Re: [Bioc-devel] BFG repo cleaner did not perfectly work

Hi Adam, I think the recommended way to remove large, inadvertently committed files from a git repo is no longer BFG or filter-branch, but a new approach called `filter-repo`. You might try it. You can read about it here: https://github.com/newren/git-filter-repo I've found it easier to use

Re: [Bioc-devel] as.list of a GRanges

For what it's worth, my package (LOLA) was one that used as.list on a GRanges or GRangesList, and those calls were broken by changes to devel. Since I was also pushing changes at the time, I assumed the devel build errors were due to my updates -- I spent quite a bit of time trying to figure

Re: [Bioc-devel] Issues with GenomicRanges updates

a a namespace (and not attached): [1] zlibbioc_1.25.0    compiler_3.5.0 tools_3.5.0 [4] XVector_0.19.8 GenomeInfoDbData_1.1.0 RCurl_1.95-4.10 [7] bitops_1.0-6 On 02/10/2018 10:40 PM, Nathan Sheffield wrote: Hi Herve, Never mind, I see now I am still a day old, looks like I was looking at y

Re: [Bioc-devel] Issues with GenomicRanges updates

] S4Vectors_0.17.31 BiocGenerics_0.25.3 -Nathan On 02/10/2018 07:33 PM, Nathan Sheffield wrote: According to my `sessionInfo` (see below), those are the versions I had been using: other attached packages: [1] GenomicRanges_1.31.19 GenomeInfoDb_1.15.5   IRanges_2.13.25 [4] S4Vectors_0.17.31

Re: [Bioc-devel] Issues with GenomicRanges updates

omeInfoDbData_1.1.0 RCurl_1.95-4.10 [7] bitops_1.0-6 On 02/10/2018 02:48 PM, Nathan Sheffield wrote: I'm having some issues getting my package LOLA to pass R CMD check using the updated dev versions of GenomicRanges et al. It seems like any time I try to apply something across a "CompressedGRanges

[Bioc-devel] Issues with GenomicRanges updates

I'm having some issues getting my package LOLA to pass R CMD check using the updated dev versions of GenomicRanges et al. It seems like any time I try to apply something across a "CompressedGRangesList" object, it's giving errors when I use mclapply from parallel. Here's a reproducible

Re: [Bioc-devel] EXTERNAL: Re: DOI for packages

assing metadata along, or perhaps it's a problem with crosscite or something? I'm not sure. Any thoughts? Nathan Sheffield, PhD Assistant Professor Center for Public Health Genomics University of Virginia www.databio.org On 10/19/2017 03:19 PM, Shepherd, Lori wrote: > Many Thanks to Sean Davis for

Re: [Bioc-devel] Git Transition Plan

Hi Nitesh and all, Can you give any status update on the SVN-to-git transition? I haven't seen any news since this exchange in March -- is the announced public beta in progress or ongoing? Are new package submissions going straight into git at this point? Or did I miss something? Thanks,

Re: [Bioc-devel] Question about R functions

HI Jing, You should export FA FB and FC, but don't export FD. If using roxygen2 for documentation you use "#' @export" on the ones to export, and just don't document FD and it won't be exported by default. Hope that helps, -Nathan On 03/30/2017 04:02 PM, Jing Wang wrote: Hi, I have

[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] GitHub and svn

Hi Kevin, Mani -- Isn't the git-svn bridge deprecated? http://bioconductor.org/developers/how-to/git-svn/ And this message: - Forwarded Message - From: "Dan Tenenbaum" To: "bioc-devel" Sent: Monday, December 28, 2015 11:08:29 AM

[Bioc-devel] New package: LOLA - Locus overlap analysis for enrichment of genomic ranges

/sheffien/LOLA). We would be eager to hear any suggestions or feedback! Nathan Sheffield and Christoph Bock ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel