Re: [Bioc-devel] Maintenance of MetaNeighbor package

2020-09-03 Thread Jesse Gillis
Hi Nitesh, That is confirmed for both me and Manthan (who was a computational science developer in my lab). Cheers, Jesse On Thu, Sep 3, 2020 at 10:00 AM Stephan Fischer wrote: > > Hi Jesse, Manthan, Nitesh, > > I wrote an e-mail earlier this week to Bioconductor support to take over > mainte

Re: [Bioc-devel] Maintenance of MetaNeighbor package

2020-09-03 Thread Stephan Fischer
Hi Jesse, Manthan, Nitesh, I wrote an e-mail earlier this week to Bioconductor support to take over maintenance of the MetaNeighbor package. Nitesh nicely offered to help me with the task, but would like to make sure that everyone agrees first. Can you please briefly confirm the change by answe

Re: [Bioc-devel] Maintenance of MetaNeighbor package

2020-09-03 Thread Nitesh Turaga
Hi Stephan, First, I’d like you to cc Dr. Jesse Gillis and also Manthan so we know that everyone is in agreement. I can help you with the permissions on the Bioconductor repo. Before you get permissions you will only be able to fetch using the HTTP protocol, i.e git remote set-url up

[Bioc-devel] List of Deprecated Packages for Bioc3.12

2020-09-03 Thread Shepherd, Lori
Please see the support site post for the current list of deprecated packages for release 3.12. These packages will be removed from Bioc3.13. It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We encour

Re: [Bioc-devel] glitches with releaseName() and seqlevelsStyle()

2020-09-03 Thread Robert Castelo
Hi Hervé, On 02/09/2020 21:44, Pages, Herve wrote: Hi Robert, On 9/2/20 11:12, Robert Castelo wrote: hi, i've found the following glitches with 'releaseName()' and 'seqlevelsStyle()', i guess due to recent changes in BSgenome and GenomeInfoDb, which is why i'm cc'ing Hervé ;) ===Bi

Re: [Bioc-devel] fetch upstream of an existing package

2020-09-03 Thread Irene Zeng
Hello, Nitesh, The FAQ is very helpful. I have the remote access to the bioconductor repository now. The package is "sparsenetgls" and now can be cloned. I have checked all the changes in the updated version. I am going to commit changes in the bioconductor repository, but received the follow