[Bioc-devel] Migration of many scater utilities to scuttle

Dear list, scater's functions have now been split into two packages: the plotting functions stay in scater while many of the non-plotting utilities (QC, normalization, aggregation) move into the new scuttle package. This has been done to prune the dependency tree by removing

Re: [Bioc-devel] How I hide non-exported function from the manual

On Wed, Jun 3, 2020 at 11:48 PM stefano wrote: > Hello Community, > > I am used to document function although hey are not exported > > I suppose you are talking about tidybulk? I am somewhat mystified by the behavior of %vjcair> R CMD build tidybulk * checking for file ‘tidybulk/DESCRIPTION’

Re: [Bioc-devel] Bioconductor package tidybulk

Thanks Lori, I have to questions 1) I got versioning error ``` rstudio-1 267 % git push upstream master Counting objects: 372, done. Delta compression using up to 32 threads. Compressing objects: 100% (276/276), done. Writing objects: 100% (290/290), 1.13 MiB | 0 bytes/s, done. Total 290

Re: [Bioc-devel] How I hide non-exported function from the manual

hi stefano what package are you talking about, what is the exact error message you are concerned about (please transcribe or copy exactly) and what version of R are you working with? thank you On Wed, Jun 3, 2020 at 11:48 PM stefano wrote: > Hello Community, > > I am used to document

[Bioc-devel] How I hide non-exported function from the manual

Hello Community, I am used to document function although hey are not exported ``` #' Get differential transcription information to a tibble using edgeR. #' #' @import dplyr #' @import tidyr #' @import tibble #' @importFrom magrittr set_colnames #' @importFrom stats model.matrix #' @importFrom

Re: [Bioc-devel] SSH Issues

Hi Nitesh, I did not change the username on purpose, maybe it happened because I submitted CoreGx under my GitHub account with Benjamin listed as the maintainer? Anyway, all of our package on Bioconductor are: * genefu * PharmacoGx * predictionnet * survcomp * Xeva *

Re: [Bioc-devel] SSH Issues

Hi Chris, Thanks for that list. I’ll give you and Benjamin access all those packages. That is what you need right? I’ll contact you when it’s done. Don’t do anything from your end just yet. Best, Nitesh > On Jun 3, 2020, at 1:26 PM, Chris Eeles wrote: > > Hi Nitesh, > > I did not change

Re: [Bioc-devel] SSH Issues

Hi Chris, I just checked and it seems you have changed the username in Benjamin’s account. Is that correct? So, the mapping is lost for all the packages Benjamin had, and your username as well has lost all of it’s mapping on Git repo. Can you tell me what packages you need access to? We

Re: [Bioc-devel] SSH Issues

Hi Chris, http://bioconductor.org/developers/how-to/git/faq/ Take a look at #13 and #14. I’ll be able to better help you with more information. Best, Nitesh > On Jun 3, 2020, at 10:49 AM, Chris Eeles > wrote: > > Hello Bioconductor

Re: [Bioc-devel] Reducing dependencies

Github Actions offers several advantages over travis-ci including longer sessions and more resources. In addition, applying package caching to a github actions workflow can essentially eliminate the time associated with package installation after the first build. See here for an example (that has

[Bioc-devel] SSH Issues

Hello Bioconductor team, I am having issues pushing updates to the development branch of the CoreGx package. When I try to push to upstream I get: "FATAL: W any packages/CoreGx gangeshberiuhn DENIED by fallthru (or you mis-spelled the reponame) Fatal: Could not read from remote repository.

Re: [Bioc-devel] Bioconductor package tidybulk

It will not be tested before integration. We assume that all maintainers and R CMD build and R CMD check before submitting changes to Bioconductor. You will need to have activated your git credentials account https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ And

Re: [Bioc-devel] Bioconductor package tidybulk

Hello Again, I would be happy to submit the github master with the patch tonight if you could please confirm the commit command. Will it be tested before integration I assume. Thanks a lot! Best wishes. *Stefano * Stefano Mangiola | Postdoctoral fellow Papenfuss Laboratory The Walter

Re: [Bioc-devel] Reducing dependencies

We have recently extended our Bioconductor package tradeSeq to allow different input formats and accommodate extended downstream analyses, by building on other R/Bioconductor packages. I would guess that the problem starts

Re: [Bioc-devel] Reducing dependencies

hi Koen, you can do some analysis of the dependencies using the BiocPkgTools as follows: library(BiocPkgTools) depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"), dependencies=c("Depends", "Imports")) ## if you get this error ## ## Error in readRDS(gzcon(con)) : ##   cannot open

Re: [Bioc-devel] Bioconductor package BEARscc

Hi Lori, Thanks for you message. I am working on this now. I believe I have resolved the issue and pushed the updated package that appears to build and check locally to both the release and devel versions of bioconductor with appropriately updated version numbers. I will check to see how