Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects

l Message- > From: Bioc-devel On Behalf Of > Vincent Carey > Sent: Sunday, December 10, 2023 1:44 PM > To: Christian Arnold > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects > > Good question.

[Bioc-devel] Missing CHM13v2.0 TxDB and OrgDb objects

Hello, I am working with the new human T2T-CHM13v2.0  assembly and while a BSgenome package already exists (BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0), I could not find the corresponding TxDb and OrgDb packages. Is there any information when they may also become available so it is easier to work with t

[Bioc-devel] Package problems due to results() function from other package?

For my package SNPhood that did not receive any code changes or updates in quite a while, I suddenly see errors with Bioc 3.18: https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/SNPhood/nebbiolo2-buildsrc.html Error: processing vignette 'workflow.Rmd' failed with diagnostics: unused ar

[Bioc-devel] Bioc-issue-bot remarks missing / wrong biocViews field in DESCRIPTION

Hi, for a new package submission (https://github.com/Bioconductor/Contributions/issues/2550), I receive an automated bot reply with the following: "The package DESCRIPTION must contain a biocViews field with one or more valid biocViews terms. Please fix your DESCRIPTION. See current biocViews

[Bioc-devel] GenomeInfoDb::fetchExtendedChromInfoFromUCSC broken again?

Hi, it appears that in the newest devel version, fetchExtendedChromInfoFromUCSC is broken (again). I found an earlier post here: https://www.mail-archive.com/bioc-devel@r-project.org/msg06193.html, which however states that this has been fixed already in the previous version 1.11.2 of the p

[Bioc-devel] lpsymphony - BiocParallel crash

Dear Bioconductor developers, I am having a somewhat mysterious and challenging problem which we believe is a bug in either (1) BiocParallel or (2) the lpsymphony library from either Bioconductor or the SYMPHONY backend. The problem is, in a nutshell, that R silently crashes or, to be more pr

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

all.packages(update[instlib == l, "Package"], l, contriburl = >>> contriburl, : >>> installation of package �S4Vectors� had non-zero exit status >>>> sessionInfo() >>> R version 3.3.0 RC (2016-04-28 r70564) >>> Platform: x86_64-apple-darwi

[Bioc-devel] Rsamtools: How to import only the first 1000 or so reads

Dear Bioc-Community, I was wondering if it is currently possible to only import the first X reads rather than all reads from an arbitrary BAM file into a list using Rsamtools with scanBam? I did not find any parameter in scanBamParam that seems to capture what I need. Specifically, I do not wa

[Bioc-devel] Reducing memory footprint of large object

mation for further processing. Do you have any idea if I can save this information more efficiently so that the overall object size is reduced? I could try an Rle, but the structure of the data does not be ideal for this... Any tips are very much appreciated! Thanks, Christian --

[Bioc-devel] Issues with R CMD check and an ExperimentalData package

n to remove vignette sources from inst/doc Any help is appreciated, thanks, Christian -- ————————— Christian Arnold, PhD Staff Bioinformatician SCB Unit - Computational Biology Joint appointment Genome Biology Joint appointment European Bioinformatics Institute (EMBL-EBI) Europe

Re: [Bioc-devel] Proper way of documenting a BiocGenerics generics with extended prototypes

within your `setMethod()` call. In particular you do _not_ need to > write an explicit `@usage` directive. > > See > https://github.com/jimhester/examplePrototype/blob/master/R/package.R > for an example package without any NOTEs for this situation. > > Jim > > On Sun, Sep 20

[Bioc-devel] Proper way of documenting a BiocGenerics generics with extended prototypes

xists, I should use it because this is exactly what my function does also... Thanks, Christian -- — Christian Arnold, PhD Staff Bioinformatician SCB Unit - Computational Biology Joint appointment Genome Biology Joint appointment European Bioinformatics Institute (EMBL-EBI) European Molec

Re: [Bioc-devel] Overloading subset operator for an S4 object with more than two dimensions

structure going to store, how should it behave? > > On Thu, May 14, 2015 at 3:35 AM, Christian Arnold > mailto:christian.arn...@embl.de>> wrote: > > Hi there, > > I am about to develop a Bioconductor package that implements a > custom S4 object, and I am

[Bioc-devel] Overloading subset operator for an S4 object with more than two dimensions

Hi there, I am about to develop a Bioconductor package that implements a custom S4 object, and I am currently thinking about a few issues, including the following: Say we have an S4 object that stores a lot of information in different slots. Assume that it does make sense to extract informat