Hi Jim, On Wed, Aug 24, 2011 at 11:16 AM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > > > On 8/24/2011 12:38 PM, Dan Tenenbaum wrote: >> >> On Wed, Aug 24, 2011 at 6:42 AM, Vincent Carey >> <stvjc at="" channing.harvard.edu=""> ?wrote: >>> >>> set ask=F in the call? ?an exclude pattern might be nice to have. >> >> Yes, setting ask=FALSE will not prompt at all. >> >> The y/n/c prompt comes from R's update.packages(), so we can't change it. > > Right. But that isn't what I asked. > > To me the issue is that new functionality has been added to biocLite(), > where the default is to update packages. This is good, and is something that > some people have been asking about for years (Hi HB). > > However, the default is to just dump people into update.packages() with ask > = TRUE. Which is fair enough. Some people would be off-put by having things > updated against their wishes. So I see the point of setting ask = TRUE as > the default. > > However, to me it is simpler to just tell people that there are some > packages that can be updated and ask them how they want to handle the > situation. Please see the attached patch. If you want, I can just increment > the version and commit. I added a modified version of your patch. If ask==TRUE, your prompting code is run, otherwise the value of ask is passed unchanged to update.packages(). Also added some code to avoid calling readLines() from a non-interactive session and in that case to behave as though the user pressed "n", as update.packages() does. This will auto-install starting tomorrow shortly after noon Seattle time. Thanks for the suggestion. Dan > > Best, > > Jim > > > > > >> >> Dan >> >>> >>> On Wed, Aug 24, 2011 at 9:26 AM, James W. MacDonald >>> <jmacdon at="" med.umich.edu="">wrote: >>> >>>> Hi, >>>> >>>> I like the new version of biocLite() where it asks if I want to update >>>> outdated package versions. However, if I have say 30 outdated packages, >>>> hitting 'y' 30 times is going to get annoying. >>>> >>>> Can it be changed to something like >>>> >>>> Available updates for 'affy' 'AnnotationDbi' 'Biostrings' etc >>>> Update all (y/N/c hit 'N' to choose by package)? >>>> >>>> And hitting N then sends the end user into the existing process? >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> -- >>>> 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 >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: http://news.gmane.org/gmane.** >>>> >>>> science.biology.informatics.**conductor<http: news.gmane.org="" gma="" ne.science.biology.informatics.conductor=""> >>>> >>> >>> ? ? ? ?[[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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