Hervé Pagès

I can't reproduce this :( ``` library(GenomicRanges) seqlevelsStyle(GRanges("chrM:1-5")) # [1] "UCSC" seqlevelsStyle(GRanges("MT:1-5")) # [1] "NCBI" "Ensembl" ``` **sessionInfo()** ``` R version 3.6.0 Patched (2019-05-02 r76454) Platform: x86_64-pc-linux-gnu (64-bit) Running under:...

There's no plan at the moment to take advantage of R's support for caching user data to save NCBI or UCSC assembly/genome information and allow `seqlevelsStyle()` to run offline. One...

Bingo! And just when we were talking about the possibility of UCSC suddenly changing the chromosome information of their genomes, they just do it! See issue #27. Note that this...

Hi @jeff-mandell , Just to let you know that I implemented an "offline mode" for `getChromInfoFromUCSC()`. This is in **GenomeInfoDb** 1.33.9. See commit 345f22c55b8c431f1cf8080af3235f78266ade9c. Note that it's only a _partial_...

There are plans to make _some_ assembly metadata available offline but there's no clear roadmap yet. In particular whether it's going to be via AnnotationHub or other means has not...

Hi Constantin, My use case is to efficiently compute: ``` f

I agree. Better not having it than having it do something that is not well defined.

This is a true positive. The unit tests in **ScaledMatrix** construct a ScaledMatrixSeed object for which `extract_array()` doesn't work (non-compliant seed). To reproduce: ``` library(ScaledMatrix) ## Define the CrippledMatrix class...

Looks like **DelayedArray** 0.26 is finally available on all platforms as of today in BioC 3.17: https://bioconductor.org/packages/3.17/DelayedArray @LliliansCalvo Can you try to install again with `BiocManager::install("DelayedArray")`?

Hi Qian, There are 2 ways to deal with this: (1) the _quick-and-dirty_ way that would only let you wrap a List object in a 1-dimensional DelayedArray object, and (2)...