Re: [Bioc-devel] new package for accessing some chemical and biological databases

Thank you all for your explanations and suggestions. I'd like first to state that the repos `biodb-repos` is not part of the package. Let me explain a bit about my package. biodb offers a unified framework for accessing very different databases. The user has to create a central instance of the cla

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

Just an FYI, *if* all you're doing is rbind():ing those data frames, then you're better of doing: df <- do.call(rbind, dfs) than df <- Reduce(rbind, dfs) because the former is faster and more memory efficient: > dfs <- rep(list(iris), times=100) > bench::mark(df <- Reduce(rbind, dfs))[,1:7

Re: [Bioc-devel] new package for accessing some chemical and biological databases

Hi, On 9/13/19 06:38, Morgan, Martin wrote: > Putting bioc-devel back in the loop. > > I think that the straight-forward answer to your original query is 'no, git > modules are not supported'. > > I think we'd carry on and say 'packages should be self-contained and conform > to the Bioconducto

Re: [Bioc-devel] new package for accessing some chemical and biological databases

I've lost track of whether the infrastructure is actually used, but certainly some package have a 'longtests' folder e.g. https://github.com/LTLA/beachmat On Fri, 13 Sep 2019 at 16:02, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > We used to have (? or at least discussed the possi

Re: [Bioc-devel] Experiment package does not appear in build report

The ENCODExplorerData package was added as an annotation package not as a data experiment package. While you should continue to push changes to the git repository please let us know when you need this annotation package updated on Bioconductor. It will need to be added manually as annotation p

Re: [Bioc-devel] new package for accessing some chemical and biological databases

We used to have (? or at least discussed the possibility of) occasional extensive checking so we could have tests long_tests (names made up). On Fri, Sep 13, 2019 at 9:50 AM Martin Morgan wrote: > Putting bioc-devel back in the loop. > > I think that the straight-forward answer to your origi

[Bioc-devel] Experiment package does not appear in build report

Hello, I maintain the ENCODExplorerData package. Recently, it has come to our attention that changes to some of the online ENCODE data we rely on broke one of our helper functions, and I pushed a fix to BioConductor devel. However, I can't see our package in the ExperimentData build log, either

Re: [Bioc-devel] new package for accessing some chemical and biological databases

Putting bioc-devel back in the loop. I think that the straight-forward answer to your original query is 'no, git modules are not supported'. I think we'd carry on and say 'packages should be self-contained and conform to the Bioconductor size and time constraints', so you cannot have a very lar

Re: [Bioc-devel] Duplicated method names in purrr and GenomicRanges

Thank you for all of your answers. Michaels solution works fine for me. I had to merge a list of data.frames. Used the solution in this thread here: https://stackoverflow.com/questions/8091303/simultaneously-merge-multiple-data-frames-in-a-list Am 12.09.19 um 13:05 schrieb Michael Lawrence via

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Thanks for these suggestions; I think they're worth considering. I've never been totally satisfied with (my function) flank(), because it's limited and its arguments are somewhat obscure in meaning. You can check out what we did in plyranges: https://rdrr.io/bioc/plyranges/man/flank-ranges.html. Y

[Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Dear bioc-devel, The ?GenomicRanges::`intra-range-methods` are very useful for range arithmetic Feedback request: would it be of general use to add the methods below to the GenomicRanges::`intra-range-method

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

I have commented on the issue on the SPB so Kayla knows to ignore these ERRORs. Cheers Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Tim P

Re: [Bioc-devel] Problems with converting GPos to GRanges.

Hi Charles, Cryptic (but short) answer: the methods package **automatically** creates a coercion method from CTSS to GRanges for you. Unfortunately this method is broken. Decryption: Warning, this will take us to the very dark side of the S4 coercion system! First this automatic method cannot