Just a short note concerning a “gotcha”.
As I have many times before, I opened an R console on my newly-upgraded (to lucid 10.04) Ubuntu machine, typed source(“http://bioconductor.org/biocLite.R”) and began a Bioconductor install with biocLite(). Only this time, I saw this:
Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so': /home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so: undefined symbol: egzread ERROR: loading failed * removing ‘/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio’
A quick email to the Bioconductor mailing list put me in touch with the very helpful Martin Morgan, who suggested that I check my zlib libraries. Sure enough, the rogue “egzread” was found in /usr/local/include/zlibemboss.h, along with a second zlib.h file, in addition to /usr/include/zlib.h.
grep egz /usr/local/include/zlibemboss.h > #define gzread egzread
I moved the rogue zlib.h out of /usr/local/include and order was restored.
So in summary, watch out when installing EMBOSS on Ubuntu – it seems to mess with things that it should not.