Re: [Bioc-devel] Git transition is happening August 16th.

installed on your system. perl: warning: Falling back to a fallback locale ("en_US.UTF-8"). Obviously, client-side LC_ALL=C suppresses this, but perhaps it can be silenced server-side, either by supporting many locales, or enforcing the default C locale without warning. Have

Re: [Bioc-devel] Passing packages as variables?

ases <- getSeq(geome::genome, Granges) Hello Zach, recently, I did something like this: requireNamespace(genome) genome <- getExportedValue(genome, genome) I am not sure if it is the best solution, but for the moment, it works. Have a nice week-end, Charles -- Charles Plessy, Ph.D. –

[Bioc-devel] GPos slower than GRanges ?

lot2_2.2.1 codetools_0.2-15 microbenchmark_1.4-2.1 [25] bitops_1.0-6RCurl_1.95-4.10 sandwich_2.4-0 compiler_3.4.3 [29] scales_0.5.0mvtnorm_1.0-6 zoo_1.8-0 (I have also made a benchmark on "real" data, which

[Bioc-devel] Help with class lost after subsetting.

ll as existing code. I am lost on how to troubleshoot this. May I ask for your help ? Best regards, -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Staff scientist in the Luscombe Unit - ~ - https:/

[Bioc-devel] [solved] Help with class lost after subsetting.

Thanks you everybody for the help and the reaction, after MultiAssayExperiment was updated, CAGEr now builds fine. Have a nice day, -- Charles ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] MultiAssayExperiment silently converting RangedSummarizedExperiments into SummarizedExperiments.

) (m<- MultiAssayExperiment(ExperimentList(exp1=rSE))) (m[[1]] <- m[[1]]) m # No change (m<- c(m, exp2=SE)) (m[[1]] <- m[[1]]) m # RangedSummarizedExperiment replaced with SummarizedExperiment sessionInfo() ``` Am I misusing the MultiAssayExperiment objects, or is this a

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

a GRanges object where the ranges are still in UnstitchedIPos class, while in the case of gpos1a and gpos1b they has been converted. I do not know how to deal with that problem and I would appreciate some help. Have a nice day, Charles -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - c

[Bioc-devel] How to add an experiment to an empty MultiAssayExperiment file ?

` and `object <- c(object, myExp=value)` but both of them fail. 2) If I want to update an experiment (for instance because I added a new assay in a SummarizedExperiment, on which I applied a normalisation method), what is the most appropriate way ? Have a nice day, Charles -- Charles Ple

[Bioc-devel] How to use initializing functions correctly ?

object in the wrapping class. Have a nice day, Charles Plessy -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu Toots from

Re: [Bioc-devel] How to use initializing functions correctly ?

alizing function so that new() can promote an UnstitchedGPos to the class, and finally a coerce method so that GRanges can be converted. The result is here: https://github.com/charles-plessy/CAGEr/blob/fix-CTSS-GPos/R/CTSS.R Not sure if you have time to have a look, but anybody's comments would be

[Bioc-devel] Best object structure for representing a pairwise genome alignment ?

se. Before I start to invest time in either direction, I wanted to check on that mailing list if there were other solutions already existing, in particularly closer to the core packages ? Have a nice day, Charles -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.j

[Bioc-devel] Resource temporarily unavailable error with rtracklayer

operator.tools_1.6.3 beanplot_1.2 [58] memoise_1.1.0VGAM_1.1-3 -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu Toots

Re: [Bioc-devel] Resource temporarily unavailable error with rtracklayer

it to GRanges first... Thanks for your help, and have a nice day, Charles -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu Toots from

Re: [Bioc-devel] Resource temporarily unavailable error with rtracklayer

On 15/07/2020 10:53, Charles Plessy wrote: On 14/07/2020 19:56, Vincent Carey wrote: Can you post an example dataset that triggers the error reproducibly? here it is: https://www.dropbox.com/s/ai9itm586clt4y9/gp.Rds?dl=0 It is a GPos object; interestingly I just realised that export.bw

[Bioc-devel] rtracklayer::import (v 1.53.1) fails on xz-compressed files.

Hello on my R 4.1.0 system, rtracklayer version 1.53.1 refuses to load XZ-compressed GFF files, throwing the error "has unsupported type: xzfile". As the function's manual page states that xz-compressed files are handled transparently, I suppose it is a bug? Have a ncie day, Char

[Bioc-devel] KEGGREST is broken and has a long reverse-dependency chain.

wondering if this bug would be a low-hanging fruit for somebody else in this list? Have a nice day, Charles Plessy -- Charles Plessy - - ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ - - charles.ple...@oist.jp Okinawa Institute of Science and Technology Graduate University Senior staff scientist ~~ Lusc