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

[Bioc-devel] Bioconductor 3.5 release: NEWS files

Hi all, One last plug to update your NEWS files. We branch on Monday so please commit changes before then. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the

Re: [Bioc-devel] How to solve warnings generated by loading other packages

Hi, I'll respond on the github issue tracker where the package review is taking place. Valerie On 04/21/2017 08:27 AM, Kristoffer Vitting-Seerup wrote: > Hi Everybody > > I'm currently in the process of adding my newest R package to Bioconductor > and the last issue I need to solve i a warning

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] Bioconductor 3.5 release: April 7 deadlines

Yes, that's what the API freeze means. The goal is to prevent last minute changes in chimeraviz from breaking downstream packages that depend on chimeraviz. By the way, the API freeze was Friday, April 7. Valerie On 04/21/2017 03:21 AM, Stian Lågstad wrote: I've added a new function to my

[Bioc-devel] How to solve warnings generated by loading other packages

Hi Everybody I'm currently in the process of adding my newest R package to Bioconductor and the last issue I need to solve i a warning generated when loading other packages (which I depend on) due to functions with identical names in those packages. More specifcally I get this error: * checking

Re: [Bioc-devel] Bioconductor 3.5 release: April 7 deadlines

I've added a new function to my package chimeraviz (so far it's in a separate branch and not commited to Bioconductor). Does the API freeze mean that I have to wait until the Bioconductor release before I commit it to the devel branch? On Fri, Apr 7, 2017 at 2:38 AM, Valerie Obenchain