AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
2
0
Entering edit mode
dilaik • 0
@dilaik-23224
Last seen 18 months ago

Hello,

I am getting a timeout error when trying to load AnnotationHub object "AH13964".

The error can be reproduced by:

> hub = AnnotationHub() 
> hub[["AH13964"]]

Output:

> Error: failed to load resource  
 name: AH13964   
title: hg19.2bit  
> reason: Timeout was reached: [annotationhub.bioconductor.org] Operation timed out after 10004 milliseconds with 0 out of 0 bytes received

Thank you!

Here is my sessionInfo():

> R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.15.1

>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  grid      stats     graphics  grDevices utils     datasets  methods   base     

>other attached packages:
 [1] httr_1.4.1                                 dplyr_0.8.5                                ggrepel_0.8.2                             
 [4] ggplot2_3.3.0                              scales_1.1.0                               broom_0.5.5                               
 [7] readxl_1.3.1                               readr_1.3.1                                plyr_1.8.6                                
[10] GenomicAlignments_1.20.1                   Rsamtools_2.0.3                            BSgenome_1.52.0                           
[13] rtracklayer_1.44.4                         AnnotationHub_2.16.1                       BiocFileCache_1.8.0                       
[16] dbplyr_1.4.2                               VennDiagram_1.6.20                         futile.logger_1.4.3                       
[19] RColorBrewer_1.1-2                         survival_3.1-11                            TCGAbiolinks_2.12.6                       
[22] biomaRt_2.40.5                             goseq_1.36.0                               geneLenDataBase_1.20.0                    
[25] BiasedUrn_1.07                             GO.db_3.8.2                                beanplot_1.2                              
[28] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.30.0                               bumphunter_1.26.0                         
[31] locfit_1.5-9.4                             iterators_1.0.12                           foreach_1.5.0                             
[34] Biostrings_2.52.0                          XVector_0.24.0                             SummarizedExperiment_1.14.1               
[37] DelayedArray_0.10.0                        BiocParallel_1.18.1                        matrixStats_0.56.0                        
[40] FDb.InfiniumMethylation.hg19_2.2.0         org.Hs.eg.db_3.8.2                         TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2   
[43] GenomicFeatures_1.36.4                     AnnotationDbi_1.46.1                       Biobase_2.44.0                            
[46] GenomicRanges_1.36.1                       GenomeInfoDb_1.20.0                        IRanges_2.18.3                            
[49] S4Vectors_0.22.1                           BiocGenerics_0.30.0                        seqLogo_1.50.0                            
[52] gplots_3.0.3                               fastcluster_1.1.25                         Rcpp_1.0.4                                
[55] mgcv_1.8-31                                nlme_3.1-145                               seqinr_3.6-1                              
[58] tidyr_1.0.2                                tibble_3.0.0                              

>loaded via a namespace (and not attached):
  [1] rappdirs_0.3.1                ggthemes_4.2.0                R.methodsS3_1.8.0             pkgmaker_0.31.1               bit64_0.9-7                  
  [6] knitr_1.28                    aroma.light_3.14.0            R.utils_2.9.2                 data.table_1.12.8             hwriter_1.3.2                
 [11] RCurl_1.98-1.1                GEOquery_2.52.0               doParallel_1.0.15             generics_0.0.2                preprocessCore_1.46.0        
 [16] lambda.r_1.2.4                RSQLite_2.2.0                 bit_1.1-15.2                  xml2_1.2.5                    httpuv_1.5.2                 
 [21] assertthat_0.2.1              xfun_0.12                     hms_0.5.3                     promises_1.1.0                fansi_0.4.1                  
 [26] scrime_1.3.5                  progress_1.2.2                caTools_1.18.0                km.ci_0.5-2                   DBI_1.1.0                    
 [31] geneplotter_1.62.0            reshape_0.8.8                 apcluster_1.4.8               EDASeq_2.18.0                 matlab_1.0.2                 
 [36] purrr_0.3.3                   import_1.1.0                  selectr_0.4-2                 ggpubr_0.2.5                  backports_1.1.5              
 [41] annotate_1.62.0               vctrs_0.2.4                   withr_2.1.2                   prettyunits_1.1.1             mclust_5.4.5                 
 [46] cluster_2.1.0                 lazyeval_0.2.2                crayon_1.3.4                  genefilter_1.66.0             edgeR_3.26.8                 
 [51] pkgconfig_2.0.3               rlang_0.4.5                   lifecycle_0.2.0               downloader_0.4                registry_0.5-1               
 [56] cellranger_1.1.0              rngtools_1.5                  base64_2.0                    Matrix_1.2-18                 KMsurv_0.1-5                 
 [61] Rhdf5lib_1.6.3                zoo_1.8-7                     GlobalOptions_0.1.1           png_0.1-7                     rjson_0.2.20                 
 [66] bitops_1.0-6                  R.oo_1.23.0                   ConsensusClusterPlus_1.48.0   KernSmooth_2.23-16            blob_1.2.1                   
 [71] DelayedMatrixStats_1.6.1      doRNG_1.8.2                   shape_1.4.4                   stringr_1.4.0                 nor1mix_1.3-0                
 [76] ShortRead_1.42.0              jpeg_0.1-8.1                  ggsignif_0.6.0                memoise_1.1.0                 magrittr_1.5                 
 [81] bibtex_0.4.2.2                gdata_2.18.0                  zlibbioc_1.30.0               compiler_3.6.0                illuminaio_0.26.0            
 [86] clue_0.3-57                   cli_2.0.2                     ade4_1.7-15                   formatR_1.7                   MASS_7.3-51.5                
 [91] tidyselect_1.0.0              stringi_1.4.6                 yaml_2.2.1                    askpass_1.1                   latticeExtra_0.6-29          
 [96] survMisc_0.5.5                tools_3.6.0                   circlize_0.4.8                rstudioapi_0.11               gridExtra_2.3                
[101] farver_2.0.3                  digest_0.6.25                 BiocManager_1.30.10           shiny_1.4.0.2                 quadprog_1.5-8               
[106] siggenes_1.58.0               later_1.0.0                   survminer_0.4.6               ComplexHeatmap_2.0.0          colorspace_1.4-1             
[111] rvest_0.3.5                   XML_3.99-0.3                  splines_3.6.0                 multtest_2.40.0               xtable_1.8-4                 
[116] jsonlite_1.6.1                futile.options_1.0.1          zeallot_0.1.0                 R6_2.4.1                      pillar_1.4.3                 
[121] htmltools_0.4.0               mime_0.9                      fastmap_1.0.1                 glue_1.3.2                    DESeq_1.36.0                 
[126] interactiveDisplayBase_1.22.0 codetools_0.2-16              utf8_1.1.4                    lattice_0.20-40               sva_3.32.1                   
[131] curl_4.3                      gtools_3.8.1                  openssl_1.4.1                 limma_3.40.6                  munsell_0.5.0                
[136] GetoptLong_0.1.8              rhdf5_2.28.1                  GenomeInfoDbData_1.2.1        HDF5Array_1.12.3              gtable_0.3.0 
> 
annotationhub • 283 views
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shepherl 2.8k
@lshep
Last seen 4 hours ago
United States

Hello, Thank you for reaching out. Could you please try again? I think this was a temporary loss of service. The source of that particular resource is from "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit" . A little while ago it seemed unavailable but now it seems to be back and I was able to download the resource.

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Thank you! It works.

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Entering edit mode
shepherl 2.8k
@lshep
Last seen 4 hours ago
United States

FWIW -- While that was an issue downloading a resource directly we started seeing some timeout ERRORs when calling AnnotationHub ( ) and ExperimentHub( ) . we are looking into the issue.

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Entering edit mode

Thank you for the update, I noticed this this morning.

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Entering edit mode

Thank you for the update, I noticed this this morning.

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