[Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

2017-04-05 Thread Pariksheet Nanda
Hi bioconductor devs, The BSgenomeViews class has been very useful in efficiently propagating metadata for running Biostring operations. I noticed something unexpected when iterating over views - it seems to return the Biostrings object instead of a single length Views object, and thus loses the

[Bioc-devel] Bioconductor 3.5 release: db0, OrgDb and TxDb packages

2017-04-05 Thread Obenchain, Valerie
Hi, The new db0, OrgDb and TxDb packages are now available in the devel branch. # db0: Updated all 19: anopheles.db0_3.4.2.tar.gz chicken.db0_3.4.2.tar.gz fly.db0_3.4.2.tar.gz pig.db0_3.4.2.tar.gz xenopus.db0_3.4.2.tar.gz arabidopsis.db0_3.4.2.tar.gz chimp.db0_3.4.2.tar.gz

[Bioc-devel] Using R Markdown for creating reproducible manuscripts – new blog post from eLife Labs

2017-04-05 Thread Emily Packer
[With apologies for cross-posting] Hi all, We have today published a blog post on eLife Labs about how scientists can use the dynamic document language, R Markdown, for creating reproducible manuscripts. At eLife, we aim to make the communication of results more beneficial for the scientific

[Bioc-devel] Commiting from git to svn

2017-04-05 Thread Lluís Revilla
Dear all, Short problem: I am a trying to sync my new package BioCor git repository with the Bioconductor svn repository. But I am failing when I do git svn dcommit. Long history of the problem I did some changes on my master branch (where I developed until now) then I used the update_remotes.sh

Re: [Bioc-devel] Check error on malbec2

2017-04-05 Thread Aimin Yan
Yes, it is. Aimin On Wed, Apr 5, 2017 at 7:20 AM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > Are these permanent system files or files that are created during > examples/vignettes? > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of

Re: [Bioc-devel] Check error on malbec2

2017-04-05 Thread Shepherd, Lori
Are these permanent system files or files that are created during examples/vignettes? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Aimin