Cannot connect to annotationnhhub server Code should be placed in three backticks as shown below
ah <- AnnotationHub(localHub = FALSE)
# Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead using 'localHub=TRUE' 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 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] pheatmap_1.0.12 sesame_1.23.6 sesameData_1.23.0 ExperimentHub_2.13.0 maftools_2.21.0
[6] lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[11] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
[16] TCGAbiolinks_2.33.0 zlibbioc_1.51.1 XVector_0.45.0 S4Arrays_1.5.1 abind_1.4-5
[21] Matrix_1.7-0 SummarizedExperiment_1.35.0 Biobase_2.65.0 GenomicRanges_1.57.1 GenomeInfoDb_1.40.1
[26] IRanges_2.38.0 S4Vectors_0.42.0 MatrixGenerics_1.16.0 matrixStats_1.3.0 AnnotationHub_3.13.0
[31] BiocFileCache_2.13.0 dbplyr_2.5.0 BiocGenerics_0.50.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 httr2_1.0.1 biomaRt_2.61.1 rlang_1.1.4 magrittr_2.0.3
[6] compiler_4.4.0 RSQLite_2.3.7 reshape2_1.4.4 png_0.1-8 vctrs_0.6.5
[11] rvest_1.0.4 pkgconfig_2.0.3 crayon_1.5.2 fastmap_1.2.0 utf8_1.2.4
[16] tzdb_0.4.0 preprocessCore_1.67.0 UCSC.utils_1.1.0 bit_4.0.5 xfun_0.45
[21] cachem_1.1.0 jsonlite_1.8.8 progress_1.2.3 blob_1.2.4 DelayedArray_0.31.1
[26] BiocParallel_1.39.0 parallel_4.4.0 prettyunits_1.2.0 R6_2.5.1 stringi_1.8.4
[31] RColorBrewer_1.1-3 DNAcopy_1.79.0 Rcpp_1.0.12 knitr_1.47 wheatmap_0.2.0
[36] downloader_0.4 splines_4.4.0 timechange_0.3.0 tidyselect_1.2.1 rstudioapi_0.16.0
[41] yaml_2.3.8 codetools_0.2-20 curl_5.2.1 lattice_0.22-6 plyr_1.8.9
[46] withr_3.0.0 KEGGREST_1.45.1 survival_3.7-0 xml2_1.3.6 Biostrings_2.73.1
[51] pillar_1.9.0 BiocManager_1.30.23 filelock_1.0.3 generics_0.1.3 BiocVersion_3.20.0
[56] hms_1.1.3 munsell_0.5.1 scales_1.3.0 glue_1.7.0 tools_4.4.0
[61] data.table_1.15.4 XML_3.99-0.16.1 grid_4.4.0 AnnotationDbi_1.67.0 colorspace_2.1-0
[66] GenomeInfoDbData_1.2.12 cli_3.6.2 rappdirs_0.3.3 fansi_1.0.6 gtable_0.3.5
[71] TCGAbiolinksGUI.data_1.25.0 digest_0.6.35 SparseArray_1.5.8 memoise_2.0.1 lifecycle_1.0.4
[76] httr_1.4.7 bit64_4.0.5
You could see if you have write access to the default cache location.
AnnotationHub::getAnnotationHubOption("CACHE")
and also provide the output to