Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Laurent Gatto
Dear all, I ended up implementing the branch specific .gitingore hack described in on Stackoverflow http://stackoverflow.com/questions/29579546/git-excludesfile-for-a-branch/29583813#29583813 My notes and implementation are available here http://lgatto.github.io/branch-specific-gitignore/

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Laurent Gatto
On 23 December 2016 18:26, Robert M. Flight wrote: > They are "orphan" branches, so they don't follow the parent. This was > the original protocol for creating project pages on github for the > longest time, you can see an example in the documentation here:https:/ > /help.github.com/articles/crea

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Robert M. Flight
They are "orphan" branches, so they don't follow the parent. This was the original protocol for creating project pages on github for the longest time, you can see an example in the documentation here: https://help.github.com/articles/creating-project-pages-using-the-command-line/ They are a pain i

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Laurent Gatto
On 23 December 2016 17:52, Kasper Daniel Hansen wrote: > Seems to be a good start. > > But I don't understand why NEWS.md is ok and NEWS.Rd is ignored, given > than NEWS.md is not (I think) compatible and NEWS.Rd is. What is irritating is that NEWS.md is not (yet?) supported by news()! I say no

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Laurent Gatto
Dear Sean and Robert, On 23 December 2016 17:24, Robert M. Flight wrote: > Yes, this seems like a time where using a non-standard site directory > on Github is useful, or as Sean said, using a separate branch to serve > the html content. It's not clear to me how a separate branch is the solutio

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Kasper Daniel Hansen
Seems to be a good start. But I don't understand why NEWS.md is ok and NEWS.Rd is ignored, given than NEWS.md is not (I think) compatible and NEWS.Rd is. Best, Kasper On Fri, Dec 23, 2016 at 12:24 PM, Robert M. Flight wrote: > Yes, this seems like a time where using a non-standard site directo

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Robert M. Flight
Yes, this seems like a time where using a non-standard site directory on Github is useful, or as Sean said, using a separate branch to serve the html content. -Robert On Fri, Dec 23, 2016 at 12:19 PM Sean Davis wrote: > Github allows you to set the branch for the docs directory if I recall. > P

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Sean Davis
Github allows you to set the branch for the docs directory if I recall. Perhaps a separate branch with a docs directory (not master) is a viable way to go? Sean > On Dec 23, 2016, at 12:16 PM, Laurent Gatto wrote: > > > There's actually another side-effect for Bioconductor. The package > we

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Laurent Gatto
There's actually another side-effect for Bioconductor. The package website is (by default) generated in the package's ./docs directory. This is very handy, as it can be set directly on Github as a Github page and becomes available as https://username.github.io/pkgname. This also means that the do

Re: [Bioc-devel] Package reference manuals in html

2016-12-23 Thread Laurent Gatto
Dear all, I'm following up re my online references suggestion with my recent experience with Hadley's pkgdown package https://github.com/hadley/pkgdown It doesn't address the cross-package issue (which is a difficult one anyway), but does pretty much everything else (with some caveats though,

Re: [Bioc-devel] Question about status of new package submission

2016-12-23 Thread Jurat Shayidin
Dear Lori : Thanks for giving prompt help on this issue. Because of I forked old version of contribution repository, my package issued on wrong place. Now I update package submission issue to the suggested repository, it can be visible the issue list. Thank you very much. Best regards : Jurat O

Re: [Bioc-devel] Question about status of new package submission

2016-12-23 Thread Shepherd, Lori
Are you sure you submitted the package to the right location? Normally we see new packages as issues on https://github.com/Bioconductor/Contributions/issues once they are submitted. Please ensure you use this link to submit your package: https://github.com/Bioconductor/Contributions/issues/new

[Bioc-devel] Question about status of new package submission

2016-12-23 Thread Jurat Shayidin
Dear Bioconductor team : Since I've issued new package submission to Bioconductor project, there is no update on assigner for my packages. I am sure that I did follow Bioconductor package submission, and contribution instruction. I believe evaluating new packages could takes time, but I don't have