Cannot connect to annotationhub server
3
0
Entering edit mode
@966734c0
Last seen 16 days ago
China

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
AnnotationHub ExperimentHub • 457 views
ADD COMMENT
0
Entering edit mode
shepherl 3.9k
@lshep
Last seen 5 hours ago
United States

Do you have a strong internet connect and/or are you behind a proxy ?

ADD COMMENT
0
Entering edit mode
@966734c0
Last seen 16 days ago
China

Yes my internet connection is fine, I have checked it and also i am not behind any proxy.

ADD COMMENT
0
Entering edit mode

You could see if you have write access to the default cache location. AnnotationHub::getAnnotationHubOption("CACHE") and also provide the output to

library(AnnotationHub)
hub=getAnnotationHubOption("URL")
readBin(hub, n=1L, what="raw")
ADD REPLY
0
Entering edit mode
@966734c0
Last seen 16 days ago
China

AnnotationHub::getAnnotationHubOption("CACHE")

[1] "C:\Users\Administrator\AppData\Local/R/cache/R/AnnotationHub"

library(AnnotationHub)

hub=getAnnotationHubOption("URL")

readBin(hub,n=1L,what = "raw")

Error in file(con, "rb"):

cannot open the connection to 'https://annotationhub.bioconductor.org'

Additionally: Warning message

In file(con, "rb") :

URL 'https://annotationhub.bioconductor.org/': Timeout of 60 seconds was reached

ADD COMMENT
0
Entering edit mode

The AnnotationHub is up and running. I think you are either behind a proxy or annotationhub.bioconductor.org is being blocked by your institution/organization

ADD REPLY

Login before adding your answer.

Traffic: 586 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6