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Kimpel, Mark W
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@kimpel-mark-w-727
Last seen 9.7 years ago
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@groton.pfizer.com>
Subject: [BioC] Makefile for installing all available packages
To: "R-Help (E-mail)" <r-help@stat.math.ethz.ch>, "BioConductor
(E-mail)" <bioconductor@stat.math.ethz.ch>
Cc: "Lawrence, JC" <jc_lawrence@groton.pfizer.com>
Message-ID:
<d7a3cfd7825bd6119b880002a58f06c20680b29e@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/html/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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