Martin Morgan
2009-May-20 23:50 UTC
[Rd] install.packages now intentionally references .Rprofile?
A post on the Bioconductor mailing list
https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html
suggests that install.packages now references .Rprofile (?), whereas
in R-2-8 it did not. Is this intentional?
The example is, in .Rprofile
library(utils)
install.packages("Biobase",
repos="http://bioconductor.org/packages/2.4/bioc")
then starting R from the command line results in repeated downloads
of Biobase
mtmorgan at mm:~/tmp> R --quiet
trying URL
'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
opened URL
=================================================downloaded 1.9 Mb
trying URL
'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
opened URL
=================================================downloaded 1.9 Mb
^C
Execution halted
> sessionInfo()
R version 2.9.0 Patched (2009-05-20 r48588)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Martin
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
Prof Brian Ripley
2009-May-21 06:17 UTC
[Rd] install.packages now intentionally references .Rprofile?
On Wed, 20 May 2009, Martin Morgan wrote:> A post on the Bioconductor mailing list > > https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html > > suggests that install.packages now references .Rprofile (?), whereas > in R-2-8 it did not. Is this intentional?Yes. And in fact it did in earlier versions, to find the default library into which to install.> > The example is, in .Rprofile > > library(utils) > install.packages("Biobase", > repos="http://bioconductor.org/packages/2.4/bioc") > > then starting R from the command line results in repeated downloads > of Biobase > > mtmorgan at mm:~/tmp> R --quiet > trying URL > 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz' > Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb) > opened URL > =================================================> downloaded 1.9 Mb > > trying URL > 'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz' > Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb) > opened URL > =================================================> downloaded 1.9 Mb > > ^C > Execution halted > >> sessionInfo() > R version 2.9.0 Patched (2009-05-20 r48588) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > Martin > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595