[Bioc-devel] new 2bit BSgenome data packages

Hi, Most BSgenome data packages have been regenerated to use UCSC 2bit format to store the sequences on disk. The new packages are currently being pushed to the BioC devel repo and should become available in the next hour or so (they'll have version 1.4.0). Some basic testing indicates that this

Re: [Bioc-devel] R CMD CHECK options

Siddharta, The development process I use, which as far as I know is the canonical "Right Way" (tm) is: (Build with no vignettes -this is often skipped) Install and test code or use devtools (repeat many times) Final install Build Check So basically, you should have already successfully installed

Re: [Bioc-devel] Slow performance on scanBam

Hi Martin, thanks for the quick response. The data is certainly shareable. Here is a link to a bam + bai + sam file that I have been using for benchmarking: https://www.dropbox.com/s/eat31mnmmco1zoh/example-bam.tar.bz2 There is a method in SAM to elide the reference names from a header, but I thin

Re: [Bioc-devel] R CMD CHECK options

- Original Message - > From: "Siddhartha Bagaria" > To: "Dan Tenenbaum" > Cc: "Craig Citro" , bioc-devel@r-project.org > Sent: Tuesday, May 13, 2014 12:02:37 AM > Subject: Re: [Bioc-devel] R CMD CHECK options > > Hi Dan, thanks. Just to be sure I understand you, are you saying that > e

Re: [Bioc-devel] Slow performance on scanBam

Hi James -- I don't think there's anything in existence to make this easier, but I'll expose something in the next 24 hours; is your data shareable? There might be deeper things to be done for processing this small-but-numerous style data. Martin On 05/12/2014 05:32 PM, James Bullard wrote: I

Re: [Bioc-devel] [BioC] granges() method for GenomicRanges objects akin to ranges()...

Hi, In summary, would it be feasible to add to 'GenomicRanges'? 1) A 'granges(x, use.mcols=FALSE, ...)' method with signature 'GRanges' that converts to a 'GRanges' object and optionally drops the mcols (if 'use.mcols' is TRUE) 2) A 'dropMcols' or 'dropmcols' method with signature 'GRanges'

Re: [Bioc-devel] R CMD CHECK options

Hi Dan, thanks. Just to be sure I understand you, are you saying that everyone manually installs all deps before running the checks? Sent from my mobile device. > On May 13, 2014, at 10:09 AM, Dan Tenenbaum wrote: > > Hi Siddartha, > > - Original Message - >> From: "Siddhartha Bagaria"