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ggmsa rlang error #64

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alslonik opened this issue Feb 8, 2024 · 0 comments
Open

ggmsa rlang error #64

alslonik opened this issue Feb 8, 2024 · 0 comments

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@alslonik
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alslonik commented Feb 8, 2024

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  `


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