Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
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Entering edit mode
@panxingxin16-22858
Last seen 20 months ago
****> library(scRNAseq)****
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:grDevices’:

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:AnnotationHub’:

    cache

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

> sce <- MacoskoRetinaData()
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'
> 
annotation singlecell rna-seq • 213 views
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Entering edit mode
shepherl 2.8k
@lshep
Last seen 13 hours ago
United States

As the ERROR indicates, you need internet connection to run the functions. As long as the function worked successfully once with internet connection it should be able to find the file again. If you have internet connection but are behind a proxy, please see ?setAnnotationHubOptions for setting a proxy.

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