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

Hi Aditya, I think straddle would be a great addition to plyranges. Happy for you to put in a PR and add you as a contributor. Maybe instead of specifying the start etc. we could dispatch on anchored ranges instead? So we’d follow the anchor_start(gr) %>% straddle(). We could also have the

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, On 9/16/19 06:35, Tiago Lubiana Alves wrote: > Hello Mike, > > Thank you for the detailed explanation. > > You are right, for the vignette, I can download it from the ExperimentHub > subset the pbmc3k dataset in the first few lines. The main point of having > a new dataset was to use

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, The following will create a similarly sized subset of the PBMC3k dataset with the counts in-memory as a sparse matrix: pbmc3k <- TENxPBMCData::TENxPBMCData("pbmc3k") mini_pbmc3k <- pbmc3k[1:1700, 1:600] assay(mini_pbmc3k) <- as(assay(mini_pbmc3k), "dgCMatrix") Cheers, Pete On Mon, 16

[Bioc-devel] New Package Submission Deadline for Bioc Release 3.10

The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.10 release is Friday October 4th. Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be

[Bioc-devel] Bioconductor 3.10 release schedule

Hi Bioconductor Community, The release of Bioconductor 3.10 will be on Wednesday October 30. Some key dates can be found on the website release schedule page: http://bioconductor.org/developers/release-schedule/ Bioconductor - Release:

[Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9

Hi All, I just got the message that my package is giving an error during the build process on Bioconductor build server. I saw the logs and found it is failing while building the vignette. I am not sure why it's happening as I have not updated the package since release and it was building without

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

It's on the right track. The case where two ranges are produced is problematic, because we would want this to be a parallel vector operation, where the length of the input is the same as the length of the output. So that last case I think might just ignore the leftend and rightstart arguments with

[Rd] Maybe bug? Using non-integer frequencies in stats::ts

I am developing a package to analyse physiological time-series and I thought that the most reliable and robust solution was to base it on the native stats::ts class. In my domain it is common to express series frequencies as samples-per-second. So ts(..., frequency=10) would mean a signal sampled

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hello Mike, Thank you for the detailed explanation. You are right, for the vignette, I can download it from the ExperimentHub subset the pbmc3k dataset in the first few lines. The main point of having a new dataset was to use it in the examples of functions. The full dataset is too big and the

Re: [Rd] [External] REprintf could be caught by tryCatch(message)

Thank you Luke, I filled https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17612 Best, Jan On Mon, Sep 16, 2019 at 2:15 AM Tierney, Luke wrote: > > You can file it as a wishlist item in the bug trackign system. Without > a compelling case or a complete and well tested patch or both I doubt >

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

Michael, actually, such a generic straddle() could be useful: straddle(leftstart=-100, rightend=100) # extended range straddle(leftstart=-100, leftend=-1) # left flank straddle(rightstart=1, rightend=100) # right flank straddle(leftstart=-100, leftend=-1, rightstart=1, rightend=100) #

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, I suspect what has happened here is that when create the mini_pbmc3k object, you're doing this by subsetting the PBMC, 3k scRNA-seq data from ExperimenHub. The assay data for that are are actually stored in an HDF5 file which will be downloaded and stored in your ExperimentHub cache on

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

Hmm no that wouldn't work, it would become messy trying to figure out when incompatible arguments are provided. Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Monday,

Re: [R-pkg-devel] References in package description file

Fantastic! Thanks! Am 16.09.2019 um 10:05 schrieb David Hugh-Jones: > Hi Wolfgang, > > You can use the CITATION file. See ?citation and ?bibentry. > > Cheers, > David > > > On Mon, 16 Sep 2019 at 08:55, Wolfgang Lenhard > > wrote: > > Hello world, >

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

Hi Michael, Thank you for the pointer to plyranges - looks very useful! > Maybe a better name is "straddle" for when ranges > straddle one of the endpoints? In keeping with the current pattern of > Ranges API, there would be a single function: straddle(x, side, left, > right,

Re: [R-pkg-devel] References in package description file

Hi Wolfgang, You can use the CITATION file. See ?citation and ?bibentry. Cheers, David On Mon, 16 Sep 2019 at 08:55, Wolfgang Lenhard < wolfgang.lenh...@uni-wuerzburg.de> wrote: > Hello world, > is there a standard way of adding references (scientific papers ...) to > the description file in

[R-pkg-devel] References in package description file

Hello world, is there a standard way of adding references (scientific papers ...) to the description file in R packages other than putting the DOI in the description text? Does a best practise exist on how much references are advisable in order not to clutter the package information? Or should

Re: [Rd] head.matrix can return 1000s of columns -- limit to n or add new argument?

Awesome. Gabe, since you already have a workshopped version, would you like to proceed? Feel free to ping me to review the patch once it's posted. On Mon, Sep 16, 2019 at 3:26 PM Martin Maechler wrote: > > Michael Chirico > > on Sun, 15 Sep 2019 20:52:34 +0800 writes: > > >

Re: [Rd] Error: package or namespace load failed for ‘utils

> Laurent Gautier > on Sun, 15 Sep 2019 15:01:09 -0400 writes: > In case a search engine leads someone with the same issue > here, I am documenting the point I reached: > I can reproduce the issue with a small example when > forcing R to not load any package at

Re: [Rd] Printing chinese characters (UTF-8) on R 3.5.2 -windows 10

On Fri, Sep 13, 2019 at 11:53 AM Tomas Kalibera wrote: > On 9/13/19 11:37 AM, IAGO GINÉ VÁZQUEZ wrote: > > But if I type > > >"會" > > the output is > > [1] "會" > > so seemingly it can be represented. Or, am I wrong? > > In RGui you can print the string, because RGui is a Windows Unicode >

Re: [Rd] Error: package or namespace load failed for‘utils

> Laurent Gautier writes: > In case a search engine leads someone with the same issue here, I am > documenting the point I reached: > I can reproduce the issue with a small example when forcing R to not load > any package at startup time (using an Renviron file): > ``` > package <- "utils" >