recountmethylation: Error in accessing database files
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Entering edit mode
Jessica • 0
@2a4e2e74
Last seen 6 weeks 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 • 124 views
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0
Entering edit mode
maden • 0
@maden-22797
Last seen 25 days ago
United States

Greetings,

Thanks for pointing this out! This seems to be a known Windows-specific issue with the SSL error thrown for RCurl. I've also seen this error being thrown periodically for the package builds. Note, the download functions should presently work for non-Windows platforms.

I will see about fixing this in a future update, probably to replace the RCurl usages. In the meantime, you may try downloading the database files outside of R using your method of choice (located at: https://recount.bio/data/).

Also note recountmethylation now includes data from 2 platforms, and the newest database files have either "hm450k" or "epic" appended to their filenames. This is reflected in the new "platform" argument for getdb functions, found on the current main (v1.2.0) and developer (v1.3.1) branches. While these new files don't yet show in ExperimentHub/AnnotationHub, they should sync there eventually.

best regards,

Sean

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