Question: Problem with AnnotationHub after crash during first download of metadata
gravatar for konstantinos.bogias
4 weeks ago by
Australia, Adelaide, University of Adelaide
konstantinos.bogias10 wrote:


I was installing AnnotationHub & ran:

ah <- AnnotationHub()

My R Session terminated half way through the metadata downloading for an unspecified crash.

Now I cannot repeat this command successfully

ah <- AnnotationHub()

Gives the message:

Error: failed to connect to local data base
  database: ‘NA’
  reason: invalid 'file' argument

The cached Hub doesn't appear to be in ~/.AnnotationHub and I can't find any local directories matching this where it might be. I was thinking that deleting these and re-running might help if they existed, but that's a dead end. Is there any way to force a re-initialisation of the cached metadata?


R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

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

[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
[1] AnnotationHub_2.16.0 BiocFileCache_1.8.0  dbplyr_1.4.2         BiocGenerics_0.30.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2                    pillar_1.4.2                  compiler_3.6.1                BiocManager_1.30.4           
 [5] later_0.8.0                   tools_3.6.1                   zeallot_0.1.0                 digest_0.6.20                
 [9] bit_1.1-14                    RSQLite_2.1.2                 memoise_1.1.0                 tibble_2.1.3                 
[13] pkgconfig_2.0.2               rlang_0.4.0                   shiny_1.3.2                   DBI_1.0.0                    
[17] rstudioapi_0.10               curl_4.0                      yaml_2.2.0                    dplyr_0.8.3                  
[21] httr_1.4.1                    IRanges_2.18.1                vctrs_0.2.0                   S4Vectors_0.22.0             
[25] rappdirs_0.3.1                stats4_3.6.1                  bit64_0.9-7                   tidyselect_0.2.5             
[29] Biobase_2.44.0                glue_1.3.1                    R6_2.4.0                      AnnotationDbi_1.46.0         
[33] purrr_0.3.2                   blob_1.2.0                    magrittr_1.5                  promises_1.0.1               
[37] backports_1.1.4               htmltools_0.3.6               assertthat_0.2.1              xtable_1.8-4                 
[41] mime_0.7                      interactiveDisplayBase_1.22.0 httpuv_1.5.1   
annotationhub • 80 views
ADD COMMENTlink modified 17 days ago by shepherl ♦♦ 1.5k • written 4 weeks ago by konstantinos.bogias10
Answer: Problem with AnnotationHub after crash during first download of metadata
gravatar for Martin Morgan
4 weeks ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Use hubCache(ah) or getAnnotationHubOption("cache") to find the location of the cache. I don't think there's a way to force re-download of the cached index.

ADD COMMENTlink written 4 weeks ago by Martin Morgan ♦♦ 23k
Answer: Problem with AnnotationHub after crash during first download of metadata
gravatar for shepherl
17 days ago by
shepherl ♦♦ 1.5k
United States
shepherl ♦♦ 1.5k wrote:

Thank you for bringing this to our attention. After further investigation, I have pinpointed the bug in the code and it has been corrected in 2.16.1 (release version) and 2.17.8 (devel version) that should propagate to the builders within the next 24 hours. Cheers.

ADD COMMENTlink written 17 days ago by shepherl ♦♦ 1.5k

I have also added a helper function refreshHub that will force redownload of the sqlite file. This is available in the devel version of the package (2.17.9)

ADD REPLYlink written 16 days ago by shepherl ♦♦ 1.5k
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