Closed sanghoonio closed 23 hours ago
jwokaty
commented
1 day ago This comes from the rtracklayer::import. I don't think it's something bedbaser should suppress since that's coming from your R session. I'm wondering what version of BiocManager you're using and if it's older. Could you share your sessionInfo()?
sanghoonio
commented
1 day ago I see, sure:
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.0.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] episcope_0.1.0 bedbaser_0.99.2
loaded via a namespace (and not attached):
[1] rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3 fs_1.6.4
[5] BiocIO_1.12.0 zlibbioc_1.48.2 vctrs_0.6.5 memoise_2.0.1
[9] Rsamtools_2.18.0 DelayedMatrixStats_1.22.6 RCurl_1.98-1.16 htmltools_0.5.8.1
[13] S4Arrays_1.2.1 BiocBaseUtils_1.4.0 usethis_2.2.3 lambda.r_1.2.4
[17] curl_5.2.1 Rhdf5lib_1.22.1 SparseArray_1.2.4 rhdf5_2.44.0
[21] htmlwidgets_1.6.4 desc_1.4.3 bsseq_1.36.0 testthat_3.2.1.1
[25] plyr_1.8.9 futile.options_1.0.1 cachem_1.1.0 GenomicAlignments_1.38.2
[29] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-1.1
[33] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0
[37] shiny_1.8.1.1 digest_0.6.36 colorspace_2.1-1 S4Vectors_0.40.2
[41] ps_1.7.7 rprojroot_2.0.4 pkgload_1.4.0 GenomicRanges_1.54.1
[45] RSQLite_2.3.7 filelock_1.0.3 fansi_1.0.6 httr_1.4.7
[49] abind_1.4-8 compiler_4.3.2 remotes_2.5.0 bit64_4.0.5
[53] withr_3.0.1 BiocParallel_1.36.0 DBI_1.2.3 pkgbuild_1.4.4
[57] HDF5Array_1.28.1 R.utils_2.12.3 DelayedArray_0.28.0 sessioninfo_1.2.2
[61] rjson_0.2.23 gtools_3.9.5 permute_0.9-7 tools_4.3.2
[65] httpuv_1.6.15 R.oo_1.26.0 glue_1.7.0 restfulr_0.0.15
[69] callr_3.7.6 rhdf5filters_1.12.1 promises_1.3.0 grid_4.3.2
[73] reshape2_1.4.4 generics_0.1.3 gtable_0.3.5 BSgenome_1.68.0
[77] R.methodsS3_1.8.2 tidyr_1.3.1 data.table_1.16.0 xml2_1.3.6
[81] utf8_1.2.4 XVector_0.42.0 BiocGenerics_0.48.1 pillar_1.9.0
[85] stringr_1.5.1 limma_3.58.1 later_1.3.2 dplyr_1.1.4
[89] BiocFileCache_2.10.2 lattice_0.22-6 rtracklayer_1.62.0 bit_4.0.5
[93] tidyselect_1.2.1 locfit_1.5-9.10 Biostrings_2.70.3 miniUI_0.1.1.1
[97] knitr_1.48 IRanges_2.36.0 SummarizedExperiment_1.32.0 xfun_0.45
[101] stats4_4.3.2 futile.logger_1.4.3 Biobase_2.62.0 statmod_1.5.0
[105] brio_1.1.5 devtools_2.4.5 matrixStats_1.4.1 DT_0.33
[109] stringi_1.8.4 yaml_2.3.10 codetools_0.2-20 tibble_3.2.1
[113] BiocManager_1.30.23 cli_3.6.3 AnVIL_1.16.2 xtable_1.8-4
[117] munsell_0.5.1 processx_3.8.4 roxygen2_7.3.2 Rcpp_1.0.13
[121] GenomeInfoDb_1.38.8 dbplyr_2.5.0 XML_3.99-0.17 rapiclient_0.1.8
[125] parallel_4.3.2 ellipsis_0.3.2 ggplot2_3.5.1 blob_1.2.4
[129] profvis_0.3.8 urlchecker_1.0.1 sparseMatrixStats_1.12.2 bitops_1.0-8
[133] scales_1.3.0 purrr_1.0.2 crayon_1.5.3 rlang_1.1.4
[137] formatR_1.14 After reinstalling a bunch of things, I am able to reproduce this. It is kind of strange. Thanks for making the issue; I'll look into it.
Running bb_to_granges() or bb_to_grangeslist() prints out the following message regarding bioconductor standard repositories. Minor issue, but I would think it can get a little annoying for large BEDsets.