Hi Terry -- Terry Therneau <[EMAIL PROTECTED]> writes:
> > Thanks for all the responses. > > I have successfully put R-devel up on a machine, and then installed the > shortread package. To start, I was trying to have a local library with the > add-ons, working with the installed R base on a shared server. This was not > a > straightforward exercise. > > A suggestion: much of my confusion was due to the fact that there were not > any > manual pages for biocLite, bioinstall, etc; or at least no documentation that > I > easily found. So I tried the standard R install (no luck), and various other The horse is out of the barn, but there is some documentation at http://bioconductor.org/install The key to making 'install.packages' work is to use the appropriate repositories, available with biocinstallRepos() once biocLite.R has been sourced. The idea of a message, e.g., 'See http://bioconductor.org/install for help' sounds good. > fruitless paths based on wrong guesses. Sean's explanation of why biocLite > does > what it does was helpful; I'd already guessed some of it by reading source > code. > Perhaps the standard install of biocLite could finish with a message pointing > one to a short 1-2 paragraph overview. When it works biocLite is nice, but > when it doesn't there isn't much hint of where to begin. It consistently > ignored my "lib" directive, for instance. And from my reading of > the source Hmm, more detail (off list, perhaps) might help, but the 'lib' argument gets passed to install.packages as expected, for me (sessionInfo() snippet below). install.packages behavior is not trivial when lib is provided. (My own approach is to set an environment variable R_LIBS. This gets incorporated into .libPaths(), and packages are installed and read from a consistent location across sessions, without explicitly providing a 'lib' argument to biocLite). > code it wouldn't have helped in the end if it had paid attention -- there is, > is > there not, an assumption that the "stubs" are in an include directory in the > R > home tree, not the user's? I don't think so. For instance, if IRanges is installed in R_HOME/library and Biostrings in /tmp/mydir, then ShortRead is compiled with appropriate paths -- along the lines of gcc -std=gnu99 -I/home/mtmorgan/arch/x86_64/R-devel/include \ -I/usr/local/include \ -I"/home/mtmorgan/arch/x86_64/R-devel/include/IRanges/include" \ -I"/tmp/mydir/Biostrings/include" \ -fpic -g -O2 -c alphabet.c -o alphabet.o It's complicated, though. > sessionInfo() R version 2.8.0 Under development (unstable) (2008-08-22 r46416) x86_64-unknown-linux-gnu > I anticipate that the Solexa, and the threat of a couple more coming in > soon, > will accelerate my familiarity with bioconductor. The shortread package > already > has repaid with interest for these install nuisances. Always good to hear! Martin > Terry T. > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
