Thanks, Jim. I appreciate the jargon update - I teach the local R course, so I should get the terminology right. I suspect that the problem may be the permissions that were set on doc/html/index.html. I will talk with our local computer guru. --Naomi At 03:41 PM 6/18/2008, you wrote: >Hi Naomi, > >Naomi Altman wrote: >>Dear Jim, >>Here is what I found. Firstly, I do not have libPaths, but I do >>have something called .libPaths which seems to have been set when >>the directory was created. > >Yes. My bad. It is .libPaths(). > >> .libPaths() >>[1] "C:\\Documents and Settings\\naomi\\My Documents/R/win- library/2.6" >>[2] "C:/PROGRA~1/R/R-26~1.1/library" >> > help.start() >>updating HTML package listing >>updating HTML search index >>fixing URLs in non-standard libraries > >The above line indicates that the correct URLs are getting set, so >you should see the BioC packages at the top of the listing when you >click on 'Packages'. > >>If nothing happens, you should open >>'C:\PROGRA~1\R\R-26~1.1\doc\html\index.html' yourself >> > .libPaths("C:/") >> > help.start() >>updating HTML package listing >>updating HTML search index >>fixing URLs in non-standard libraries >>If nothing happens, you should open >>'C:\PROGRA~1\R\R-26~1.1\doc\html\index.html' yourself >>One thing I noticed is that the directory holding the bioconductor >>libraries, C:\\Documents and Settings\\naomi\\My >>Documents/R/win-library/2.6 does not have a doc folder and so >>presumably the html files have not been downloaded. Was there some >>flag I should have set when downloading the libraries? > >They are technically *packages* that are downloaded to a *library* >(I can hear Martin Maechler's teeth grinding from here ;-D). >Pedantic notes aside, no you don't need to set any flags, just use >biocLite(<packagename>. Anyway, there isn't a doc folder. The HTML >is in the html directory of the package. > >Best, > >Jim > > >>--Naomi >> >>At 02:31 PM 6/18/2008, James W. MacDonald wrote: >>>Did you set your library paths? >>> >>>I did the following and it works for me on both R-2.7.0 and R-devel. >>> >>>libPaths("C:/") >>>biocLite("drosophila2probe") >>> >>>then >>> >>>help.start() >>> >>>brings up the HTML help with the heading >>> >>>Packages in C:\ >>>Cross-links from this library to other libraries may not work. >>> >>>drosophila2probe [snip] >>> >>>Packages in the standard library >>> >>>[snip] >>> >>>Best, >>> >>>Jim >>> >>> >>> >>>Naomi Altman wrote: >>>>Thanks to increased security here, I now have to download >>>>Bioconductor routines into my own library rather than the R >>>>program library. (Thanks to whoever implemented this - works great.) >>>>However, I am a huge fan of the html "help" and the Bioconductor >>>>packages no longer appear. Any suggestions? >>>>Thanks, >>>>Naomi S. Altman 814-865-3791 (voice) >>>>Associate Professor >>>>Dept. of Statistics 814-863-7114 (fax) >>>>Penn State University 814-865-1348 (Statistics) >>>>University Park, PA 16802-2111 >>>>_______________________________________________ >>>>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 >>> >>>_______________________________________________ >>>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 >>Naomi S. Altman 814-865-3791 (voice) >>Associate Professor >>Dept. of Statistics 814-863-7114 (fax) >>Penn State University 814-865-1348 (Statistics) >>University Park, PA 16802-2111 > >-- >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 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111