Re: [Bioc-devel] Vignette update after change in git mirror repo

Thanks for your help, this makes much more sense. Best, Maia On Sun, Apr 23, 2017 at 7:16 PM, Hervé Pagès wrote: > Nothing strange about this. As I said, all packages are built and > checked daily and the build report is updated every day with the new > results. But there

Re: [Bioc-devel] Vignette update after change in git mirror repo

Nothing strange about this. As I said, all packages are built and checked daily and the build report is updated every day with the new results. But there is a lag between your changes in svn and what you see in the build report. More precisely, yesterday's report didn't reflect your latest

Re: [Bioc-devel] Vignette update after change in git mirror repo

Thanks, Hervé. Very strange, when I checked that link earlier today, it appeared to still have errors. All good now! On Sun, Apr 23, 2017 at 4:49 PM, Hervé Pagès wrote: > Hi Maia, > > On 04/23/2017 10:09 AM, Maia Smith wrote: > >> Just an update - the checked in code is

Re: [Bioc-devel] Vignette update after change in git mirror repo

Hi Maia, On 04/23/2017 10:09 AM, Maia Smith wrote: Just an update - the checked in code is passing R CMD check on my computer (no errors, 1 warning), and has a version bump from 0.99.9 to 0.99.10, but I still haven't seen a build attempt on bioconductor since I committed the code a few days

Re: [Bioc-devel] Vignette update after change in git mirror repo

Sorry I lead you astray, earlier, Maia. In general, you do not need to install the package in the vignette. The first code block in the vignette where you did "eval=FALSE" is the way to go. The second code block where you actually do the installation is unnecessary. The package is installed by R

Re: [Bioc-devel] Vignette update after change in git mirror repo

I suppose it's a circular problem - the biocLite code can't be updated until the vignette works, and the vignette doesn't work because the biocLite code is not updated and the vignette depends on the updated code, etc. On Fri, Apr 21, 2017 at 3:20 PM, Maia Smith wrote: > Thanks

Re: [Bioc-devel] Vignette update after change in git mirror repo

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

Re: [Bioc-devel] Vignette update after change in git mirror repo

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

Re: [Bioc-devel] Vignette update after change in git mirror repo

I believe I did (see diff in DESCRIPTION file in the commit - https://github.com/Bioconductor-mirror/timescape/commit/13597696049eda5858b755ca2777486f5b88f588 ). Maia On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis wrote: > Be sure that you bumped the version number to

Re: [Bioc-devel] Vignette update after change in git mirror repo

Be sure that you bumped the version number to trigger a build. Sean On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith 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

Re: [Bioc-devel] Vignette update after change in git mirror repo

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

Re: [Bioc-devel] Vignette update after change in git mirror repo

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

[Bioc-devel] Vignette update after change in git mirror repo

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