Closed elaplant closed 3 years ago
sanchit-saini
commented
3 years ago Hi @elaplant
This issue will get fixed in the upcoming release that is on 20 May(Bioconductor 3.13). BiocGenerics contains the characterORconnection which was renamed to character_OR_connection. Effectively it was also renamed in the rtracklayer package. But because of failed checks, it wasn't propagated on the Bioconductor.
lawremi
commented
3 years ago @sanchit-saini is there some way for us to fix this now, instead of waiting for the release?
sanchit-saini
commented
3 years ago @lawremi For now, I think the user can declare class union themself after importing rtracklayer with
setClassUnion("character_OR_connection", c("character", "connection"))How long will it take for the updated rtracklayer to propagate to the Bioconductor repository?
sanchit-saini
commented
3 years ago The changes are already present in the Bioconductor devel branch and I think this branch will be used for the next release. So therefore it will be propagated on 20 May.
elaplant
commented
3 years ago Setting the class union works so I'll be able to use that until the update. Thank you!
I’m trying to use rtracklayer 1.48.0 to search UCSC genome browser tables. When I try to set up the session and then add the appropriate genome I get an error:
Session info below:
R version 4.0.0 (2020-04-24) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] forcats_0.5.0 stringr_1.4.0 purrr_0.3.4 tibble_3.0.1 tidyverse_1.3.0 dplyr_0.8.5 survminer_0.4.7 ggpubr_0.3.0
[9] survival_3.1-12 devtools_2.3.0 usethis_1.6.1 readr_1.3.1 data.table_1.12.8 EDec_0.9 tidyr_1.0.3 rtracklayer_1.48.0
[17] GenomicRanges_1.40.0 GenomeInfoDb_1.24.0 IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.36.1 pROC_1.16.2 caret_6.0-86 ggplot2_3.3.0
[25] lattice_0.20-41 CTD_1.0.0 gmp_0.6-2 igraph_1.2.5
loaded via a namespace (and not attached): [1] readxl_1.3.1 backports_1.1.6 plyr_1.8.6 splines_4.0.0 BiocParallel_1.24.1 digest_0.6.25
[7] foreach_1.5.0 gdata_2.18.0 fansi_0.4.1 magrittr_1.5 memoise_1.1.0 openxlsx_4.2.2
[13] remotes_2.1.1 recipes_0.1.12 Biostrings_2.56.0 modelr_0.1.8 gower_0.2.1 matrixStats_0.56.0
[19] prettyunits_1.1.1 colorspace_1.4-1 blob_1.2.1 rvest_0.3.5 haven_2.3.0 xfun_0.14
[25] callr_3.4.3 crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.6.1 zoo_1.8-8 iterators_1.0.12
[31] glue_1.4.0 gtable_0.3.0 ipred_0.9-9 zlibbioc_1.34.0 XVector_0.28.0 DelayedArray_0.14.0
[37] car_3.0-8 pkgbuild_1.0.8 abind_1.4-5 scales_1.1.1 DBI_1.1.0 rstatix_0.5.0
[43] Rcpp_1.0.4.6 xtable_1.8-4 foreign_0.8-78 km.ci_0.5-2 lava_1.6.7 prodlim_2019.11.13
[49] httr_1.4.1 gplots_3.0.3 ellipsis_0.3.0 farver_2.0.3 pkgconfig_2.0.3 XML_3.99-0.3
[55] nnet_7.3-13 dbplyr_1.4.4 labeling_0.3 tidyselect_1.1.0 rlang_0.4.6 reshape2_1.4.4
[61] munsell_0.5.0 cellranger_1.1.0 tools_4.0.0 cli_2.0.2 generics_0.0.2 broom_0.5.6
[67] yaml_2.2.1 ModelMetrics_1.2.2.2 processx_3.4.2 knitr_1.28 fs_1.4.1 zip_2.0.4
[73] survMisc_0.5.5 caTools_1.18.0 nlme_3.1-147 xml2_1.3.2 compiler_4.0.0 rstudioapi_0.11
[79] curl_4.3 testthat_2.3.2 ggsignif_0.6.0 reprex_0.3.0 stringi_1.4.6 ps_1.3.3
[85] desc_1.2.0 Matrix_1.2-18 KMsurv_0.1-5 vctrs_0.3.0 pillar_1.4.4 lifecycle_0.2.0
[91] bitops_1.0-6 R6_2.4.1 KernSmooth_2.23-16 gridExtra_2.3 rio_0.5.16 sessioninfo_1.1.1
[97] codetools_0.2-16 MASS_7.3-51.6 gtools_3.8.2 assertthat_0.2.1 pkgload_1.0.2 SummarizedExperiment_1.18.2 [103] rprojroot_1.3-2 withr_2.2.0 GenomicAlignments_1.24.0 Rsamtools_2.4.0 GenomeInfoDbData_1.2.3 hms_0.5.3
[109] grid_4.0.0 rpart_4.1-15 timeDate_3043.102 class_7.3-16 carData_3.0-4 Biobase_2.50.0
[115] lubridate_1.7.8