Lately my R-program is not working properly (Sun Solaris). It used to be easy and smooth. I am using the AFFY mouse expression set 430A and I need to have the package "moe430acdf" in my working directory. I have run this analysis before already without problems. However, lately, it is not loading the package "moe430acdf" and instead it is removing the package "moe430acdf". Why is that? I used these commands: > source("http://www.bioconductor.org/getBioC.R") > getBioC(relLevel="release", destdir="~/r181/library") Running getBioC version 1.2.50.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Synching your local package management information ... Packages which have been removed: XML MAGEML moe430acdf Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users I tried also to install the package "moe430cdf" using these commands: > options(CRAN = "http://www.bioconductor.org/") > options(CRAN = "http://www.bioconductor.org/") > install.packages("moe430acdf", lib= "~/r181/library") trying URL `http://www.bioconductor.org//src/contrib/PACKAGES' Content type `text/plain' length 18474 bytes opened URL .......... ........ downloaded 18Kb Warning message: No package "moe430acdf" on CRAN. in: download.packages(pkgs, destdir = tmpd, available = available, Thanks for the help. Roger Roger L. Vallejo, Ph.D. Assist. Professor of Genomics & Bioinformatics The Pennsylvania State University Department of Dairy & Animal Science 305 Henning Building University Park, PA 16802 Phone: (814) 865-1846 Fax: (814) 863-6042 Email: rvallejo@psu.edu <mailto:rvallejo@psu.edu> [[alternative HTML version deleted]]

> > getBioC(relLevel="release", destdir="~/r181/library") > Synching your local package management information ... > Packages which have been removed: > XML > MAGEML > moe430acdf What this implies is that these packages were not installed properly on a previous run - what currently happens in reposTools (and isn't the most clear thing, I will look to change this in the very near future) is that when it attempts to install a package it adds it to the database - then the next time something calls syncLocalLibList() (which getBioC does), if the package actually failed to install then it sees that the package isnt' there and in the eyes of syncLocalLibLIst() it looks like the package was removed. I need to add in some code to detect that the package actually failed to install. XML and MAGEML both use C code, and that can sometimes cause installation problems - but I don't know why the CDF package would fail. > > options(CRAN = "http://www.bioconductor.org/") > > install.packages("moe430acdf", lib= "~/r181/library") > No package "moe430acdf" on CRAN. in: download.packages(pkgs, destdir = > tmpd, available = available, The CDF packages aren't currently available via our CRAN style repositories. What happens if you download the package manually from the website and do a 'R INSTALL moe430acdf'?