Cannot connect to AnnotationHub server

[reliscu]

First command:

ah=AnnotationHub()
Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : 
  Invalid Cache: sqlite file
  Hub has not been added to cache
  Run again with 'localHub=FALSE'

Then:

ah=AnnotationHub(localHub=F)
Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : 
  Invalid Cache: sqlite file
  Hub has not been added to cache
  Run again with 'localHub=FALSE'

Session info:

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /wynton/home/cbi/shared/software/CBI/R-4.0.2/lib64/R/lib/libRblas.so
LAPACK: /wynton/home/cbi/shared/software/CBI/R-4.0.2/lib64/R/lib/libRlapack.so

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

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

other attached packages:
 [1] AnnotationHub_2.20.2      BiocFileCache_1.12.1     
 [3] dbplyr_1.4.4              ensembldb_2.12.1         
 [5] AnnotationFilter_1.12.0   GenomicFeatures_1.40.1   
 [7] GenomicRanges_1.40.0      GenomeInfoDb_1.24.2      
 [9] biomaRt_2.44.1            huex10stprobeset.db_8.7.0
[11] org.Hs.eg.db_3.11.4       AnnotationDbi_1.50.3     
[13] IRanges_2.22.2            S4Vectors_0.26.1         
[15] Biobase_2.48.0            BiocGenerics_0.34.0      
[17] BiocManager_1.30.10       data.table_1.12.8        
[19] gprofiler2_0.1.9         

loaded via a namespace (and not attached):
 [1] httr_1.4.2                    tidyr_1.1.1                  
 [3] bit64_4.0.2                   jsonlite_1.6.1               
 [5] viridisLite_0.3.0             shiny_1.5.0                  
 [7] assertthat_0.2.1              interactiveDisplayBase_1.26.3
 [9] askpass_1.1                   blob_1.2.1                   
[11] GenomeInfoDbData_1.2.3        Rsamtools_2.4.0              
[13] yaml_2.2.1                    progress_1.2.2               
[15] BiocVersion_3.11.1            pillar_1.4.4                 
[17] RSQLite_2.2.0                 lattice_0.20-41              
[19] glue_1.4.1                    digest_0.6.25                
[21] promises_1.1.1                XVector_0.28.0               
[23] colorspace_1.4-1              httpuv_1.5.4                 
[25] htmltools_0.5.0               Matrix_1.2-18                
[27] XML_3.99-0.5                  pkgconfig_2.0.3              
[29] zlibbioc_1.34.0               xtable_1.8-4                 
[31] purrr_0.3.4                   scales_1.1.1                 
[33] later_1.1.0.1                 BiocParallel_1.22.0          
[35] tibble_3.0.1                  openssl_1.4.2                
[37] generics_0.0.2                ggplot2_3.3.1                
[39] ellipsis_0.3.1                SummarizedExperiment_1.18.2  
[41] lazyeval_0.2.2                mime_0.9                     
[43] magrittr_1.5                  crayon_1.3.4                 
[45] memoise_1.1.0                 tools_4.0.2                  
[47] prettyunits_1.1.1             hms_0.5.3                    
[49] lifecycle_0.2.0               matrixStats_0.56.0           
[51] stringr_1.4.0                 plotly_4.9.2.1               
[53] munsell_0.5.0                 DelayedArray_0.14.1          
[55] Biostrings_2.56.0             compiler_4.0.2               
[57] rlang_0.4.7                   grid_4.0.2                   
[59] RCurl_1.98-1.2                rappdirs_0.3.1               
[61] htmlwidgets_1.5.1             bitops_1.0-6                 
[63] gtable_0.3.0                  DBI_1.1.0                    
[65] curl_4.3                      R6_2.4.1                     
[67] GenomicAlignments_1.24.0      dplyr_1.0.2                  
[69] rtracklayer_1.48.0            fastmap_1.0.1                
[71] bit_4.0.4                     ProtGenerics_1.20.0          
[73] stringi_1.4.6                 Rcpp_1.0.5                   
[75] vctrs_0.3.2                   tidyselect_1.1.0        

[reliscu]

The source of this issue is addressed here:

https://github.com/Bioconductor/AnnotationHub/issues/20

[lshep]

Since there is a more detailed description and background in issue #20 I'm closing this issue to track there. Are you behind a proxy that needed to be set?

[HenrikBengtsson]

Sorry, I missed that @reliscu already posted about this problem. Yes, this should be on the same HPC environment that I describe in #20.