recountmethylation: Error in accessing database files
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Jessica • 0
@2a4e2e74
Last seen 4 days ago
United States

Hello,

I'm trying to access database files using getdb() on the recountmethylation package. I use the following code:

library(recountmethylation) 
library(SMFilter)
library(minfi)
library(tidyverse)
library(BiocFileCache)
hub = ExperimentHub::ExperimentHub()
rmdat <- AnnotationHub::query(hub, "recountmethylation") # query the hubs

getdb_h5se_gr(verbose=TRUE)

Then, I get the following error:

library(recountmethylation) 
> library(SMFilter)
> library(minfi)
> library(BiocFileCache)
> hub = ExperimentHub::ExperimentHub()
snapshotDate(): 2020-10-27
> rmdat <- AnnotationHub::query(hub, "recountmethylation") # query the hubs
> 
> getdb_h5se_gr(verbose=TRUE) 
Downloading database...
Retrieving data dirnames from server...
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Download completed.
Error in getdb_h5se_gr(verbose = TRUE) : Problem with dbpath.

This is the output from the traceback():

> traceback()
2: stop("Problem with dbpath.")
1: getdb_h5se_gr(verbose = TRUE)
Warning message:
call dbDisconnect() when finished working with a connection 
>

This is my sessionInfo():

 sessionInfo()
R version 4.0.5 (2021-03-31)
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  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] forcats_0.5.1               stringr_1.4.0               dplyr_1.0.6                
 [4] purrr_0.3.4                 readr_1.4.0                 tidyr_1.1.3                
 [7] tibble_3.1.2                ggplot2_3.3.3               tidyverse_1.3.1            
[10] minfi_1.36.0                bumphunter_1.32.0           locfit_1.5-9.4             
[13] iterators_1.0.13            foreach_1.5.1               Biostrings_2.58.0          
[16] XVector_0.30.0              SummarizedExperiment_1.20.0 MatrixGenerics_1.2.1       
[19] matrixStats_0.59.0          GenomicRanges_1.42.0        GenomeInfoDb_1.26.7        
[22] IRanges_2.24.1              S4Vectors_0.28.1            SMFilter_1.0.3             
[25] recountmethylation_1.0.0    GEOmetadb_1.52.0            GEOquery_2.58.0            
[28] Biobase_2.50.0              ExperimentHub_1.16.1        AnnotationHub_2.22.1       
[31] BiocFileCache_1.14.0        dbplyr_2.1.1                BiocGenerics_0.36.1        
[34] RSQLite_2.2.7              

loaded via a namespace (and not attached):
  [1] readxl_1.3.1                  backports_1.2.1              
  [3] plyr_1.8.6                    splines_4.0.5                
  [5] BiocParallel_1.24.1           digest_0.6.27                
  [7] htmltools_0.5.1.1             fansi_0.5.0                  
  [9] magrittr_2.0.1                memoise_2.0.0                
 [11] limma_3.46.0                  annotate_1.68.0              
 [13] modelr_0.1.8                  askpass_1.1                  
 [15] siggenes_1.64.0               prettyunits_1.1.1            
 [17] colorspace_2.0-1              rvest_1.0.0                  
 [19] blob_1.2.1                    rappdirs_0.3.3               
 [21] haven_2.4.1                   xfun_0.23                    
 [23] jsonlite_1.7.2                crayon_1.4.1                 
 [25] RCurl_1.98-1.3                genefilter_1.72.1            
 [27] survival_3.2-10               glue_1.4.2                   
 [29] gtable_0.3.0                  zlibbioc_1.36.0              
 [31] DelayedArray_0.16.3           Rhdf5lib_1.12.1              
 [33] HDF5Array_1.18.1              scales_1.1.1                 
 [35] DBI_1.1.1                     rngtools_1.5                 
 [37] Rcpp_1.0.6                    xtable_1.8-4                 
 [39] progress_1.2.2                bit_4.0.4                    
 [41] mclust_5.4.7                  preprocessCore_1.52.1        
 [43] httr_1.4.2                    RColorBrewer_1.1-2           
 [45] ellipsis_0.3.2                pkgconfig_2.0.3              
 [47] reshape_0.8.8                 XML_3.99-0.6                 
 [49] utf8_1.2.1                    tidyselect_1.1.1             
 [51] rlang_0.4.11                  later_1.2.0                  
 [53] AnnotationDbi_1.52.0          cellranger_1.1.0             
 [55] munsell_0.5.0                 BiocVersion_3.12.0           
 [57] tools_4.0.5                   cachem_1.0.5                 
 [59] cli_2.5.0                     generics_0.1.0               
 [61] broom_0.7.6                   evaluate_0.14                
 [63] fastmap_1.1.0                 yaml_2.2.1                   
 [65] fs_1.5.0                      knitr_1.33                   
 [67] bit64_4.0.5                   beanplot_1.2                 
 [69] scrime_1.3.5                  nlme_3.1-152                 
 [71] doRNG_1.8.2                   sparseMatrixStats_1.2.1      
 [73] mime_0.10                     nor1mix_1.3-0                
 [75] xml2_1.3.2                    biomaRt_2.46.3               
 [77] compiler_4.0.5                rstudioapi_0.13              
 [79] curl_4.3.1                    interactiveDisplayBase_1.28.0
 [81] reprex_2.0.0                  stringi_1.6.2                
 [83] GenomicFeatures_1.42.3        lattice_0.20-41              
 [85] Matrix_1.3-2                  multtest_2.46.0              
 [87] vctrs_0.3.8                   pillar_1.6.1                 
 [89] lifecycle_1.0.0               rhdf5filters_1.2.1           
 [91] BiocManager_1.30.15           data.table_1.14.0            
 [93] bitops_1.0-7                  httpuv_1.6.1                 
 [95] rtracklayer_1.50.0            R6_2.5.0                     
 [97] promises_1.2.0.1              codetools_0.2-18             
 [99] MASS_7.3-53.1                 assertthat_0.2.1             
[101] rhdf5_2.34.0                  openssl_1.4.4                
[103] withr_2.4.2                   GenomicAlignments_1.26.0     
[105] Rsamtools_2.6.0               GenomeInfoDbData_1.2.4       
[107] hms_1.1.0                     quadprog_1.5-8               
[109] grid_4.0.5                    base64_2.0                   
[111] rmarkdown_2.8                 DelayedMatrixStats_1.12.3    
[113] illuminaio_0.32.0             lubridate_1.7.10             
[115] shiny_1.6.0

I'm using the Bioconductor User Guide (https://www.bioconductor.org/packages/devel/bioc/vignettes/recountmethylation/inst/doc/recountmethylation_users_guide.html#obtain-the-test-database) to get access to the database files.

I believe the error might have to do with BiocFileCache. Any help is greatly appreciated - thank you!

getdb recountmethylation dbpath • 43 views
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