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Warnes, Gregory R
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460
@warnes-gregory-r-43
Last seen 10.2 years ago
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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