Failure to download resources (MeSHDb) from AnnotationHub
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@steve-lianoglou-2771
Last seen 1 hour ago
United States

Comrades! Long time no repartee ...

I thought it would be nigh time to upgrade my bioc install to the latest and greatest (bioc3.22), so I gave it a whirl.

I've recently been trying to do some magic with MeSH terms, and wanted to download the latest mouse (AH121915) and human (AH121907) MeSHDb files (v010) from AnnotationHub, however it's throwing an error while trying to download the files .. something about not being able to resolve the host (bioconductorhubs.blob.core.windows.net) that it looks like it's trying to pull these files from.

Witness:

library(AnnotationHub)
ah <- AnnotationHub()

# Note that these are the files I'm after
ah[c("AH121915", "AH121907")]]
# ...
#              title                                
#   AH121915 | MeSHDb for Mus musculus (Mouse, v010)
#   AH121907 | MeSHDb for Homo sapiens (Human, v010)

Trying to download either of these files, like so:

mesh.hs <- ah[["AH121915"]]

Results in the following error:

downloading 1 resources
retrieving 1 resource
Error loading resource.
 attempting to re-download
downloading 1 resources
retrieving 1 resource
Warning messages:
1: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/128661'
  local file path: '/Users/steve/Library/Caches/org.R-project.R/R/AnnotationHub/7b382f3dffdf_128661'
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Could not resolve hostname [bioconductorhubs.blob.core.windows.net]:
Could not resolve host: bioconductorhubs.blob.core.windows.net 
2: bfcadd() failed; resource removed
  rid: BFC22
  fpath: 'https://annotationhub.bioconductor.org/fetch/128661'
  reason: download failed 
3: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/128661'
  cache resource: 'AH121915 : 128661'
  reason: bfcadd() failed; see warnings() 
4: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/128661'
  local file path: '/Users/steve/Library/Caches/org.R-project.R/R/AnnotationHub/7b38f69a1b4_128661'
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Could not resolve hostname [bioconductorhubs.blob.core.windows.net]:
Could not resolve host: bioconductorhubs.blob.core.windows.net 
5: bfcadd() failed; resource removed
  rid: BFC23
  fpath: 'https://annotationhub.bioconductor.org/fetch/128661'
  reason: download failed 
6: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/128661'
  cache resource: 'AH121915 : 128661'
  reason: bfcadd() failed; see warnings() 
Error:
! failed to load resource
  name: AH121915
  title: MeSHDb for Mus musculus (Mouse, v010)
  reason: 1 resources failed to download

Am I doing something wrong, or?

Also, here is my sessionInfo, thanks!

R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.7.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] AnnotationHub_4.0.0 BiocFileCache_3.0.0 dbplyr_2.5.1        BiocGenerics_0.56.0 generics_0.1.4     

loaded via a namespace (and not attached):
 [1] bit_4.6.0            crayon_1.5.3         dplyr_1.1.4          compiler_4.5.2       BiocManager_1.30.26  filelock_1.0.3       tidyselect_1.2.1     Biobase_2.70.0      
 [9] blob_1.2.4           Biostrings_2.78.0    Seqinfo_1.0.0        IRanges_2.44.0       png_0.1-8            yaml_2.3.10          fastmap_1.2.0        XVector_0.50.0      
[17] R6_2.6.1             curl_7.0.0           httr2_1.2.1          tibble_3.3.0         AnnotationDbi_1.72.0 DBI_1.2.3            pillar_1.11.1        rlang_1.1.6         
[25] KEGGREST_1.50.0      cachem_1.1.0         bit64_4.6.0-1        RSQLite_2.4.3        memoise_2.0.1        cli_3.6.5            withr_3.0.2          magrittr_2.0.4      
[33] rappdirs_0.3.3       lifecycle_1.0.4      S4Vectors_0.48.0     vctrs_0.6.5          glue_1.8.0           stats4_4.5.2         purrr_1.2.0          BiocVersion_3.22.0  
[41] httr_1.4.7           tools_4.5.2          pkgconfig_2.0.3
MeSHDb AnnotationHub • 43 views
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shepherl 4.2k
@lshep
Last seen 58 minutes ago
United States

apologies. These are contributed by someone outside the core team. On upload I did not realize they included the older Bioconductor storage location. I have updated the entries to pull from the correct location. Please try again at your earliest convenience.

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That fixed it, thanks Lori!

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