Question: Question: Problem fetching resources from AnnotationHub, AH62557,error 403
0
gravatar for kathy240424
7 months ago by
kathy2404240 wrote:

Dear all,

I'm currently struggling to fetch data from AnnotationHub:

> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2018-04-30
> query(ah, "coprinopsis cinerea")
AnnotationHub with 2 records
# snapshotDate(): 2018-04-30 
# $dataprovider: Inparanoid8, ftp:...
# $species: Coprinopsis cinerea, C...
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid,
#   genome, description,
#   coordinate_1_based, maintainer,
#   rdatadateadded, preparerclass,
#   tags, rdatapath, sourceurl,
#   sourcetype 
# retrieve records with, e.g.,
#   'object[["AH10386"]]' 

            title                    
  AH10386 | hom.Coprinopsis_cinere...
  AH62557 | org.Coprinopsis_cinere...
> query(ah, "coprinopsis cinerea")
AnnotationHub with 2 records
# snapshotDate(): 2018-04-30 
# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Coprinopsis cinerea, Coprinopsis cinerea_okayama7#130
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer,
#   rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH10386"]]' 

            title                                         
  AH10386 | hom.Coprinopsis_cinerea.inp8.sqlite           
  AH62557 | org.Coprinopsis_cinerea_okayama7#130.eg.sqlite
> ccin <- ah [['AH62557']]
downloading 1 resources
retrieving 1 resource
Downloading: 240 B     
Error: failed to load resource
  name: AH62557
  title: org.Coprinopsis_cinerea_okayama7#130.eg.sqlite
  reason: 1 resources failed to download
In addition: Warning message:
download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/69303'
  cache path: '/Users/kathy_chan//.AnnotationHub/69303'
  reason: Forbidden (HTTP 403). 

while I try AH10386, it was OK, and the hub path of AH62557 can't open in webbrowser. is there something wrong with the source file of AH62557?

My R:

> sessionInfo()
R version 3.5.0 (2018-04-23)
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/3.5/Resources/lib/libRlapack.dylib

locale:
[1] C

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

other attached packages:
 [1] AnnotationHub_2.12.1  BiocInstaller_1.30.0  XML_3.98-1.16         pathview_1.20.0      
 [5] org.Hs.eg.db_3.6.0    AnnotationDbi_1.42.1  IRanges_2.14.12       S4Vectors_0.18.3     
 [9] Biobase_2.40.0        BiocGenerics_0.26.0   KEGGREST_1.20.2       gage_2.30.0          
[13] dplyr_0.7.6           clusterProfiler_3.8.1

loaded via a namespace (and not attached):
 [1] enrichplot_1.0.2              bit64_0.9-7                   httr_1.3.1                   
 [4] UpSetR_1.3.3                  Rgraphviz_2.24.0              tools_3.5.0                  
 [7] R6_2.3.0                      DBI_1.0.0                     lazyeval_0.2.1               
[10] colorspace_1.3-2              tidyselect_0.2.4              gridExtra_2.3                
[13] bit_1.1-14                    curl_3.2                      compiler_3.5.0               
[16] graph_1.58.1                  labeling_0.3                  KEGGgraph_1.40.0             
[19] scales_1.0.0                  ggridges_0.5.1                stringr_1.3.1                
[22] digest_0.6.17                 DOSE_3.6.1                    XVector_0.20.0               
[25] htmltools_0.3.6               pkgconfig_2.0.2               rlang_0.2.2.9000             
[28] rstudioapi_0.8                RSQLite_2.1.1                 shiny_1.1.0                  
[31] bindr_0.1.1                   BiocParallel_1.14.2           GOSemSim_2.6.2               
[34] magrittr_1.5                  GO.db_3.6.0                   Matrix_1.2-14                
[37] Rcpp_0.12.19                  munsell_0.5.0                 viridis_0.5.1                
[40] yaml_2.2.0                    stringi_1.2.4                 ggraph_1.0.2                 
[43] MASS_7.3-50                   zlibbioc_1.26.0               plyr_1.8.4                   
[46] qvalue_2.12.0                 grid_3.5.0                    blob_1.1.1                   
[49] promises_1.0.1                ggrepel_0.8.0                 DO.db_2.9                    
[52] crayon_1.3.4                  lattice_0.20-35               Biostrings_2.48.0            
[55] cowplot_0.9.3                 splines_3.5.0                 pillar_1.3.0                 
[58] fgsea_1.6.0                   igraph_1.2.2                  reshape2_1.4.3               
[61] fastmatch_1.1-0               glue_1.3.0                    data.table_1.11.8            
[64] httpuv_1.4.5                  png_0.1-7                     tweenr_1.0.0                 
[67] gtable_0.2.0                  purrr_0.2.5                   tidyr_0.8.1                  
[70] assertthat_0.2.0              ggplot2_3.0.0                 ggforce_0.1.3                
[73] mime_0.6                      xtable_1.8-3                  later_0.7.5                  
[76] viridisLite_0.3.0             tibble_1.4.2                  rvcheck_0.1.1                
[79] memoise_1.1.0                 units_0.6-1                   bindrcpp_0.2.2               
[82] interactiveDisplayBase_1.18.0

 

 

looking forward to your reply, thank you!!

annotation • 200 views
ADD COMMENTlink modified 7 months ago by shepherl ♦♦ 1.4k • written 7 months ago by kathy2404240
Thank you for reporting this. It appears to be an ERROR in the AnnotationHub with how it handles special characters in the download link (ie. #). I will be investigating immediately and let you know when we have fixed the bug.
ADD REPLYlink written 7 months ago by shepherl ♦♦ 1.4k

Thank you and looking forward to your reply.

ADD REPLYlink written 7 months ago by kathy2404240
Answer: Question: Problem fetching resources from AnnotationHub, AH62557,error 403
0
gravatar for shepherl
7 months ago by
shepherl ♦♦ 1.4k
United States
shepherl ♦♦ 1.4k wrote:

We apologize for the inconvenience. We have fixed the bug in the code and you should now be able to download the resource. Please let us know if you have any further issues.

ADD COMMENTlink modified 7 months ago • written 7 months ago by shepherl ♦♦ 1.4k
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