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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!
