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_queryAnnotationHub 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
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?
Session info