Re: [Rd] How to assign NULL value to pairlist element while keeping it a pairlist?

2016-10-15 Thread Martin Maechler
> Michael Lawrence > on Wed, 12 Oct 2016 15:21:13 -0700 writes: > Thanks, this was what I expected. There is a desire to > eliminate the usage of pairlist from user code, which > suggests the alternative of allowing for function > arguments

[Rd] Inconsistent behavior of summary

2016-10-15 Thread Kaiyin Zhong
Here is the code: summary(c(1:5, NA)) summary(c("a", NA)) It seems in the firs case the number of NAs is reported, but not in the second. Tested with R 3.3.1 on a mac. Best regards, Kaiyin ZHONG [[alternative HTML version deleted]] __

[Bioc-devel] Version on GitHub mirror different than Bioconductor

2016-10-15 Thread Raymond Cavalcante
Hello, My recently accepted package (thanks!) annotatr, has mismatching versions on the GitHub mirror (v0.99.20 https://github.com/Bioconductor-mirror/annotatr/blob/master/DESCRIPTION ) and Bioconductor/devel (v0.99.19

Re: [Bioc-devel] Version on GitHub mirror different than Bioconductor

2016-10-15 Thread Martin Morgan
On 10/15/2016 07:53 AM, Raymond Cavalcante wrote: Hello, My recently accepted package (thanks!) annotatr, has mismatching versions on the GitHub mirror (v0.99.20 https://github.com/Bioconductor-mirror/annotatr/blob/master/DESCRIPTION

Re: [Bioc-devel] GitHub and svn

2016-10-15 Thread Gabe Becker
Mani, Related to what Kasper said, one thing you can do is commit directly to the canonical repo for your package (which again is not on github once the package is accepted) from rstudio. It supports svn. ~G On Oct 15, 2016 11:38 AM, "Kasper Daniel Hansen" < kasperdanielhan...@gmail.com> wrote:

Re: [Bioc-devel] GitHub and svn

2016-10-15 Thread Kevin RUE
Dear Mani, That's actually where I think the git-svn bridge becomes useful. If you take the time once to synchronise the devel branch of your package from the Bioconductor-mirror to one of the branch on your GitHub repository (for me the master branch), you could then: 1) commit changes to your

Re: [Bioc-devel] Version on GitHub mirror different than Bioconductor

2016-10-15 Thread Raymond Cavalcante
I noticed that v0.99.20 on the Bioc build servers have an error because of a missing file (inst/extdata/test_annotations_6_tx_gene_symbol.bed). Oddly, that file is present in rcavalcante/annotatr v0.99.20 (added in commit acc43cb), but didn't make it when migrated to Bioc for some reason.

Re: [Bioc-devel] GitHub and svn

2016-10-15 Thread Nathan Sheffield
Hi Kevin, Mani -- Isn't the git-svn bridge deprecated? http://bioconductor.org/developers/how-to/git-svn/ And this message: - Forwarded Message - From: "Dan Tenenbaum" To: "bioc-devel" Sent: Monday, December 28, 2015 11:08:29 AM

Re: [Bioc-devel] GitHub and svn

2016-10-15 Thread Henrik Bengtsson
Hi folks, I'm a person who prefers to use Git as my main source for my Bioc packages. These Git repositories are then synced online to GitHub for each collaboration yada yada. This also means that these days I also tend to think of the Bioconductor SVN repository mostly as a communication

Re: [Bioc-devel] SVN repo and git mirror for accepted package

2016-10-15 Thread Martin Morgan
On 10/15/2016 10:01 AM, Lukas Weber wrote: Hi, Is there anything we need to do to set up the svn repository and git mirror for new packages accepted last week? The issue in the GitHub contributions repo for our package is closed/accepted (

Re: [Bioc-devel] GitHub and svn

2016-10-15 Thread Kasper Daniel Hansen
Not at the moment. We are in the (long) process of changing this, but there is no ETA for it. The complications we currently have, as soon as a package is accepted in Bioconductor, is that the "true" repository then becomes Bioconductor SVN and your Github repository is just a way for you to

[Bioc-devel] SVN repo and git mirror for accepted package

2016-10-15 Thread Lukas Weber
Hi, Is there anything we need to do to set up the svn repository and git mirror for new packages accepted last week? The issue in the GitHub contributions repo for our package is closed/accepted ( https://github.com/Bioconductor/Contributions/issues/128), but the git mirror repo isn't there yet

Re: [Bioc-devel] SVN repo and git mirror for accepted package

2016-10-15 Thread Lukas Weber
Ok that's great, thank you! Lukas On Sat, Oct 15, 2016 at 10:15 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 10/15/2016 10:01 AM, Lukas Weber wrote: > >> Hi, >> >> Is there anything we need to do to set up the svn repository and git >> mirror >> for new packages accepted last

Re: [Bioc-devel] SVN repo and git mirror for accepted package

2016-10-15 Thread Marcel Ramos
Hi Lukas, You will be receiving SVN credentials soon for upload. Please expect a message from Martin Morgan. Regards, Marcel On Sat, Oct 15, 2016 at 10:02 AM Lukas Weber wrote: > Hi, > > Is there anything we need to do to set up the svn repository and git mirror > for new