Problem with AnnotationHub after crash during first download of metadata
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Entering edit mode
@konstantinosbogias-21699
Last seen 2.1 years ago
Australia, Adelaide, University of Adel…

Hi,

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?

Thanks

sessionInfo()
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

locale:
[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 • 268 views
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Entering edit mode
@martin-morgan-1513
Last seen 3 months ago
United States

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.

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Entering edit mode
shepherl 2.8k
@lshep
Last seen 1 hour ago
United States

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.

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Entering edit mode

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)

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