AnnotationHub: failed to load resource name
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hxwanghxw • 0
@82c1708d
Last seen 4 months ago
United States

I tried to repeat the code we learned in Coursera >> Bioconductor for Genomic Data Science.

library(rtracklayer)
library(AnnotationHub)
ahub <- AnnotationHub()
table(ahub$rdataclass)
ahub.bw = subset(ahub, rdataclass == "BigWigFile" & species == "Homo sapiens")
bw = ahub.bw[[1]]

The error printed was:

downloading 1 resources
retrieving 1 resource
Error: failed to load resource
  name: AH32002
  title: E001-H3K4me1.fc.signal.bigwig
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/37442’
  local file path: ‘~/Library/Caches/AnnotationHub/a42f440187eb_37442’
  reason: SSL certificate problem: Invalid certificate chain 
2: bfcadd() failed; resource removed
  rid: BFC25
  fpath: ‘https://annotationhub.bioconductor.org/fetch/37442’
  reason: download failed 
3: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/37442’
  cache resource: ‘AH32002 : 37442’
  reason: bfcadd() failed; see warnings()

What should I do to get this work?

DFP • 320 views
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What is your sessionInfo()?

I just tried this and it seemed to work okay:

> library(AnnotationHub)
> ahub = AnnotationHub()
snapshotDate(): 2021-06-24
> ahub.bw = subset(ahub, rdataclass == "BigWigFile" & species == "Homo sapiens")
> bw = ahub.bw[[1]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
require("rtracklayer")
> bw
BigWigFile object
resource: /home/shepherd/.cache/R/AnnotationHub/21a222c8af02_37442
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Thank you very much for your reply. I tried it again. It still showed same error.

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] rtracklayer_1.46.0          GenomicAlignments_1.22.1    Rsamtools_2.2.3             Biostrings_2.54.0          
 [5] XVector_0.26.0              SummarizedExperiment_1.16.1 DelayedArray_0.12.3         BiocParallel_1.20.1        
 [9] matrixStats_0.59.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.1        
[13] IRanges_2.20.2              S4Vectors_0.24.4            AnnotationHub_2.18.0        BiocFileCache_1.10.2       
[17] dbplyr_1.3.0                BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6                    lattice_0.20-44               assertthat_0.2.1             
 [4] digest_0.6.27                 utf8_1.2.1                    mime_0.11                    
 [7] R6_2.5.0                      RSQLite_2.2.7                 httr_1.4.2.9000              
[10] pillar_1.6.1                  zlibbioc_1.32.0               rlang_0.4.11                 
[13] curl_4.3.2                    rstudioapi_0.13               blob_1.2.1                   
[16] Matrix_1.3-4                  RCurl_1.98-1.3                bit_4.0.4                    
[19] shiny_1.6.0                   compiler_3.6.3                httpuv_1.6.1                 
[22] pkgconfig_2.0.3               htmltools_0.5.1.1             tidyselect_1.1.1             
[25] tibble_3.1.2                  GenomeInfoDbData_1.2.2        interactiveDisplayBase_1.24.0
[28] XML_3.99-0.3                  fansi_0.5.0                   crayon_1.4.1                 
[31] dplyr_0.8.0                   later_1.2.0                   bitops_1.0-7                 
[34] rappdirs_0.3.3                grid_3.6.3                    xtable_1.8-4                 
[37] lifecycle_1.0.0               DBI_1.1.1                     magrittr_2.0.1               
[40] cachem_1.0.5                  promises_1.2.0.1              ellipsis_0.3.2               
[43] vctrs_0.3.8                   tools_3.6.3                   bit64_4.0.5                  
[46] glue_1.4.2                    purrr_0.3.4                   BiocVersion_3.10.1           
[49] fastmap_1.1.0                 yaml_2.2.1                    AnnotationDbi_1.48.0         
[52] BiocManager_1.30.16           memoise_2.0.0
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Are you behind a proxy that would have to be set?

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I have checked the Proxies under network. Nothing is selected.

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what is the result of running the following: httr::HEAD("http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E001-H3K4me1.fc.signal.bigwig")

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It showed:

Error in curl::curl_fetch_memory(url, handle = handle) : Could not resolve host: egg2.wust1.edu

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httr::HEAD("http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E001-H3K4me1.fc.signal.bigwig")

Sorry, it showed the following error.

Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: Invalid certificate chain

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This seems specific to your system and suggests that it might be on your computer's end. I did some quick google searches that suggest cleaning your browser cache and making sure the computer date and time are set correctly. I'm not a mac user so I'm not sure if someone else has some other suggestions.

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Thank you very much for your help. The date and time are right. I am cleaning the browser cache to see whether it will work.

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