Error: failed to load 'AnnotationHub' resource
2
1
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@borowczakmarc-9168
Last seen 5.9 years ago
United States

When attempting to download a gene, obtained the following error message. Here is my code:

library(AnnotationHub)
ah <- AnnotationHub()
ah.bw <- subset(ah, rdataclass == "BigWigFile" & species == "Homo sapiens")
qhs<-query(ah.bw, c("E055","H3K27me3","fc.signal"))
qhs[1]$genome
# [1] "hg19"
genes=qhs[[1]]

and the error message:

downloading from ‘https://annotationhub.bioconductor.org/fetch/37910’
retrieving 1 resource
Error: failed to load 'AnnotationHub' resource
  name: AH32470
  title: E055-H3K27me3.fc.signal.bigwig
  reason: 1 resources failed to download
In addition: There were 50 or more warnings (use warnings() to see the first 50)

The sessionInfo follows:

R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 GenomicFeatures_1.22.4            AnnotationDbi_1.32.0             
 [4] Biobase_2.30.0                    BSgenome_1.38.0                   Biostrings_2.38.0                
 [7] XVector_0.10.0                    rtracklayer_1.30.1                GenomicRanges_1.22.1             
[10] GenomeInfoDb_1.6.1                IRanges_2.4.1                     S4Vectors_0.8.1                  
[13] AnnotationHub_2.2.2               BiocGenerics_0.16.1               RevoUtilsMath_3.2.2              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.0                  BiocInstaller_1.20.0         futile.logger_1.4.1          bitops_1.0-6                
 [5] futile.options_1.0.0         tools_3.2.2                  zlibbioc_1.16.0              biomaRt_2.26.0              
 [9] digest_0.6.8                 RSQLite_1.0.0                shiny_0.12.2                 DBI_0.3.1                   
[13] curl_0.9.3                   httr_1.0.0                   stringr_1.0.0                R6_2.1.1                    
[17] XML_3.98-1.3                 BiocParallel_1.4.0           lambda.r_1.1.7               magrittr_1.5                
[21] Rsamtools_1.22.0             htmltools_0.2.6              GenomicAlignments_1.6.1      SummarizedExperiment_1.0.1  
[25] mime_0.3                     interactiveDisplayBase_1.8.0 xtable_1.7-4                 httpuv_1.3.3                
[29] stringi_0.5-5                RCurl_1.95-4.7   

Any help is welcome at this point. Thanks in advance.

Marc

biomart annotationhub • 2.0k views
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0
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Can you edit your question to include the R code you were evaluating, I guess something like hub[["AH12345"]] ? Post a comment when you've edited. 

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@martin-morgan-1513
Last seen 3 months ago
United States

For the original question, AnnotationHub tries to retrieve the resource from it's source

> qhs$sourceurl
[1] "http://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E055-H3K27me3.fc.signal.bigwig"

And pasting the source url into the browser or otherwise trying to retrieve this url (e.g., with wget) times out, so the server is not available. I'm not sure whether this is temporary or more permanent... The second example suggests a similar problem.

 

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I've confirmed Martin's observation that the server is unavailable.

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K ▴ 50
@k-8495
Last seen 3.1 years ago
United States

I have the exact same problem with AnnotationHub. This is the error I get in the command line:

> ah <- AnnotationHub()
snapshotDate(): 2015-11-05
> q3a <- query(ah, c("H3K4me3","EpigenomeRoadMap","H1 Cells")) # returns 6 records
> h3k4m3.h1.epi.narrow <- q3a[["AH29884"]] #getting narrow peak file
require(“rtracklayer”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/35324’
retrieving 1 resource
There were 50 or more warnings (use warnings() to see the first 50)
Error: failed to load 'AnnotationHub' resource
  name: AH29884
  title: E003-H3K4me3.narrowPeak.gz
  reason: error in evaluating the argument 'con' in selecting a method for function 'import': Error in cache(yy) : 1 resources failed to download

No idea what is happening. Everything was working fine till yesterday. So when this issue happened, I updated my R, Rstudio, and Bioconductor to the latest versions.

I get this error in Rstudio

> library(AnnotationHub)
> ah = AnnotationHub()
Error in AnnotationHub() : could not find function "dbfile"
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The problem in Rstudio looks like a version mis-match; does BiocInstaller::biocValid() report problems that you can address?

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This is what I get now in Rstudio

​> BiocInstaller::biocValid()
[1] TRUE
> h3k4m3.h1.epi.narrow <- q3a[[2]]
downloading from ‘https://annotationhub.bioconductor.org/fetch/35324’
retrieving 1 resource
There were 50 or more warnings (use warnings() to see the first 50)
Error: failed to load 'AnnotationHub' resource
  name: AH29884
  title: E003-H3K4me3.narrowPeak.gz
  reason: error in evaluating the argument 'con' in selecting a method for function 'import': Error in cache(yy) : 1 resources failed to download

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Can you please be more specific in your response. Please EDIT your response to confirm that this is in Rstudio. Please also be sure to start a new session, and to provide the complete transcript including sessionInfo().

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Sorry about that, I was typing too fast ! Yes, this is in Rstudio. I started a new session, and tried the following commands. Also shown below is sessionInfo().
​Thanks !

> ah <- AnnotationHub()
snapshotDate(): 2015-11-05
> BiocInstaller::biocValid()
[1] TRUE
> q3a <- query(ah, c("H3K4me3","EpigenomeRoadMap","H1 Cells")) # returns 6 records
> h3k4m3.h1.epi.narrow <- q3a[[2]]
require(“rtracklayer”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/35324’
retrieving 1 resource
There were 50 or more warnings (use warnings() to see the first 50)
Error: failed to load 'AnnotationHub' resource
  name: AH29884
  title: E003-H3K4me3.narrowPeak.gz
  reason: error in evaluating the argument 'con' in selecting a method for function 'import': Error in cache(yy) : 1 resources failed to download
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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_1.30.1   GenomicRanges_1.22.1 GenomeInfoDb_1.6.1   IRanges_2.4.1      
[5] S4Vectors_0.8.1      AnnotationHub_2.2.2  BiocGenerics_0.16.1 

loaded via a namespace (and not attached):
[1] Rcpp_0.12.1                  BiocInstaller_1.20.0         futile.logger_1.4.1        
[4] XVector_0.10.0               bitops_1.0-6                 futile.options_1.0.0       
[7] tools_3.2.2                  zlibbioc_1.16.0              digest_0.6.8               
[10] RSQLite_1.0.0                shiny_0.12.2                 DBI_0.3.1                  
[13] curl_0.9.3                   httr_1.0.0                   stringr_1.0.0              
[16] Biostrings_2.38.0            Biobase_2.30.0               R6_2.1.1                   
[19] AnnotationDbi_1.32.0         XML_3.98-1.3                 BiocParallel_1.4.0         
[22] lambda.r_1.1.7               magrittr_1.5                 Rsamtools_1.22.0           
[25] htmltools_0.2.6              GenomicAlignments_1.6.1      SummarizedExperiment_1.0.1 
[28] mime_0.4                     interactiveDisplayBase_1.8.0 xtable_1.8-0               
[31] httpuv_1.3.3                 stringi_1.0-1                RCurl_1.95-4.7             
> 
 
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I think that the immediate problem is that the server is unavailable. There is an outstanding issue with importing some narrowPeaks files, but I'm not sure if that is also a problem here.

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Is there an alternate way to access these files - any other server or source ? I believe its not so hard to get the BED file, but it would be nice to get the BED file in the format of a GRanges object. 

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FYI this has been fixed. The new snapshotDate() is Nov 19:

> ah <- AnnotationHub()
snapshotDate(): 2015-11-19

Let us know if you still have problems with these or any other files.

Thanks.

Valerie

 

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