HTTP 403 Forbidden when trying to download available record

Non vengono indicati file o test del repository. Inizia riproducendo l’esempio R con AnnotationHub e ispeziona la richiesta fallita a https://annotationhub.bioconductor.org/fetch/126071, verificando anche se le modifiche all’Ensembl API hanno effetto su di essa. Il lavoro è completato quando la risorsa AH119325 viene scaricata correttamente oppure il problema è stato ricondotto a una modifica di un servizio esterno con un workaround documentato.

Hello, I have been running the following code over the past few months and now errors. Steps to reproduce included.

Not sure where it may be going wrong, maybe it's due to the ongoing changes to the Ensembl API?

library(ensembldb)
library(AnnotationHub)

# Get db cache
ah <- AnnotationHub(cache = ".cache")

# Query for human EnsDb object
ens_query <- query(ah, c("Ensembl", "113", "homo sapiens"))
ens_query

AnnotationHub with 1 record
# snapshotDate(): 2025-10-29
# names(): AH119325
# $dataprovider: Ensembl
# $species: Homo sapiens
# $rdataclass: EnsDb
# $rdatadateadded: 2024-10-28
# $title: Ensembl 113 EnsDb for Homo sapiens
# $description: Gene and protein annotations for Homo sapiens based on Ensembl version 113.
# $taxonomyid: 9606
# $genome: GRCh38
# $sourcetype: ensembl
# $sourceurl: http://www.ensembl.org
# $sourcesize: NA
# $tags: c("113", "Annotation", "AnnotationHubSoftware", "Coverage", "DataImport", "EnsDb", "Ensembl", "Gene", "Protein", "Sequencing",
#   "Transcript") 
# retrieve record with 'object[["AH119325"]]' 

# Download db
ah[["AH119325"]]

downloading 1 resources
retrieving 1 resource
Error loading resource.
 attempting to re-download
downloading 1 resources
retrieving 1 resource
Error: failed to load resource
  name: AH119325
  title: Ensembl 113 EnsDb for Homo sapiens
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/126071'
  local file path: '.cache/2819d6e228c7f_126071'
  reason: HTTP 403 Forbidden. 
2: bfcadd() failed; resource removed
  rid: BFC7
  fpath: 'https://annotationhub.bioconductor.org/fetch/126071'
  reason: download failed 
3: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/126071'
  cache resource: 'AH119325 : 126071'
  reason: bfcadd() failed; see warnings() 
4: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/126071'
  local file path: '.cache/2819d40183cc1_126071'
  reason: HTTP 403 Forbidden. 
5: bfcadd() failed; resource removed
  rid: BFC8
  fpath: 'https://annotationhub.bioconductor.org/fetch/126071'
  reason: download failed 
6: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/126071'
  cache resource: 'AH119325 : 126071'
  reason: bfcadd() failed; see warnings() 

Session info

> sessionInfo()
R version 4.5.3 (2026-03-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Australia/Sydney
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] AnnotationHub_4.0.0     BiocFileCache_3.0.0     dbplyr_2.5.2            ensembldb_2.34.0        AnnotationFilter_1.34.0 GenomicFeatures_1.62.0 
 [7] AnnotationDbi_1.72.0    Biobase_2.70.0          GenomicRanges_1.62.1    Seqinfo_1.0.0           IRanges_2.44.0          S4Vectors_0.49.1-1     
[13] BiocGenerics_0.56.0     generics_0.1.4         

loaded via a namespace (and not attached):
 [1] KEGGREST_1.50.0             SummarizedExperiment_1.40.0 httr2_1.2.2                 rjson_0.2.23                xfun_0.57                  
 [6] lattice_0.22-9              vctrs_0.7.3                 tools_4.5.3                 bitops_1.0-9                curl_7.1.0                 
[11] parallel_4.5.3              tibble_3.3.1                RSQLite_3.52.0              blob_1.3.0                  pkgconfig_2.0.3            
[16] Matrix_1.7-4                cigarillo_1.0.0             lifecycle_1.0.5             compiler_4.5.3              Rsamtools_2.26.0           
[21] Biostrings_2.78.0           codetools_0.2-20            GenomeInfoDb_1.46.2         htmltools_0.5.9             RCurl_1.98-1.18            
[26] yaml_2.3.12                 lazyeval_0.2.3              pillar_1.11.1               crayon_1.5.3                BiocParallel_1.44.0        
[31] cachem_1.1.0                DelayedArray_0.36.1         abind_1.4-8                 tidyselect_1.2.1            digest_0.6.39              
[36] purrr_1.2.2                 BiocVersion_3.22.0          dplyr_1.2.1                 restfulr_0.0.16             fastmap_1.2.0              
[41] grid_4.5.3                  cli_3.6.6                   SparseArray_1.10.10         magrittr_2.0.5              S4Arrays_1.10.1            
[46] XML_3.99-0.23               withr_3.0.2                 filelock_1.0.3              rappdirs_0.3.4              UCSC.utils_1.6.1           
[51] bit64_4.8.2                 rmarkdown_2.31              XVector_0.50.0              httr_1.4.8                  matrixStats_1.5.0          
[56] bit_4.6.0                   otel_0.2.0                  png_0.1-9                   memoise_2.0.1               evaluate_1.0.5             
[61] knitr_1.51                  BiocIO_1.20.0               rtracklayer_1.70.1          rlang_1.2.0                 glue_1.8.1                 
[66] DBI_1.3.0                   BiocManager_1.30.27         rstudioapi_0.18.0           jsonlite_2.0.0              R6_2.6.1                   
[71] MatrixGenerics_1.22.0       GenomicAlignments_1.46.0    ProtGenerics_1.42.0