Re: [Bioc-devel] peculiar warning in BiocOncoTK

2019-12-19 Thread Vincent Carey
On Thu, Dec 19, 2019 at 3:11 PM Martin Morgan wrote: > I'd guess that 'car' is trying to use globalVariables() with saying > Imports: utils in the DESCRIPTION and / or importFrom(utils, > globalVariables) in the NAMESPACE? > yes -- "without" ... I will contact John Fox. The error messaging

Re: [Bioc-devel] Trigger a new build after version bump

2019-12-19 Thread Martin Morgan
It seems like in your vignette you are trying to install your own package. But if you needed to install the package, then the vignette wouldn't be available to install it from... ;) In this code chunk ```{r results='hide',message=FALSE,warning=FALSE} if (!requireNamespace("BiocManager", quietly

Re: [Bioc-devel] peculiar warning in BiocOncoTK

2019-12-19 Thread Martin Morgan
I'd guess that 'car' is trying to use globalVariables() with saying Imports: utils in the DESCRIPTION and / or importFrom(utils, globalVariables) in the NAMESPACE? Martin On 12/19/19, 2:22 PM, "Bioc-devel on behalf of Vincent Carey" wrote: I can't get a handle on this apparent issue

[Bioc-devel] peculiar warning in BiocOncoTK

2019-12-19 Thread Vincent Carey
I can't get a handle on this apparent issue with 'car' -- there is some indication of this globalVariables error at https://rdrr.io/github/hadley/tibble/f/revdep/problems.md but I don't see an explanation. The pernicious aspect of this, which seems limited to mac, is that it stops the

Re: [Bioc-devel] Trigger a new build after version bump

2019-12-19 Thread Ahmed Metwally
Hi, The built is has been done on the updates I pushed. Here you see that the release version has been bumped to 1.2.1 instead of 1.2.0 and dev version has been bumped to 1.3.3 instead of 1.3.0. However, I still see the same error as before. Here is the OS built results for the release

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

2019-12-19 Thread Turaga, Nitesh
Hi Ludwig, Thank you for volunteering to take over as maintainer for PathNet and PathNetData. You should now have access to both packages as the maintainer. They should show up on the build machine tomorrow. You should port your fix(s) to the build machine for the PathNet package when you

Re: [Bioc-devel] Question regarding pruning release of large files

2019-12-19 Thread Turaga, Nitesh
Hi Saskia, Mike is correct, you cannot force push to the Bioconductor git repo. If you point me to the GitHub location, and you are confident that you want your repo overwritten, let me know I'll force push it for you. Best, Nitesh > On Dec 19, 2019, at 8:49 AM, Mike Smith wrote: > > Hi

Re: [Bioc-devel] Bioconductor Developers Forum - Thursday 19th December

2019-12-19 Thread Mike Smith
Dear all, Just a reminder that this is happening today. It appears I am resolutely wishing for summer time still - the intended time is 09:00 PST/ 12:00 EST / 18:00 CET Best wishes, Mike On Mon, 16 Dec 2019 at 15:49, Mike Smith wrote: > Dear all, > > The next Bioconductor Developers' Forum

Re: [Bioc-devel] Question regarding pruning release of large files

2019-12-19 Thread Mike Smith
Hi Saskia, There's some documentation on this at https://bioconductor.org/developers/how-to/git/remove-large-data/ I guess the most pertinent part is "The Bioconductor git server does not allow -f or to force push to the git.bioconductor.org location. Please email bioc-devel@r-project.org