.r-project.org/src/contrib/PACKAGES.html"

bioconductor: bioCmain bioCcontrib bioCdata


	$(WGET) "http://www.bioconductor.org/contrib/index.html"

	$(WGET) "http://www.bioconductor.org/data/metaData.html"

install: $(PACKAGE_LOGS)

%.log: %.tar.gz
	$(RCMD) INSTALL $< > $@.broken 2>&1 
	mv $@.broken $@

LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}


Bioconductor mailing list
Bioconductor at stat.math.ethz.ch

End of Bioconductor Digest, Vol 14, Issue 19
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Mark W. Kimpel MD (mkimpel at iupui.edu).vcf
Type: text/x-vcard
Size: 366 bytes
Desc: Mark W. Kimpel MD (mkimpel at iupui.edu).vcf
Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments/20040414/40495989/MarkW.KimpelMDmkimpeliupui.edu.vcf

More information about the Bioconductor mailing list