Re: [Bioc-devel] Error in Vignette of package

Hi all,  I've also followed this thread as the FELLA package has problems with the vignette as well.  I have two issues (link) First:Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim "

[Bioc-devel] Cairo dependency problem in the OSX machine

Hello all, Recently, a package I submitted to Bioconductor failed with an error message in the OS X system. This is the link for the build: http://bioconductor.org/spb_reports/PubScore_buildreport_20191208212325.html#celaya2_buildsrc_anchor The problem was with the Cairo package, which is a depe

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

Hi Alex, The easiest way to do this is literally just "fetch and merge". 5371 git clone g...@github.com:al2na/methylKit.git 5372 cd methylKit 5377 git remote add upstream g...@git.bioconductor.org:packages/methylKit 5378 git fetch --a

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

As you can see in the branch network https://github.com/al2na/methylKit/network , I already rebased all commits to a copy of bioc master and checked the build on travis, but I was wondering whether this is the best way to do it. Because this way I am r

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

The package I am talking about is methylKit, (https://github.com/al2na/methylKit ). > On 9. Dec 2019, at 16:29, Turaga, Nitesh > wrote: > > Hi, > > Please let me know which package you are talking about. > > Also, give me your GitHub package name. >

Re: [Bioc-devel] How to move package from workflow to software

Hi Julien, After re-considering how this package should go forward. Please submit your package to the https://github.com/Bioconductor/Contributions. This will put your package through the Single Package Builder which will help us review your package better. There have been significant code ch

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

Hi, Please let me know which package you are talking about. Also, give me your GitHub package name. Nitesh > On Dec 9, 2019, at 7:24 AM, Alexander Gosdschan wrote: > > Hi, > > Somehow I missed to push a large number of commits to the bloc git master > branch before the latest release and

[Bioc-devel] Rebasing possible on bioconductor git ?

Hi, Somehow I missed to push a large number of commits to the bloc git master branch before the latest release and now I have 50 commits on GitHub that happened before the release. What would be the best way to get the git remotes in sync again? Is it possible to rebase commits on the bioc ma

Re: [Bioc-devel] Error in Vignette of package

Hi Simina, thank you for reporting the remaining problem on Windows builders. I have just made an adjustment to BiocStyle which should resolve the issue. Cheers, Andrzej On Sun, Dec 8, 2019 at 4:18 PM Simina Boca wrote: > Hi all, > I've been following this conversation as I was having the same