Hi,
I started to work with AnnotationHub package but it seems no matter what options I give for cache, it is not able to create a local hub. Firstly, I used default cache path for windows which is under "C:/Users/user.name/AppData/Local/AnnotationHub/AnnotationHub/Cache/" by hub <- AnnotationHub()
and then I tried to specifically set a cache directory in the "C" drive by hub <- AnnotationHub(cache = "C:/Temp/RtmpsZf3Ul/cache")
Both of them produce (except for the cache path):
snapshotDate(): 2020-04-27
Error in value[[3L]](cond) : failed to create index
hubCache(): C:/Temp/RtmpsZf3Ul/cache
reason: unable to open database file
Besides there are functions in the manual that don't exist in the package:
getAnnotationHubCache
and setAnnotationHubCache
!!!
Any help is appreciated.
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
[7] methods base
other attached packages:
[1] AnnotationHub_2.20.0 BiocFileCache_1.12.0 dbplyr_1.4.4
[4] BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lattice_0.20-41
[3] prettyunits_1.1.1 Rsamtools_2.4.0
[5] Biostrings_2.56.0 assertthat_0.2.1
[7] digest_0.6.25 mime_0.9
[9] R6_2.4.1 GenomeInfoDb_1.24.2
[11] stats4_4.0.2 RSQLite_2.2.0
[13] httr_1.4.1 pillar_1.4.5
[15] zlibbioc_1.34.0 rlang_0.4.6
[17] GenomicFeatures_1.40.1 progress_1.2.2
[19] curl_4.3 rstudioapi_0.11
[21] blob_1.2.1 S4Vectors_0.26.1
[23] Matrix_1.2-18 BiocParallel_1.22.0
[25] stringr_1.4.0 RCurl_1.98-1.2
[27] bit_1.1-15.2 biomaRt_2.44.1
[29] shiny_1.5.0 DelayedArray_0.14.0
[31] httpuv_1.5.4 compiler_4.0.2
[33] rtracklayer_1.48.0 pkgconfig_2.0.3
[35] askpass_1.1 htmltools_0.5.0
[37] openssl_1.4.2 tidyselect_1.1.0
[39] SummarizedExperiment_1.18.1 interactiveDisplayBase_1.26.3
[41] tibble_3.0.2 GenomeInfoDbData_1.2.3
[43] IRanges_2.22.2 matrixStats_0.56.0
[45] XML_3.99-0.4 later_1.1.0.1
[47] crayon_1.3.4 dplyr_1.0.0
[49] GenomicAlignments_1.24.0 bitops_1.0-6
[51] rappdirs_0.3.1 grid_4.0.2
[53] xtable_1.8-4 lifecycle_0.2.0
[55] DBI_1.1.0 magrittr_1.5
[57] stringi_1.4.6 XVector_0.28.0
[59] promises_1.1.1 ellipsis_0.3.1
[61] generics_0.0.2 vctrs_0.3.1
[63] tools_4.0.2 bit64_0.9-7
[65] BSgenome_1.56.0 Biobase_2.48.0
[67] glue_1.4.1 purrr_0.3.4
[69] BiocVersion_3.11.1 hms_0.5.3
[71] fastmap_1.0.1 yaml_2.2.1
[73] AnnotationDbi_1.50.1 BiocManager_1.30.10
[75] GenomicRanges_1.40.0 memoise_1.1.0
[77] VariantAnnotation_1.34.0