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traceback for using GENCODE in bioconductor; need CENTREannotation attached to avoid this
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| > 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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