I tried to install Bioconductor 1.3 in R 1.9.0. for linux suse 8.0. I was able to install some libraries, but for some of them the installation fails. One of these is affy: when the installation file tries to install the manual the message obtained is: -------------------------------------------------- ........ normalize.constant text html latex normalize.contrast text html latex example normalize.invariantset text html latex ERROR: command (e.g. \url) inside \link ERROR: building help failed for package 'affy' ** Removing '/cineca/prod/Bioinf/R/R-1.9.0/library/affy' ------------------------------------------------- I found the problem. There is a sintax error in the code generating the help for the function loess.normalize. I solved the problem: Unpacking the affy_1.3.28.tar.gz editing the file normalize.loess.Rd in man subdirectory of affy: on line 38 change the line: \link {loess.normalize} for a complete description with: \code{\link {loess.normalize}} for a complete description zip the file again and launch the function R CMD INSTALL again. Hope this is helpful! ----------------------------------------------------------- Dr Francesco Falciano CINECA (High Performance Systems) via Magnanelli, 6/3 40033 Casalecchio di Reno (BO)-ITALY tel: +39-051-6171724 fax: +39-051-6132198 e-mail: f.falciano@cineca.it [[alternative HTML version deleted]]