Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

Good day, It might be useful to readers to have a comparison table (ticks and crosses) in the MultiAssayExperiment vignette that compares the features available in it to those available in SummarizedExperiment, to allow quicker decision making. -- Dario

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi Anusha, On Wed, Oct 18, 2017 at 2:30 PM, Anusha Nagari < anusha.nag...@utsouthwestern.edu> wrote: > > Can you please let me know how to go about the following NOTE. Or if this is something that should be really taken care of for a successful package build and install: > > * checking

Re: [Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

> Sounds great; please make a pull request against > > https://github.com/Bioconductor/Rsamtools I will send a pull request tomorrow. I will probably have some technical questions on testing and may ask you there on github. Thanks for the quick response. Heng > On Oct 18, 2017, at 16:40,

Re: [Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

On 10/18/2017 04:32 PM, Heng Li wrote: Hi, I am not sure whether I should send the request to this mailing list in this case, but I am not sure what is the best place to ask. Anyway, an alignment with >65535 operators can't be encoded in the current BAM format. Unfortunately, a tiny fraction

[Bioc-devel] Updating Rsamtools to support BAMs with >65535 CIGAR operators

Hi, I am not sure whether I should send the request to this mailing list in this case, but I am not sure what is the best place to ask. Anyway, an alignment with >65535 operators can't be encoded in the current BAM format. Unfortunately, a tiny fraction of ultra-long nanopore reads will be

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

> > On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson > wrote: > >> I think the main reason for reusing/subclassing core classes that users >> can >> appreciate is that it makes it much easier for users to integrate multiple >> packages into a single workflow. Only the most

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi Herve, Thank you for your response. >In other words putting everything in Imports can hurt >usability/friendliness. The approach should be more nuanced. It's >good that the 'R CMD check' NOTE reminds us about the Depends vs >Imports trade-off but for Bioconductor packages the choices made >by

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

Good points. I think Levi hit on the direct reuse argument (via inheritance and composition), and, you're right, interoperability is another big one. On Wed, Oct 18, 2017 at 10:26 AM, Ryan Thompson wrote: > I think the main reason for reusing/subclassing core classes that

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi, On 10/18/2017 09:19 AM, Pariksheet Nanda wrote: Hi Anusha On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari wrote: Depends: includes the non-default packages: ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘GenomicAlignments’

Re: [Bioc-devel] Why should Bioconductor developers re-use core classes?

I think the main reason for reusing/subclassing core classes that users can appreciate is that it makes it much easier for users to integrate multiple packages into a single workflow. Only the most basic of pipelines uses just a single Bioconductor package. For instance, an "edgeR" pipeline

Re: [Bioc-devel] Help with R CMD check NOTEs

Hi Anusha On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari wrote: > > Depends: includes the non-default packages: > ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ > ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’ > Adding so many packages to the

[Bioc-devel] Fail to push changes on RELEASE_3_5

Hi every one I am Mohammed OE the maintainer of cellbaseR package. I am getting this error while trying to push a bug fix to RELEASE branch remote: FATAL: W refs/heads/RELEASE_3_5 packages/cellbaseR m.abdallah DENIED by fallthru remote: error: hook declined to update refs/heads/RELEASE_3_5 To

Re: [Bioc-devel] ShortRead readFasta UniProt Incorrect Import

Hi, I just modified the Sequence Data workflow to suggest the use of readDNAStringSet() and family to read in a FASTA file. Cheers, H. On 10/18/2017 08:03 AM, Martin Morgan wrote: On 10/18/2017 01:00 AM, Dario Strbenac wrote: Good day, If I have a FASTA file that contains

Re: [Bioc-devel] ShortRead readFasta UniProt Incorrect Import

On 10/18/2017 01:00 AM, Dario Strbenac wrote: Good day, If I have a FASTA file that contains sp|Q9NYW0|T2R10_HUMAN Taste receptor type 2 member 10 OS=Homo sapiens GN=TAS2R10 PE=1 SV=3 MLRVVEGIFIFVVVSESVFGVLGNGFIGLVNCIDCAKNKLSTIGFILTGLAISRIFLIWI

Re: [Bioc-devel] EXTERNAL: Cardinal duplicate commits

Hi Kylie, I have reset your package to its original state. The best way to proceed is with this documentation, http://master.bioconductor.org/developers/how-to/git/sync-existing-repositories/ You specifically want to take a look at point#8

Re: [Bioc-devel] EXTERNAL: FW: attract problems reported by the "Build/check report" for BioC 3.5

Thank you very much! Best, Sam On Oct 17, 2017, at 9:58 PM, Obenchain, Valerie > wrote: Yes, if all is green on the build report you can ignore it. Thanks. Valerie On 10/17/2017 11:46 AM, Samuel E Zimmerman wrote:

Re: [Bioc-devel] EXTERNAL: Git push error and duplicate commits

Hi Matthew, I’ve reset your package to the original clean state. Same place we were last time when this happened. I encourage you to ask questions on bioc-devel if you are not sure about a certain command, or are facing problems. Best, Nitesh > On Oct 13, 2017, at 3:31 PM, Turaga, Nitesh

Re: [Bioc-devel] EXTERNAL: Needs access to devel Git Repository

We process the keys manually at noon EST every business day. You submitted at 17/10/2017 21:54:46 . Please wait. Best, Nitesh > On Oct 17, 2017, at 11:33 PM, Yang Liao wrote: > > Dear Bioconductor maintainers, > > > I'm the co-maintainer of the Rsubread package. When