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Last active January 9, 2026 13:42
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traceback for using GENCODE in bioconductor; need CENTREannotation attached to avoid this
> query(ah, c("GENCODE", "human"))
AnnotationHub with 87 records
# snapshotDate(): 2025-10-29
# $dataprovider: GENCODE, Gencode, BroadInstitute, ENCODE
# $species: Homo sapiens
# $rdataclass: GRanges, list, TxDb, SQLiteConnection
# additional mcols(): taxonomyid, genome, description,
# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
# rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH49010"]]'
title
AH49010 | gen10.gtf.gz
AH49011 | gen10.long.gtf.gz
AH49012 | gen10.long.partition.unstr.gtf.gz
AH49554 | gencode.v23.2wayconspseudos.gff3.gz
AH49555 | gencode.v23.annotation.gff3.gz
... ...
AH75191 | TxDb for Gencode v32 on hg38 coordinates
AH75192 | Annotated genes for Gencode v32 on hg38 coordinates
AH75193 | GenomicState for Gencode v32 on hg38 coordinates
AH107317 | hg19.Crawford.wgEncodeDukeMapabilityRegionsExcludable
AH116730 | GENCODE basic gene annotation v40
> g40 = ah[["AH116730"]]
loading from cache
Error loading resource.
attempting to re-download
downloading 1 resources
retrieving 1 resource
loading from cache
Error: failed to load resource
name: AH116730
title: GENCODE basic gene annotation v40
reason: this db is of type CENTREannotDb but this is not a defined class
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Enter a frame number, or 0 to exit
1: ah[["AH116730"]]
2: ah[["AH116730"]]
3: .local(x, i, j = j, ...)
4: .Hub_get1(x[idx], force = force, verbose = verbose, config = config, progre
5: tryCatch({
fls <- cache(getHub(class), config = config, progress = progr
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatchOne(expr, names, parentenv, handlers[[1]])
8: value[[3]](cond)
9: tryCatch({
message("Error loading resource.", "\n attempting to re-downl
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatchOne(expr, names, parentenv, handlers[[1]])
12: value[[3]](cond)
Selection:
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