Perhaps someone has seen this behavior and can help: I am working with a student who has a Windows vista laptop. She had installed R 2.6.2 and Bioconductor. When working with the swirl sample data set and trying to normalize within arrays, an error with the lowess function was occurring. I checked the limma version and it was 2.9.7, so we tried to install limma 2.12, but got a warning that the prior version of limma cannot be removed. Oddly, the machine is in a state such that if from the R GUI we choose Packages->Load Package, limma does not appear on the list (which makes sense because there is no limma folder in C:\Program Files\R\R-2.6.2\library). Yet if we try to install limma, we see the 'cannot remove prior version' error. We even uninstalled R and re-installed it, but the same problem with installing limma persists. I guess I never should have joked early on that we could probably blame this problem on Vista...but it's looking like that may be the case. Any ideas would be appreciated. Thanks, Susan J. Miller Manager, Scientific Data Analysis Biotechnology Computing Facility Arizona Research Laboratories (520) 626-2597

Hi Susan, Usually this happens when you get a half-deleted package, often when there isn't anything in the e.g., <rhome>/library/limma directory, but the directory still exists. Check to see if there is a limma directory in your library directory, if so, delete it by hand and then try re-installing using biocLite(). Best, Jim Susan J. Miller wrote: > Perhaps someone has seen this behavior and can help: > > I am working with a student who has a Windows vista laptop. She had > installed R 2.6.2 and Bioconductor. When working with the swirl sample > data set and trying to normalize within arrays, an error with the lowess > function was occurring. I checked the limma version and it was 2.9.7, > so we tried to install limma 2.12, but got a warning that the prior > version of limma cannot be removed. Oddly, the machine is in a state > such that if from the R GUI we choose Packages->Load Package, limma does > not appear on the list (which makes sense because there is no limma > folder in C:\Program Files\R\R-2.6.2\library). Yet if we try to install > limma, we see the 'cannot remove prior version' error. We even > uninstalled R and re-installed it, but the same problem with installing > limma persists. > > I guess I never should have joked early on that we could probably blame > this problem on Vista...but it's looking like that may be the case. Any > ideas would be appreciated. > > Thanks, > > Susan J. Miller > Manager, Scientific Data Analysis > Biotechnology Computing Facility > Arizona Research Laboratories > (520) 626-2597 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623