Re: [Bioc-devel] How to set dimnames inside constructor function?

2020-06-25 Thread Hervé Pagès
Hi Muad, I'm not able to reproduce this. With a naked 'count' matrix: library(SummarizedExperiment) count <- matrix(1:15, ncol=3) row_data <- DataFrame(stuff=runif(5)) se1 <- SummarizedExperiment(list(count=count), rowData=row_data) dimnames(se1) <- list(sprintf("Gene%04d", 1:5),

Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

2020-06-25 Thread Hervé Pagès
Hi Ahmed, Just a heads up that Lori's workaround (reinstalling iheatmap from source on all the builders) should be considered a temporary one and that the fundamental problem remains. The fundamental problem being that the iheatmap's Windows and Mac binaries that are on CRAN are broken. And

Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

2020-06-25 Thread Erik Christensen
Thank you! @return was the correct tag. -Original Message-From: Mike Smith To: Erik Christensen Cc: bioc-devel Subject: Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.Date: Thu, 25 Jun 2020 17:39:18 +0200 Hi Erik, I think the #' @return tag will create the \value{} section in

Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

2020-06-25 Thread Mike Smith
Hi Erik, I think the #' @return tag will create the \value{} section in the Rd file. Mike On Thu, 25 Jun 2020 at 17:24, Erik Christensen wrote: > Hello, > > Is there a way to add the value section in man pages using roxygen tags? I > am currently using "@section Value: ..." but this fails

Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

2020-06-25 Thread Shepherd, Lori
I think it's looking for details on the return value for the functions. I believe the correct syntax is @return to add a return value section in roxygen Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton

[Bioc-devel] Passing BiocCheck with roxygen2 tags.

2020-06-25 Thread Erik Christensen
Hello, Is there a way to add the value section in man pages using roxygen tags? I am currently using "@section Value: ..." but this fails biocheck with "WARNING: Add non-empty \value sections to the following...{{dropped:18}} ___

[Bioc-devel] New maintainer request for GAPGOM package

2020-06-25 Thread Casper van Mourik
Dear Bioconductor, I wish to transfer the package maintainer for the GAPGOM Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.GAPGOM). The new maintainer would be Rezvan Ehsani (rezvanehsan...@gmail.com). Thanks in advance. With kind regards, Casper van Mourik [[alternative