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kasperdanielhansen / genbioconductor

Materials for Genomics Data Science: Introduction to Bioconductor
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OrgDb download failed #12

Open cparsania opened 5 years ago

cparsania commented 5 years ago

Hi,

I tried to download the OrgDB object sourced by fungidb through annotationhub. Somehow it failed. See the commands and error below 

library("AnnotationHub")
hub <- AnnotationHub()

> hub
AnnotationHub with 46259 records
# snapshotDate(): 2019-05-02 
# $dataprovider: BroadInstitute, Ensembl, UCSC, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Haemcode, FungiDB, Inparanoid8, TriTrypDB, PlasmoDB, AmoebaDB
# $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Bos taurus, Rattus norvegicus, Pan troglodytes, Danio rerio, Gallus gallus, Mono...
# $rdataclass: GRanges, BigWigFile, TwoBitFile, OrgDb, Rle, ChainFile, EnsDb, Inparanoid8Db, TxDb, data.frame
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH5012"]]' 

            title                                                     
  AH5012  | Chromosome Band                                           
  AH5013  | STS Markers                                               
  AH5014  | FISH Clones                                               
  AH5015  | Recomb Rate                                               
  AH5016  | ENCODE Pilot                                              
  ...       ...                                                       
  AH73812 | org.Plasmodium_vivax.eg.sqlite                            
  AH73813 | org.Burkholderia_mallei_ATCC_23344.eg.sqlite              
  AH73814 | org.Bacillus_cereus_(strain_ATCC_14579_|_DSM_31).eg.sqlite
  AH73815 | org.Bacillus_cereus_ATCC_14579.eg.sqlite                  
  AH73816 | org.Schizosaccharomyces_cryophilus_OY26.eg.sqlite    

hub_subset <- query(hub , c("fungidb" ,"OrgDb"))

> hub_subset
AnnotationHub with 277 records
# snapshotDate(): 2019-05-02 
# $dataprovider: FungiDB
# $species: Naganishia albida, Albugo candida 2VRR, Albugo laibachii Nc14, Allomyces macrogynus ATCC 38327, Aphanomyces astaci, Aphanomyces invad...
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH71411"]]' 

            title                                                         
  AH71411 | Transcript information for Albugo candida 2VRR                
  AH71412 | Transcript information for Albugo laibachii Nc14              
  AH71413 | Transcript information for Allomyces macrogynus ATCC 38327    
  AH71414 | Transcript information for Aspergillus aculeatus ATCC 16872   
  AH71415 | Transcript information for Aspergillus brasiliensis CBS 101740
  ...       ...                                                           
  AH71937 | Transcript information for Phytophthora sojae P6497           
  AH71938 | Transcript information for Pythium vexans DAOM BR484          
  AH71939 | Transcript information for Saccharomyces cerevisiae S288c     
  AH71940 | Transcript information for Scedosporium apiospermum IHEM 14462
  AH71941 | Transcript information for Yarrowia lipolytica CLIB89 W29   

> hub_subset[["AH71940"]]
downloading 1 resources
retrieving 1 resource
Downloading: 240 B     
Error: failed to load resource
  name: AH71940
  title: Transcript information for Scedosporium apiospermum IHEM 14462
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/78686’
  local file path: ‘/Users/chirag/Library/Caches/AnnotationHub/25d6f57295d_78686’
  reason: Forbidden (HTTP 403). 
2: bfcadd() failed; resource removed
  rid: BFC16
  fpath: ‘https://annotationhub.bioconductor.org/fetch/78686’
  reason: download failed 
3: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/78686’
  cache resource: ‘AH71940 : 78686’
  reason: bfcadd() failed; see warnings() 

> hub_subset[["AH71412"]]
downloading 1 resources
retrieving 1 resource
Downloading: 240 B     
Error: failed to load resource
  name: AH71412
  title: Transcript information for Albugo laibachii Nc14
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/78158’
  local file path: ‘/Users/chirag/Library/Caches/AnnotationHub/25d435cd1c6_78158’
  reason: Forbidden (HTTP 403). 
2: bfcadd() failed; resource removed
  rid: BFC17
  fpath: ‘https://annotationhub.bioconductor.org/fetch/78158’
  reason: download failed 
3: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/78158’
  cache resource: ‘AH71412 : 78158’
  reason: bfcadd() failed; see warnings()

However, GRanges objects provided by fungidb are working fine.

Help would be highly appreciated.

Thanks.