Re: [Bioc-devel] No Windows binary for GenomicRanges

2018-03-28 Thread Hervé Pagès
Hi Gordon, The TIMEOUT that was preventing the Windows binary of GenomicRanges from propagating has been addressed. The latest version of the package (1.31.23) is now available for BioC devel users on all platforms via biocLite(). Cheers, H. On 03/19/2018 10:01 AM, Hervé Pagès wrote: Hi Gordo

Re: [Bioc-devel] Tensorflow support for bioconductor packages

2018-03-28 Thread Hervé Pagès
On 03/28/2018 02:41 PM, Hervé Pagès wrote: Hi Kieran, Note that you can execute arbitrary code at load time by defining an .onLoad() hook in your package. So you *could* put something like this in your package:   .onUnload <- function(libpath)   {     if (!reticulate::py_module_available("te

Re: [Bioc-devel] Tensorflow support for bioconductor packages

2018-03-28 Thread Hervé Pagès
Hi Kieran, Note that you can execute arbitrary code at load time by defining an .onLoad() hook in your package. So you *could* put something like this in your package: .onUnload <- function(libpath) { if (!reticulate::py_module_available("tensorflow")) tensorflow::install_tensorf

[Bioc-devel] How to access git repository as a new maintainer

2018-03-28 Thread Hu, Zicheng
Dear bio-devel, I will be maintaining the package RImmPort in the future. However, I can�t push my changes to its repository in BioConductor. I filled out the google sheet (titled: "git / svn transition: ssh keys") a couple of days ago to request for access but haven�t heard from bioC. What els

[Bioc-devel] FW: GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

2018-03-28 Thread Zhu, Lihua (Julie)
Nitesh, I am trying to fix the following error in the released version by adding the correct encoding in the DESCRIPTION file. However, I encountered the following message. Could you please help? Thanks! Best regards, Julie git push upstream RELEASE_3_6 Counting objects: 401, done. Delta com

Re: [Bioc-devel] Tensorflow support for bioconductor packages

2018-03-28 Thread Michael Lawrence
Presumably the installation of tensor flow only has to happen once, so you could factor your interface such that it installs tensor flow lazily. Michael On Wed, Mar 28, 2018 at 9:23 AM, Kieran Campbell wrote: > Hi all, > > Rstudio have released the Tensorflow package for R - > https://tensorflo

Re: [Bioc-devel] Moving Package from SVN to Git

2018-03-28 Thread Turaga, Nitesh
I just processed the keys today. Please try again. Best, Nitesh > On Mar 28, 2018, at 1:12 PM, Tomasz Stokowy wrote: > > Dear bioc-devel, > > I am moving my package RareVariantVis to GitHub following steps listed here: > https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ >

[Bioc-devel] Moving Package from SVN to Git

2018-03-28 Thread Tomasz Stokowy
Dear bioc-devel, I am moving my package RareVariantVis to GitHub following steps listed here: https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ I submitted my rsa key to Bioconductor and Github and I can connect to Github: Tomaszs-MBP:.ssh tomaszstokowy$ ssh -T g...@gith

Re: [Bioc-devel] hook declined or non-fast-forward problem

2018-03-28 Thread Martin Morgan
On 03/28/2018 11:51 AM, Hongxu Ding wrote: Thank you Martin! I made the updates according to reviewers' comments from Bioinformatics, so I would say these are "new features". So does this mean I'm all set and the updates will be available on Bioconducotr for the next release? yes the cha

Re: [Bioc-devel] hook declined or non-fast-forward problem

2018-03-28 Thread Hongxu Ding
Thank you very much Martin! 2018-03-28 12:51 GMT-04:00 Martin Morgan : > > > On 03/28/2018 11:51 AM, Hongxu Ding wrote: > >> Thank you Martin! >> >> I made the updates according to reviewers' comments from Bioinformatics, >> so I would say these are "new features". >> >> So does this mean I'm all

[Bioc-devel] Tensorflow support for bioconductor packages

2018-03-28 Thread Kieran Campbell
Hi all, Rstudio have released the Tensorflow package for R - https://tensorflow.rstudio.com/tensorflow/ - and we have started incorporating it into some of our genomics packages for the heavy numerical computation. We would ideally like these to be submitted to Bioconductor, but there's a custom

Re: [Bioc-devel] hook declined or non-fast-forward problem

2018-03-28 Thread Martin Morgan
On 03/28/2018 11:19 AM, Hongxu Ding wrote: Thank you very much Morgan! I followed your suggestions and solved the problem. I think the problem is the version is 1.1.0 on Bioconductor, and the version of my new update is 1.0.1. I bumped the version to 1.1.1 and used *_git push g...@git.bioco

Re: [Bioc-devel] hook declined or non-fast-forward problem

2018-03-28 Thread Hongxu Ding
Thank you Martin! I made the updates according to reviewers' comments from Bioinformatics, so I would say these are "new features". So does this mean I'm all set and the updates will be available on Bioconducotr for the next release? Best, Ding 2018-03-28 11:45 GMT-04:00 Martin Morgan : > > >

Re: [Bioc-devel] hook declined or non-fast-forward problem

2018-03-28 Thread Hongxu Ding
Thank you very much Morgan! I followed your suggestions and solved the problem. I think the problem is the version is 1.1.0 on Bioconductor, and the version of my new update is 1.0.1. I bumped the version to 1.1.1 and used *git push g...@git.bioconductor.org:packages/iterClust.git master* for upda

Re: [Bioc-devel] hook declined or non-fast-forward problem

2018-03-28 Thread Martin Morgan
On 03/27/2018 11:14 AM, Hongxu Ding wrote: Dear Nitesh, I think I have similar problem... I tried to push some updates to Bioconductor using *git push upstream master *and having the following problem*:* *To git.bioconductor.org:packages/iterClust.git ! [rejected]master -> mas