Thanks for your feedback James. I'm not sure why this error is appearing, because the latest svn commit *changed* that error, and shouldn't be looking for "frac" any longer - here is the code copied from the bioconductor mirror -
stop("Perturbations data frame must have the following column names: ", "\"pert_name\", \"prev_tp\"") On Fri, Apr 21, 2017 at 1:53 PM, James W. MacDonald <jmac...@uw.edu> wrote: > The update won't get built if there is an error during check: > > Quitting from lines 42-54 (timescape_vignette.Rmd) > Error: processing vignette 'timescape_vignette.Rmd' failed with > diagnostics: > Perturbations data frame must have the following column names: > "pert_name", "prev_tp", "frac" > Execution halted > > You can either check the build page (which you should be doing, since > packages that fail check won't be part of the release on MONDAY): > http://bioconductor.org/checkResults/devel/bioc-LATEST/ or (better yet), > you should build and check locally before you check in your changes. > > On Fri, Apr 21, 2017 at 4:41 PM, Maia Smith <ma...@sfu.ca> wrote: > >> I believe I did (see diff in DESCRIPTION file in the commit - >> https://github.com/Bioconductor-mirror/timescape/commit/1359 >> 7696049eda5858b755ca2777486f5b88f588 >> ). >> >> Maia >> >> >> >> On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis <seand...@gmail.com> wrote: >> >> > Be sure that you bumped the version number to trigger a build. >> > >> > Sean >> > >> > >> > On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith <ma...@sfu.ca> wrote: >> > >> >> Hi Sean, >> >> >> >> Thanks for your response, perhaps I was unclear. I used "Scenario 1: >> Use >> >> Git Locally, No GitHub Repository" in the how-to page, and committed >> to svn >> >> (I think!). The changes are reflected in the bioconductor mirror ( >> >> https://github.com/Bioconductor-mirror/timescape) but not in the >> >> vignette (https://bioconductor.org/packages/devel/bioc/vignettes/time >> >> scape/inst/doc/timescape_vignette.html). Perhaps I made an error >> >> somewhere? >> >> >> >> Best, >> >> Maia >> >> >> >> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis <seand...@gmail.com> >> wrote: >> >> >> >>> Hi, Maia. >> >>> >> >>> The git mirror is not used for building packages. Instead, you will >> >>> need to commit to svn for changes to show up on Bioconductor. See >> here for >> >>> details of working with git and svn together. >> >>> >> >>> https://www.bioconductor.org/developers/how-to/git-mirrors/ >> >>> >> >>> If I misunderstood what you are saying, could you clarify a bit? >> >>> >> >>> Sean >> >>> >> >>> >> >>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith <ma...@sfu.ca> wrote: >> >>> >> >>>> How long does it take for the html vignette to update after a change >> in >> >>>> the >> >>>> git mirror has taken place? I changed my code in the git mirror a few >> >>>> days >> >>>> ago, and the html vignette hasn't incorporated these changes yet. >> >>>> >> >>>> Thanks in advance for your help. >> >>>> >> >>>> Maia >> >>>> >> >>>> [[alternative HTML version deleted]] >> >>>> >> >>>> _______________________________________________ >> >>>> Bioc-devel@r-project.org mailing list >> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >>>> >> >>> >> >> >> > >> > >> > -- >> > Sean Davis, MD, PhD >> > Center for Cancer Research >> > National Cancer Institute >> > National Institutes of Health >> > Bethesda, MD 20892 >> > https://seandavi.github.io/ >> > https://twitter.com/seandavis12 >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel