Re: [Bioc-devel] Git error when pushing to bioconductor

2018-06-07 Thread Turaga, Nitesh
Hi Divy, Can you send me the output of your git status git remote -v Best, Nitesh > On Jun 4, 2018, at 12:50 PM, Kangeyan, Divy wrote: > > Hi Nitesh, >I followed the resolve merge conflict article you provided > step by step. There was no error

Re: [R-pkg-devel] How do I know if/when my package is fit for CRAN?

2018-06-07 Thread Duncan Murdoch
On 07/06/2018 6:23 AM, Voeten, C.C. wrote: Dear list, I have been working on an R package for the past two years. It started as a programming exercise for me to get acquainted with R, and because I had some issues with lmerTest::step (the aim of my package was to automate the protocol I use

Re: [Bioc-devel] workflows are missing from landing pages

2018-06-07 Thread Shepherd, Lori
Sorry the announcement got delayed. We were making updates to the views and website code that displays the landing pages. They are temporarily missing but will be regenerated after the build report completes. This should be remedied over the next day. Lori Shepherd Bioconductor Core Team

Re: [Bioc-devel] workflows are missing from landing pages

2018-06-07 Thread Shepherd, Lori
The devel pages have the documentation displayed. The release pages are being regenerated today. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] html documents not on landing pages

2018-06-07 Thread Shepherd, Lori
Hello everyone, We are implementing some changes to how the documents are displayed on the landing pages. Any vignette/documentation that is currently in HTML format is unavailable temporarily until after the next daily build report posts. All the HTML documents will reappear later this

[Bioc-devel] workflows are missing from landing pages

2018-06-07 Thread Michael Love
It seems like the vignettes are not showing up here: https://bioconductor.org/packages/release/workflows/ https://bioconductor.org/packages/release/workflows/html/rnaseqGene.html https://bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html

Re: [R-pkg-devel] How do I know if/when my package is fit for CRAN?

2018-06-07 Thread Voeten, C.C.
Dear Michael and Rune, Yes, when I started I was hoping that my tinkering might eventually be absorbed into lmerTest. Unfortunately, at the time, my knowledge of R and lmerTest was not sufficient for me to hack at lmerTest, and once I had achieved what I needed for LMMs in my own way (as a

Re: [R-pkg-devel] How do I know if/when my package is fit for CRAN?

2018-06-07 Thread Rune Haubo
On 7 June 2018 at 13:00, Michael Dewey wrote: > > One thing which occurs to me though is whether the maintaner of lmerTest > would accept it into the package? If it has a different philosophy probably > not but perhaps worth asking? In the lmerTest-team we are always open to collaborations. A

Re: [R-pkg-devel] How do I know if/when my package is fit for CRAN?

2018-06-07 Thread Michael Dewey
Comments in-line On 07/06/2018 11:23, Voeten, C.C. wrote: Dear list, I have been working on an R package for the past two years. It started as a programming exercise for me to get acquainted with R, and because I had some issues with lmerTest::step (the aim of my package was to automate the

Re: [Bioc-devel] eval() and evalq() of BiocGenerics used in Rcpp causes segfault in some cases

2018-06-07 Thread Martin Morgan
On 06/07/2018 04:56 AM, Joris Meys wrote: Dear all, the following issue drew my attention. The new package "conflicted" manipulates the search path and by doing so, highlighted that Rcpp is using the BiocGenerics version of evalq() in case BiocGenerics is loaded. Otherwise it uses the base

[Bioc-devel] eval() and evalq() of BiocGenerics used in Rcpp causes segfault in some cases

2018-06-07 Thread Joris Meys
Dear all, the following issue drew my attention. The new package "conflicted" manipulates the search path and by doing so, highlighted that Rcpp is using the BiocGenerics version of evalq() in case BiocGenerics is loaded. Otherwise it uses the base version. This is easily fixed in Rcpp by using

Re: [Bioc-devel] Submit package under a Github organization

2018-06-07 Thread Diogo P. P. Branco
Dear Leonardo, Thank you for the response. I guess I will do the submission normally then. Best, 2018-06-06 19:53 GMT+02:00 Leonardo Collado Torres : > Hi, > > I don't think that anything changes. At least, I don't remember that > being the case (I have a few packages hosted in organization >

Re: [Rd] encoding argument of source() in 3.5.0

2018-06-07 Thread Tomas Kalibera
Thanks, the fix is now in R-patched and will be included in 3.5.1. Tomas On 06/06/2018 09:54 PM, Stephen Berman wrote: On Tue, 5 Jun 2018 16:03:54 +0200 Tomas Kalibera wrote: Thanks for the report, fixed in R-devel (74848). Best Tomas FTR, I confirm that the problem I reported is now