[Bioc-sig-seq] Shortreads

Terry Therneau therneau at mayo.edu
Mon Aug 25 20:48:39 CEST 2008

  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 
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 
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 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.
  	Terry T.

More information about the Bioc-sig-sequencing mailing list