I can't run PhyloProfile
Entering edit mode
S.t ▴ 10
Last seen 21 months ago

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

[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
AnnotationHubData PhyloProfile • 1.1k views
Entering edit mode

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.

Entering edit mode

Hi, may be you can try this one. Best, Vinh

Entering edit mode

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.


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