[Bioc-devel] SRAdb::sraConvert returns results in arbitrary order

2016-11-17 Thread Ryan C. Thompson
Hello, I was recently bitten by an unexpected behavior in the sraConvert function from the SRAdb package. I wanted to fetch the other SRA IDs associated with the SRX numbers of 32 samples, and I used the sraConvert function to do so. However, I did not realized that sraConvert returns the

Re: [Bioc-devel] adding new features to current release branch

2016-11-17 Thread Kasper Daniel Hansen
No, you should not add new functions to the release branch. The documentation is pretty clear. The only thing you should change is bug fixes (and perhaps documentation improvements which could be thought of as bug fixes). Kasper On Thu, Nov 17, 2016 at 4:13 AM, Anand MT

Re: [Bioc-devel] adding new features to current release branch

2016-11-17 Thread Martin Morgan
On 11/17/2016 04:13 AM, Anand MT wrote: Hi Mods, My package maftools is now in release branch. Since the release, I haven't made any bug fixes or any sort of changes. Now I have few bug fixes and new functions that I want to add as they are helpful to users. Since, its mentioned only bug fixes

Re: [Bioc-devel] vmatchPattern Returns Out of Bounds Indices

2016-11-17 Thread Hervé Pagès
Hi, These questions really belong to the support site. On 11/16/2016 04:00 PM, Dario Strbenac wrote: Hello, If using vmatchPattern to find a sequence in another sequence, the resulting end index can be beyond the length of the subject XStringSet. For example: forwardPrimer <-

Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster

2016-11-17 Thread Pariksheet Nanda
On Tue, Nov 15, 2016 at 7:34 PM, Martin Morgan wrote: > On 11/15/2016 09:52 AM, Obenchain, Valerie wrote: >> On 11/15/2016 03:32 AM, Pariksheet Nanda wrote: >>> >>> It would be great to have an OrganismDb package for >>> Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and >>>