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 $@ LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}} ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 14, Issue 19 ******************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: Mark W. Kimpel MD (mkimpel@iupui.edu).vcf Type: text/x-vcard Size: 366 bytes Desc: Mark W. Kimpel MD (mkimpel@iupui.edu).vcf Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040414/40495989/MarkW.KimpelMDmkimpeliupui.edu.vcf

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@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/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 $@ LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}} ------------------------------ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor End of Bioconductor Digest, Vol 14, Issue 19