Re: [Bioc-devel] updating and syncing existing package with Github

2017-11-28 Thread Obenchain, Valerie
On 11/28/2017 01:45 PM, Obenchain, Valerie wrote: Hi Mehrnoush, When posting a question, try to provide as many details as possible. Show commands you've tried, any error messages you see, or point us to links that may be useful. The more details we have the easier it is to help you. >From loo

Re: [Bioc-devel] updating and syncing existing package with Github

2017-11-28 Thread Obenchain, Valerie
Hi Mehrnoush, When posting a question, try to provide as many details as possible. Show commands you've tried, any error messages you see, or point us to links that may be useful. The more details we have the easier it is to help you. >From looking around I found that flowDensity was in the rel

Re: [Bioc-devel] Pandoc issues

2017-11-28 Thread Vladimir Kiselev
Hi Herve, Thanks for your reply! scmap::getSankey() didn't really work in the release, so I switched it off quite long ago by setting `eval = FALSE`. Regarding rmarkdown: I remember when I updated Pandoc I got a different error from rmarkdown, then I googled it and found that it was related to th

Re: [Bioc-devel] SummarizedExperiment: structure loss, when mixing matrix and data.frame data

2017-11-28 Thread Hervé Pagès
Hi, Looks like at an even lower level, S4Vectors:::listElementType() is at the origin of the problem: > S4Vectors:::listElementType(list(matrix(), data.frame())) [1] "vector" Should return "ANY" here. Will try to fix. H. On 11/26/2017 07:03 AM, Martin Morgan wrote: It would seem to be a

Re: [Bioc-devel] Pandoc issues

2017-11-28 Thread Hervé Pagès
Hi Vladimir, mmh... scmap::getSankey() used to work (and still works in the release version of scmap) so I wonder what could have changed in the devel version or in one of its dependencies to cause it to fail now... Anyway we'll look into updating pandoc to the latest version (currently at versi

[Bioc-devel] updating and syncing existing package with Github

2017-11-28 Thread Mehrnoush Malek
?Hello, I tried to sync my package (flowDensity) and followed the instruction, but for some reason I don't see it in bioC check result. It would be great if someone can help, or guide me. Thanks in advance, Mehrnoush ___ Bioc-devel@r-project.org

[Bioc-devel] Pandoc issues

2017-11-28 Thread Vladimir Kiselev
Hi, I am not able to plot Sankey diagrams using `googleVis` in the vignette of my package (scmap). Here is error message: http://bioconductor.org/checkResults/devel/bioc-LATEST/scmap/malbec2-buildsrc.html It says: pandoc: Could not fetch https://www.google.com/jsapi?callback=displayChartSankeyID6