On Thu, Dec 1, 2011 at 2:35 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Thu, Dec 1, 2011 at 2:32 PM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> There used to be the canonical update method: >> >> biocLite("Biobase") >> library(Biobase) >> z <- biocReposList() >> update.packages(repos = z, ask = FALSE) >> >> Which is the only context in which I remember biocLite() and ask = FALSE >> being used in close enough proximity that one might 'misremember' (to quote >> our esteemed ex-president) using biocLite() with that argument. >> > > BTW, there's still a way to do that, as documented here: > > http://bioconductor.org/install/#update-bioconductor-packages Actually, the more up-to-date and concise way to do it is: biocLite(character(), ask=FALSE) Dan > > Dan > > >> Best, >> >> Jim >> >> >> >> >> On 12/1/2011 3:14 PM, Dan Tenenbaum wrote: >>> >>> Hi Kasper, >>> >>> On Thu, Dec 1, 2011 at 11:41 AM, Kasper Daniel Hansen >>> <kasperdanielhansen at="" gmail.com=""> ?wrote: >>>> >>>> I just used biocLite in R-2.13 (.2 patched) with ask=FALSE and got an >>>> error: >>>> >>>> Using R version 2.13.2, biocinstall version 2.8.4. >>>> Installing Bioconductor version 2.8 packages: >>>> [1] "fdrtool" >>>> Please wait... >>>> >>>> Error in download.file(url, destfile, method, mode = "wb", ...) : >>>> ?unused argument(s) (ask = FALSE) >>>> Warning in download.packages(pkgs, destdir = tmpd, available = available, >>>> ?: >>>> ?download of package 'fdrtool' failed >>>> >>>> Seems like the ... argument is passed to download.file. ?Not sure if >>>> this is a "bug" but biocLite used to accept ask=FALSE. >>> >>> Are you sure? I looked in older versions, and it doesn't seem like we >>> ever has an "ask" argument. Incidentally, install.packages() doesn't >>> either, and it passes its ... to download.file() which also doesn't >>> have an "ask" argument. >>> >>>> Btw, it works >>>> in 2.14, so it might not be worth fixing. >>>> >>> Dan >>> >>> >>>> Kasper >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> 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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues