I can't use AnnotationHub()
1
0
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755606975 • 0
@755606975-22698
Last seen 4.2 years ago
>library(AnnotationHub)
> ah<-AnnotationHub()
No internet connection using 'localHub=TRUE'
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'


> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
[1] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.2         BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3                    later_1.0.0                  
 [3] pillar_1.4.3                  compiler_3.6.2               
 [5] BiocManager_1.30.10           tools_3.6.2                  
 [7] zeallot_0.1.0                 digest_0.6.23                
 [9] bit_1.1-14                    RSQLite_2.2.0                
[11] memoise_1.1.0                 lifecycle_0.1.0              
[13] tibble_2.1.3                  gtable_0.3.0                 
[15] pkgconfig_2.0.3               rlang_0.4.2                  
[17] shiny_1.4.0                   DBI_1.1.0                    
[19] rstudioapi_0.10               yaml_2.2.0                   
[21] curl_4.3                      fastmap_1.0.1                
[23] dplyr_0.8.3                   httr_1.4.1                   
[25] IRanges_2.20.1                S4Vectors_0.24.1             
[27] vctrs_0.2.1                   rappdirs_0.3.1               
[29] stats4_3.6.2                  bit64_0.9-7                  
[31] grid_3.6.2                    tidyselect_0.2.5             
[33] Biobase_2.46.0                glue_1.3.1                   
[35] R6_2.4.1                      AnnotationDbi_1.48.0         
[37] ggplot2_3.2.1                 purrr_0.3.3                  
[39] blob_1.2.0                    magrittr_1.5                 
[41] promises_1.1.0                htmltools_0.4.0              
[43] scales_1.1.0                  backports_1.1.5              
[45] assertthat_0.2.1              xtable_1.8-4                 
[47] mime_0.8                      interactiveDisplayBase_1.24.0
[49] colorspace_1.4-1              httpuv_1.5.2                 
[51] lazyeval_0.2.2                munsell_0.5.0                
[53] BiocVersion_3.10.1            crayon_1.3.4 
AnnotationHub • 2.6k views
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So did you check if you have internet connection? or some of the proposed solutions of the error?

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I have the internet connection.

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0
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Did you use localHub = FALSE ?

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> ah<-AnnotationHub(localHub=F)
No internet connection using 'localHub=TRUE'
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'

> ah<-AnnotationHub(localHub=T)
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'

> refreshHub(hub,cache,proxy,hubClass=c("AnnotationHub","ExperimentHub"))
Error in refreshHub(hub, cache, proxy, hubClass = c("AnnotationHub", "ExperimentHub")) : 
  This function requires internet connection

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shepherl 3.8k
@lshep
Last seen 15 hours ago
United States

The message does indicate it is not finding internet connection

Using localHub=FALSE would not work in this case if the hub had never been created and if there is no internet connection; it would need to work at least once to use the localHub option.

Are you behind a proxy that would prevent internet connection? If you are behind a proxy, please set the proxy by either using proxy= in the constructor or by setting globally with setAnnotationHubOption.

We check the internet connection by checking first if the proxy is set, and then by using curl::has_internet().

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Also in the future please tag the post with the package that is in question. I did not receive a notification because the tag did not include the package name annotationhub. Cheers.

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I finally get it. I run this code, and all problems be solved. Thank you very much! Bless you. AnnotationHub(proxy='127.0.0.1:10801')

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glad that was the issue. Cheers.

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