[BioC] problems with Greg's installer script

[Liaw, Andy]

Doesn't look like the Makefile would work on Windoze.  I believe it's meant
to work only on Unix-like OSes.

Andy

> From: Kimpel, Mark W
> 
> 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
> 
> 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>
> Message-ID:
> 	<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.  
> 
> -Greg
> 
> # Download and install all available R packages from the CRAN and
> Bioconductor 
> # 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
> 
> cran: 
> 	$(WGET) "http://cran.r-project.org/src/contrib/PACKAGES.html"
> 
> bioconductor: bioCmain bioCcontrib bioCdata
> 
> bioCmain:
> 	$(WGET)
> "http://www.bioconductor.org/repository/release1.3/package/htm
l/index.html"

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

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

install: $(PACKAGE_LOGS)

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



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End of Bioconductor Digest, Vol 14, Issue 19