Hi, I'm new to R/Biocunductor and trying to access AnnotationHub. I get an error message whenever I try to run the script
> ah=AnnotationHub()
updating metadata: retrieving 1 resource
Error: database is corrupt; remove it and try again
database: ‘/Users/ian//.AnnotationHub/annotationhub.sqlite3’
reason: missing tables
In addition: Warning message:
download failed
hub path: ‘https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3’
cache path: ‘/Users/ian//.AnnotationHub/annotationhub.sqlite3’
reason: there is no package called ‘curl’
I've searched through the previous topics and found the fixes that have been posted previously (link below), however, when I run them I receive the same error message. AnnotationHub corrupt database
Session info:
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] AnnotationHub_2.6.5 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 IRanges_2.8.2 digest_0.6.12
[4] mime_0.5 R6_2.2.0 xtable_1.8-2
[7] DBI_0.6-1 stats4_3.3.3 RSQLite_1.1-2
[10] BiocInstaller_1.24.0 httr_1.2.1 S4Vectors_0.12.2
[13] tools_3.3.3 Biobase_2.34.0 shiny_1.0.1
[16] yaml_2.1.14 httpuv_1.3.3 AnnotationDbi_1.36.2
[19] memoise_1.0.0 htmltools_0.3.5 interactiveDisplayBase_1.12.0
>
Thank you in advance
