Question

Annotationhub V2.16.1 Error info

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chaimol • 0

@chaimol-22021

Last seen 5.5 years ago

In China use Annotationhub_2.16.1 have some err :

    > hub <- AnnotationHub()

Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) : 
  bfcadd() failed; see warnings()
In addition: Warning messages:
1: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
  local file path: ‘C:\Users\Frank\AppData\Local\AnnotationHub\AnnotationHub\Cache/2d54133d1b0a_annotationhub.sqlite3’
  reason: Timeout was reached: [annotationhub.bioconductor.org] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received 
2: bfcadd() failed; resource removed
  rid: BFC10
  fpath: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
  reason: download failed

> sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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_2.16.1 BiocFileCache_1.8.0  dbplyr_1.4.2         BiocGenerics_0.30.0 
[5] curl_4.2

annotation software error • 1.8k views

ADD COMMENT • link updated 5.5 years ago by Martin Morgan 25k • written 5.5 years ago by chaimol • 0

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Entering edit mode

If you run the following what do you get back?

BiocManager::install("httr")
library(httr)
HEAD("https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3")

Are you also trying to access from behind a proxy? There is an argument to AnnotationHub to set a proxy if this is the case.

ADD REPLY • link 5.5 years ago shepherl 4.1k