AnnotationHub Error in value[[3L]](cond) : failed to create index

Question

[Parham]

Hi, I started to work with AnnotationHub package but it seems no matter what options I give for cache, it is not able to create a local hub. Firstly, I used default cache path for windows which is under "C:/Users/user.name/AppData/Local/AnnotationHub/AnnotationHub/Cache/" by hub <- AnnotationHub() and then I tried to specifically set a cache directory in the "C" drive by hub <- AnnotationHub(cache = "C:/Temp/RtmpsZf3Ul/cache") Both of them produce (except for the cache path):

    snapshotDate(): 2020-04-27
Error in value[[3L]](cond) : failed to create index
  hubCache(): C:/Temp/RtmpsZf3Ul/cache
  reason: unable to open database file

Besides there are functions in the manual that don't exist in the package: getAnnotationHubCache and setAnnotationHubCache !!!

Any help is appreciated.

    sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

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

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

other attached packages:
[1] AnnotationHub_2.20.0 BiocFileCache_1.12.0 dbplyr_1.4.4        
[4] BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5                    lattice_0.20-41              
 [3] prettyunits_1.1.1             Rsamtools_2.4.0              
 [5] Biostrings_2.56.0             assertthat_0.2.1             
 [7] digest_0.6.25                 mime_0.9                     
 [9] R6_2.4.1                      GenomeInfoDb_1.24.2          
[11] stats4_4.0.2                  RSQLite_2.2.0                
[13] httr_1.4.1                    pillar_1.4.5                 
[15] zlibbioc_1.34.0               rlang_0.4.6                  
[17] GenomicFeatures_1.40.1        progress_1.2.2               
[19] curl_4.3                      rstudioapi_0.11              
[21] blob_1.2.1                    S4Vectors_0.26.1             
[23] Matrix_1.2-18                 BiocParallel_1.22.0          
[25] stringr_1.4.0                 RCurl_1.98-1.2               
[27] bit_1.1-15.2                  biomaRt_2.44.1               
[29] shiny_1.5.0                   DelayedArray_0.14.0          
[31] httpuv_1.5.4                  compiler_4.0.2               
[33] rtracklayer_1.48.0            pkgconfig_2.0.3              
[35] askpass_1.1                   htmltools_0.5.0              
[37] openssl_1.4.2                 tidyselect_1.1.0             
[39] SummarizedExperiment_1.18.1   interactiveDisplayBase_1.26.3
[41] tibble_3.0.2                  GenomeInfoDbData_1.2.3       
[43] IRanges_2.22.2                matrixStats_0.56.0           
[45] XML_3.99-0.4                  later_1.1.0.1                
[47] crayon_1.3.4                  dplyr_1.0.0                  
[49] GenomicAlignments_1.24.0      bitops_1.0-6                 
[51] rappdirs_0.3.1                grid_4.0.2                   
[53] xtable_1.8-4                  lifecycle_0.2.0              
[55] DBI_1.1.0                     magrittr_1.5                 
[57] stringi_1.4.6                 XVector_0.28.0               
[59] promises_1.1.1                ellipsis_0.3.1               
[61] generics_0.0.2                vctrs_0.3.1                  
[63] tools_4.0.2                   bit64_0.9-7                  
[65] BSgenome_1.56.0               Biobase_2.48.0               
[67] glue_1.4.1                    purrr_0.3.4                  
[69] BiocVersion_3.11.1            hms_0.5.3                    
[71] fastmap_1.0.1                 yaml_2.2.1                   
[73] AnnotationDbi_1.50.1          BiocManager_1.30.10          
[75] GenomicRanges_1.40.0          memoise_1.1.0                
[77] VariantAnnotation_1.34.0

Answer 1

[Kevin Blighe]

Could you possibly try to re-install AnnotationHub as the development version, and then try again?

BiocManager::install(version='devel')
BiocManager::install("AnnotationHub")

Also, I trust that you have already done the standard things like closing your R session after each use, and re-starting your machine when your memory cache has become crammed with junk and needs wiping(?)

Kevin