Hervé Pagès

Thanks Michael. I kind of had a premonition that this was actually going to be considered a "feature". It still doesn't really explain why this breaks `callNextMethod()` though. Mimicking the...

see https://stat.ethz.ch/pipermail/bioc-devel/2023-May/019696.html for some context

See issue #26 for a discussion about this. TLDR: One concern is that there's a (small) risk that the cache data become stale after the online NCBI or UCSC data...

Hi @jorainer , See https://github.com/jorainer/ensembldb/issues/88#issuecomment-1212482235. Would that work for you? H.

Hi Robert, It doesn't work here for this particular GAlignments object because its genome is unknown: ``` > seqinfo(gal1) Seqinfo object with 2 sequences from an unspecified genome: seqnames seqlengths...

> Looking at the code of the package of **GenomicAlignments**, the line that builds the Seqinfo object etc... Indeed. I just changed this in **GenomicAlignments** 1.39.4 so now `readGAlignments(file, ...)`...

What's `GetGRangesFromEnsDb`? Where is this function defined? How am I supposed to reproduce this? Please provide a reproducible example and show your `sessionInfo()`. Best

Already reported and discussed in issue #99 with no satisfying solution so far. > So I think it'd be preferable to check if the output of getURL2 is an html...

> Personally I find a not-quite-robust solution that tends to work and sometimes fails is still better than it not working at all. Not from a package maintainer perspective. But...

@Urja25 Are you also behind an http-only proxy? Please show the output of `list_ftp_dir("https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/")`. FWIW here is what I get: ``` > library(GenomeInfoDb) > list_ftp_dir("ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/") [1] "GCF_000001405.10_NCBI34" "GCF_000001405.11_NCBI35" [3] "GCF_000001405.12_NCBI36"...