AnnotationHub() returns only one record !?
2
0
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@jeanmonlong-9845
Last seen 5.7 years ago

Hi,

When I want to use AnnotationHub, I can access only one record. Before it was working for me as usual but not anymore.

> ah = AnnotationHub()
updating AnnotationHub metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2016-02-23
> ah
AnnotationHub with 1 record
# snapshotDate(): 2016-02-23
# names(): EH1
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: ExpressionSet
# $title: RNA-Sequencing and clinical data for 7706 tumor samples from The C...
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706 tum...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: TCGA, RNA-seq, Expression, Count
# retrieve record with 'object[["EH1"]]'

As you can see 'ah' has only one record available. I tried it in a docker instance (bioconductor/release_core) and have the same problem so I don't think it's my installation.

Anyone else has this problem ? Is it a problem of the snapshot ? Has the syntax changed ?

Thanks,

Jean

EDIT: My session info is

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=fr_CA.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_CA.UTF-8        LC_COLLATE=fr_CA.UTF-8    
 [5] LC_MONETARY=fr_CA.UTF-8    LC_MESSAGES=fr_CA.UTF-8   
 [7] LC_PAPER=fr_CA.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_CA.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3   IRanges_2.4.8       
[4] S4Vectors_0.8.11     AnnotationHub_2.2.3  BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3                  AnnotationDbi_1.32.3        
 [3] XVector_0.10.0               zlibbioc_1.16.0             
 [5] xtable_1.8-2                 R6_2.1.2                    
 [7] httr_1.1.0                   tools_3.2.3                 
 [9] Biobase_2.30.0               DBI_0.3.1                   
[11] htmltools_0.3                digest_0.6.9                
[13] interactiveDisplayBase_1.8.0 shiny_0.13.1                
[15] curl_0.9.6                   RSQLite_1.0.0               
[17] mime_0.4                     compiler_3.2.3              
[19] BiocInstaller_1.20.1         httpuv_1.3.3                

 

 
annotationhub • 915 views
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I don't see this behavior. Can you EDIT your question to include the output of sessionInfo(), and then post a COMMENT to let us know that you've edited the question?

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I added my session information. Sorry about that.

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@jeanmonlong-9845
Last seen 5.7 years ago

It must have been a snapshot problem. When I try it now it uses a previous snapshot (Jan 25) and it works as before.

Now I get:

> ah = AnnotationHub()
snapshotDate(): 2016-01-25
> ah
AnnotationHub with 36200 records
# snapshotDate(): 2016-01-25
# $dataprovider: BroadInstitute, UCSC, Ensembl, ftp://ftp.ncbi.nlm.nih.gov/g...
# $species: Homo sapiens, Mus musculus, Bos taurus, Pan troglodytes, Danio r...
# $rdataclass: GRanges, BigWigFile, FaFile, ChainFile, OrgDb, TwoBitFile, In...
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
#   sourcetype
# retrieve records with, e.g., 'object[["AH2"]]'

            title                                               
  AH2     | Ailuropoda_melanoleuca.ailMel1.69.dna.toplevel.fa   
  AH3     | Ailuropoda_melanoleuca.ailMel1.69.dna_rm.toplevel.fa
  AH4     | Ailuropoda_melanoleuca.ailMel1.69.dna_sm.toplevel.fa
  AH5     | Ailuropoda_melanoleuca.ailMel1.69.ncrna.fa          
  AH6     | Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa        
  ...       ...                                                 
  AH50415 | Tupaia_belangeri.TREESHREW.83.gtf                   
  AH50416 | Tursiops_truncatus.turTru1.83.gtf                   
  AH50417 | Vicugna_pacos.vicPac1.83.gtf                        
  AH50418 | Xenopus_tropicalis.JGI_4.2.83.gtf                   
  AH50419 | Xiphophorus_maculatus.Xipmac4.4.2.83.gtf            

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@valerie-obenchain-4275
Last seen 2.0 years ago
United States

Hi Jean,

This was my fault. I was modifying some records and messed up the db replacement. The new snapshot date should be today 

> ah <- AnnotationHub()
snapshotDate(): 2016-03-03

and all should be well. Let me know if you don't get the updated version.

Valerie

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The new snapshot works for me, thanks for the quick fix !

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