Hello! I was recently just trying to install bioconductor using the source() and then biocLite() commands, but the only problem was that it wasn't able to access: "http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15" Upon going to "http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/", I found that the v2.15 has been removed and only v3.0 is there now. To download that, how should I change the commands? Or will you guys update it soon? Also, after using biocLite(), it prompts me about whether I would like to update all/some/none packages (a/s/n), but it doesn't respond to any inputs ('a', 'all', etc.) and I'm forced to quit it using 'esc'. Any idea what the problem might be?? Thanks! -- output of sessionInfo(): > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 Warning: package ???Biobase??? is in use and will not be installed trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/IRanges_1.16.6.zip' Content type 'application/zip' length 2048190 bytes (2.0 Mb) opened URL downloaded 2.0 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/AnnotationDbi_1.20.7.zip' Content type 'application/zip' length 4200978 bytes (4.0 Mb) opened URL downloaded 4.0 Mb package ???IRanges??? successfully unpacked and MD5 sums checked package ???AnnotationDbi??? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Rishi\AppData\Local\Temp\RtmpmETHDq\downloaded_packages Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15 Old packages: 'cluster', 'foreign', 'KernSmooth', 'lattice', 'Matrix', 'mgcv', 'nnet', 'rpart', 'snow', 'survival', 'XML' Update all/some/none? [a/s/n]: all Update all/some/none? [a/s/n]: all Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: a Update all/some/none? [a/s/n]: s Update all/some/none? [a/s/n]: s Update all/some/none? [a/s/n]: d Update all/some/none? [a/s/n]: d Update all/some/none? [a/s/n]: n Update all/some/none? [a/s/n]: -- Sent via the guest posting facility at bioconductor.org.

Hi Rishi, On Thu, May 23, 2013 at 1:04 PM, Rishi Sinha [guest] <guest at="" bioconductor.org=""> wrote: > > Hello! > > I was recently just trying to install bioconductor using the source() and then biocLite() commands, but the only problem was that it wasn't able to access: > > "http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15" What do you mean "install bioconductor"? What packages are you trying to install? Can you show us the `biocLite(...)` command you are using? If you are not trying to install the custom CDFs that the brainarray people provide, then you have no problem. If you look closely at the message that is being printed, it is only issuing a warning, but you can carry on with your business. > Upon going to "http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/", I found that the v2.15 has been removed and only v3.0 is there now. > > To download that, how should I change the commands? Or will you guys update it soon? What is "that" that you want to download? If you really want to access older versions of their custom CDFs, you can browse what they have here: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp If worse comes to worst, you can download the package you want and install manually from the local package. > Also, after using biocLite(), it prompts me about whether I would like to update all/some/none packages (a/s/n), but it doesn't respond to any inputs ('a', 'all', etc.) and I'm forced to quit it using 'esc'. Any idea what the problem might be?? I haven't experienced that before (but I've also never run R on windows). How are you running R? Are you, for instance, using rstudio, emacs/ess, or? -steve -- Steve Lianoglou Computational Biologist Department of Bioinformatics and Computational Biology Genentech

Hi Rishi, Please use "reply all" when replying to emails on the list so that discussion stays on the list. This way you will likely get better help since more eyeballs are looking at your problems, and the list can be used as a resource for people in the future. On May 23, 2013, at 1:37 PM, RISHI SINHA <rishi.z.sinha at="" berkeley.edu=""> wrote: > Hi Steve, > > Sorry, I guess I really don't know exactly what I'm downloading from Bioconductor. I'm using a book, Applied Statistics for Bioinformatics Using R, and it says: > "Bioconductor is primarily based on R and can be installed, as > follows. > > source("http://www.bioconductor.org/biocLite.R") > > biocLite()" Ahh, I see. The packages that get installed by default have likely changed since that book was published. Still, you can likely broadly apply much of what's there, although you may run into bumps. The `biocLite()` function installs thing from bioconductor's repositories. You can use it to specify packages you'd like, so you could do: R> source("http://bioconductor.org/biocLite.R") R> biocLite("multtest") R> library(multtest) R> library(golub) and you can continue on your way, you will like need to install some other things. I suspect installing "limma" depends on enough other things that it should get you on your way: R> biocLite("limma") > I don't think I skipped any steps according to the book, but if there are any intermediate steps I missed, that would be nice to know. You haven't skipped anything it seems, but the world of bioconductor (and the defaults) has moved on since that book was published in 2009 .. I guess you are using this one, right? http://cran.r-project.org/doc/contrib/Krijnen- IntroBioInfStatistics.pdf I've never read that particular work, but I'd suggest as you go through it and new packages are introduced, I'd go here: http://bioconductor.org/packages/release/BiocViews.html#___Software to find the package (if it's a bioconductor one). Click through to the package's main page, install it via the instructions you see there, and read the vignettes that it comes with (under the "Documentation" section) before continuing with the book. Have fun, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech