Open alslonik opened 7 months ago
Hi, ggmsa command with your protein example gives the following: What can be done to debug?
` rlang::last_trace() <error/rlib_error_dots_nonempty> Error in `vctrs::vec_as_subscript()`: ! `...` must be empty. x Problematic argument: • call = call
Backtrace: ▆ 1. └─ggmsa::ggmsa(OG_msa_example) 2. └─ggmsa::tidy_msa(msa, start = start, end = end) 3. ├─tidyr::gather(alndf, "position", "character", cn) 4. └─tidyr:::gather.data.frame(alndf, "position", "character", cn) 5. ├─base::unname(tidyselect::vars_select(tbl_vars(data), !!!quos)) 6. └─tidyselect::vars_select(tbl_vars(data), !!!quos) 7. └─tidyselect:::eval_select_impl(...) 8. ├─tidyselect:::with_subscript_errors(...) 9. │ └─rlang::try_fetch(...) 10. │ └─base::withCallingHandlers(...) 11. └─tidyselect:::vars_select_eval(...) 12. └─tidyselect:::walk_data_tree(expr, data_mask, context_mask) 13. └─tidyselect:::eval_c(expr, data_mask, context_mask) 14. └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init) 15. └─tidyselect:::walk_data_tree(init, data_mask, context_mask) 16. └─tidyselect:::as_indices_sel_impl(...) 17. └─tidyselect:::as_indices_impl(...) 18. └─vctrs::vec_as_subscript(x, logical = "error", call = call, arg = arg) Run rlang::last_trace(drop = FALSE) to see 4 hidden frames.`
`> sessionInfo() R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3 locale: [1] LC_CTYPE=he_IL.UTF-8 LC_NUMERIC=C LC_TIME=he_IL.UTF-8 LC_COLLATE=he_IL.UTF-8 [5] LC_MONETARY=he_IL.UTF-8 LC_MESSAGES=he_IL.UTF-8 LC_PAPER=he_IL.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=he_IL.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] ggmsa_1.4.0 msa_1.30.1 RSQLite_2.2.20 RPostgres_1.4.6 Biostrings_2.62.0 [6] GenomeInfoDb_1.34.4 XVector_0.34.0 IRanges_2.24.1 S4Vectors_0.28.1 BiocGenerics_0.44.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.9 ape_5.7-1 lattice_0.21-8 tidyr_1.2.1 [5] assertthat_0.2.1 digest_0.6.31 proj4_1.0-14 utf8_1.2.3 [9] ggforce_0.4.1 R6_2.5.1 ggplot2_3.3.6 pillar_1.8.1 [13] ggfun_0.1.4 yulab.utils_0.1.4 zlibbioc_1.44.0 rlang_1.1.1 [17] lazyeval_0.2.2 rstudioapi_0.14 extrafontdb_1.0 blob_1.2.4 [21] extrafont_0.19 ggalt_0.4.0 RCurl_1.98-1.3 polyclip_1.10-4 [25] bit_4.0.5 munsell_0.5.0 compiler_4.2.2 pkgconfig_2.0.3 [29] gridGraphics_0.5-1 seqmagick_0.1.6 tidyselect_1.2.0 tibble_3.1.2 [33] GenomeInfoDbData_1.2.9 fansi_1.0.3 crayon_1.5.2 dplyr_1.0.6 [37] withr_3.0.0 MASS_7.3-58.1 bitops_1.0-7 grid_4.2.2 [41] jsonlite_1.8.4 nlme_3.1-161 Rttf2pt1_1.3.12 gtable_0.3.3 [45] lifecycle_1.0.4 DBI_1.2.1 magrittr_2.0.3 scales_1.2.1 [49] KernSmooth_2.23-21 tidytree_0.4.6 cli_3.1.0 cachem_1.0.8 [53] farver_2.1.1 fs_1.6.3 ggtree_3.2.1 ellipsis_0.3.2 [57] generics_0.1.3 vctrs_0.3.8 ash_1.0-15 RColorBrewer_1.1-3 [61] treeio_1.22.0 tools_4.2.2 bit64_4.0.5 ggplotify_0.1.1 [65] glue_1.5.0 purrr_0.3.4 tweenr_2.0.2 maps_3.4.1 [69] hms_1.1.3 parallel_4.2.2 fastmap_1.1.1 colorspace_2.0-2 [73] aplot_0.2.2 R4RNA_1.26.0 memoise_2.0.1 patchwork_1.1.2 `
Hi, ggmsa command with your protein example gives the following: What can be done to debug?