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I found this page: "I can't use AnnotationHub() " but I still couldn't slive my problem. Does it mean that my internet setting has some problem? Looking forward to someone giving me an answer. Thanks.
> library(PhyloProfile)
> runPhyloProfile()
Using 'localHub=TRUE'
If offline, please also see BiocManager vignette section on offline use
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 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=Japanese_Japan.utf8 LC_CTYPE=Japanese_Japan.utf8 LC_MONETARY=Japanese_Japan.utf8 LC_NUMERIC=C
[5] LC_TIME=Japanese_Japan.utf8
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ExperimentHub_2.4.0 AnnotationHub_3.4.0 BiocFileCache_2.4.0 dbplyr_2.1.1 zoo_1.8-10 OmaDB_2.12.0
[7] plyr_1.8.7 httr_1.4.3 shinyjs_2.1.0 shinyFiles_0.9.1 shinyBS_0.61.1 RColorBrewer_1.1-3
[13] gridExtra_2.3 GO.db_3.15.0 AnnotationDbi_1.58.0 ggplot2_3.3.6 GenomeInfoDbData_1.2.8 energy_1.7-10
[19] data.table_1.14.2 colourpicker_1.1.1 Biostrings_2.64.0 GenomeInfoDb_1.32.1 XVector_0.36.0 IRanges_2.30.0
[25] S4Vectors_0.34.0 bioDist_1.68.0 KernSmooth_2.23-20 Biobase_2.56.0 BiocGenerics_0.42.0 ape_5.6-2
[31] shiny_1.7.1 PhyloProfile_1.11.1
loaded via a namespace (and not attached):
[1] nlme_3.1-157 matrixStats_0.62.0 bitops_1.0-7 fs_1.5.2
[5] bit64_4.0.5 filelock_1.0.2 tools_4.2.0 utf8_1.2.2
[9] R6_2.5.1 DT_0.23 DBI_1.1.2 colorspace_2.0-3
[13] withr_2.5.0 tidyselect_1.1.2 bit_4.0.4 curl_4.3.2
[17] compiler_4.2.0 graph_1.74.0 cli_3.3.0 SparseM_1.81
[21] xml2_1.3.3 topGO_2.48.0 scales_1.2.0 rappdirs_0.3.3
[25] digest_0.6.29 rmarkdown_2.14 pkgconfig_2.0.3 htmltools_0.5.2
[29] fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.0.2 RSQLite_2.2.14
[33] generics_0.1.2 jsonlite_1.8.0 dplyr_1.0.9 RCurl_1.98-1.6
[37] magrittr_2.0.3 Rcpp_1.0.8.3 munsell_0.5.0 fansi_1.0.3
[41] lifecycle_1.0.1 yaml_2.3.5 zlibbioc_1.42.0 blob_1.2.3
[45] parallel_4.2.0 promises_1.2.0.1 crayon_1.5.1 miniUI_0.1.1.1
[49] lattice_0.20-45 KEGGREST_1.36.0 knitr_1.39 pillar_1.7.0
[53] GenomicRanges_1.48.0 boot_1.3-28 glue_1.6.2 BiocVersion_3.15.2
[57] evaluate_0.15 BiocManager_1.30.17 png_0.1-7 vctrs_0.4.1
[61] httpuv_1.6.5 gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1
[65] cachem_1.0.6 xfun_0.30 mime_0.12 xtable_1.8-4
[69] later_1.3.0 gsl_2.1-7.1 tibble_3.1.7 memoise_2.0.1
[73] ellipsis_0.3.2 interactiveDisplayBase_1.34.0 BiocStyle_2.24.0
Are you connected to the internet? At least the first run you will need internet access to use; After it is cached you should be able to use offline use. If you have internet this may indicate a problem with a default setting in PhyloProfile.
Hi, may be you can try this one. Best, Vinh
It works! Finally! Yesterday it drives me crazy. I was really sorry that I didn't check Q&A carefully. The "Problem with ExperimentHub" part solves this problem perfectly.
Thank you very much! Bless you.