Re: [Bioc-devel] IRanges findOverlaps and queryHits

Hi Nathan, Direct slot access is strongly discouraged, for this very reason. Please stick to using the accessor. And yes, Hits was redefined in terms of a graph model last devel cycle. Michael On Tue, Dec 20, 2016 at 12:16 PM, Nathan Sheffield wrote: > Did the

[Bioc-devel] IRanges findOverlaps and queryHits

Did the findOverlaps return object get a @queryHits slot removed recently? I recently got this error running some of my code: Error: no slot of name "queryHits" for this object of class "SortedByQueryHits" My workflow is basically, fo = findOverlaps(...) fo@queryHits Using queryHits(fo)

Re: [Bioc-devel] Initial setup of git svn with existing GitHub repo - upstream working tree history error

Thanks, Lukas! You are correct that the problem was due to some of the commits between master and devel and I was able to remedy the issue by 'git cherry-pick’ on them one-by-one. Best, Keegan > On Dec 20, 2016, at 9:57 AM, Lukas Weber wrote: > > Hi Keegan, > > I'm

Re: [Bioc-devel] Initial setup of git svn with existing GitHub repo - upstream working tree history error

Hi Keegan, I'm not sure how much this will help you, but I had some similar issues recently. I also wanted to keep my pre-existing development history in my personal GitHub repo, which wasn't straightforward. I ended up solving it by only using 'git cherry-pick' (instead of 'git merge') to

Re: [Bioc-devel] change of maintainer's mail address on release branch

Hi Thomas, Yes, follow the guide lines at the link you cited. ## check out release svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/yourPackage ## make the email change, bump the version and check in cd myPackage svn ci Valerie On 12/20/2016 05:56 AM, Thomas

[Bioc-devel] change of maintainer's mail address on release branch

Dear Bioc-devel community, I face the problem that the validity of my email address runs out soon (I changed the university). This mail address is currently used in one package on release. On the devel branch, the DESCRIPTION file and man pages contain already the most recent email address. The

Re: [Bioc-devel] ‘gWidgets2RGtk2’ is not available in malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64

Hi valerie, It is fine now. Hemi > 在 2016年12月19日，下午9:52，Obenchain, Valerie > 写道： > > It looks like this has cleared up. We couldn't find anything > reproducible so maybe it was a glitch. > > Valerie > > > > On 12/13/2016 07:00 AM, Obenchain, Valerie

Re: [Bioc-devel] New Package submission request to Bioconductor Project

Dear Lori : Thanks for your prompt response. Yes, I did follow new package submission guideline from Bioconductor site, package contribution page helped me how to create new issue, Now I opened the issue for new package submission. Thanks again for Bioconductor team on kind evaluation of my

Re: [Bioc-devel] New Package submission request to Bioconductor Project

We Thank you for taking the time and diligence to try and have a clean R CMD check and BiocCheck before submission. If these are your only issues and you feel the package is ready to be reviewed please submit http://bioconductor.org/developers/package-submission/ and your assigned reviewer

[Bioc-devel] New Package submission request to Bioconductor Project

Dear BiocDevel, Bioconductor Team : I've read Bioconductor contribution repository, and new package submission with full instruction, and make sure I am ready to submit my packages -- MSPC -- to Bioconductor projects. However, my package both succeed with R CMD check, R CMD BiocCheck without any