shinyDAG
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GerkeLab
error when adding a new link
Just stumbled on this app, looks like it doesnt work with R 4.3.3 or perhaps with later versions of **tidyr**?
This error occurs when trying to add any link to any node.
When debugging the I tried changing the nest and unnest functions to unnest_legacy. This removed the warnings.
https://www.tidyverse.org/blog/2019/09/tidyr-1-0-0/#nesting
But the Error ! object 'to.y' not found persists and I dont know how to debug it.
Warning: Supplying `...` without names was deprecated in tidyr 1.0.0.
ℹ Please specify a name for each selection.
ℹ Did you want `data = -to`?
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: Supplying `...` without names was deprecated in tidyr 1.0.0.
ℹ Please specify a name for each selection.
ℹ Did you want `data = -from`?
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: Supplying `...` without names was deprecated in tidyr 1.0.0.
ℹ Please specify a name for each selection.
ℹ Did you want `data = -to`?
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: Supplying `...` without names was deprecated in tidyr 1.0.0.
ℹ Please specify a name for each selection.
ℹ Did you want `data = -from`?
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: `cols` is now required when using `unnest()`.
ℹ Please use `cols = c(data)`.
Warning: `cols` is now required when using `unnest()`.
ℹ Please use `cols = c(data)`.
Warning: `cols` is now required when using `unnest()`.
ℹ Please use `cols = c(data)`.
Warning: `cols` is now required when using `unnest()`.
ℹ Please use `cols = c(data)`.
Warning: Error in mutate: ℹ In argument: `d_y = to.y - from.y`.
Caused by error:
! object 'to.y' not found
160: <Anonymous>
159: signalCondition
158: signal_abort
157: abort
156: h
155: .handleSimpleError
154: eval
153: mask$eval_all_mutate
152: mutate_col
150: mutate_cols
149: mutate.data.frame
148: mutate
147: select
146: %>%
145: edge_points [R/edge.R#74]
144: <reactive:arrows> [R/module/clickpad.R#102]
128: arrows
127: layout.plotly
126: layout
125: %||%
122: modify_list
121: config
120: %||%
119: shiny_defaults_set
118: shiny_event_add
117: plotly::event_register
116: %||%
115: shiny_defaults_set
114: shiny_event_add
113: plotly::event_register
112: %||%
111: shiny_defaults_set
110: shiny_event_add
109: plotly::event_register
108: %||%
107: shiny_defaults_set
106: shiny_event_add
105: plotly::event_register
104: addHook
103: htmlwidgets::onRender
102: %>%
101: renderPlotly [R/module/clickpad.R#224]
100: func
97: shinyRenderWidget
96: func
83: renderFunc
82: output$clickpad-plot
1: runApp
Input to asJSON(keep_vec_names=TRUE) is a named vector. In a future version of jsonlite, this option will not be supported, and named vectors will be translated into arrays instead of objects. If you want JSON object output, please use a named list instead. See ?toJSON.
No scatter mode specifed:
Setting the mode to markers
Read more about this attribute -> https://plotly.com/r/reference/#scatter-mode
No scatter mode specifed:
Setting the mode to markers
Read more about this attribute -> https://plotly.com/r/reference/#scatter-mode
Warning: Error in tidyr::gather: Can't select columns that don't exist.
✖ Column `from` doesn't exist.
176: <Anonymous>
175: signalCondition
174: signal_abort
173: cnd_signal
172: <Anonymous>
171: signalCondition
170: signal_abort
169: abort
168: stop_subscript
167: stop_subscript_oob
166: <Anonymous>
165: vctrs::vec_as_location
164: chr_as_locations
163: as_indices_impl
162: as_indices_sel_impl
161: walk_data_tree
160: eval_colon
159: walk_data_tree
158: reduce_sels
157: eval_c
156: walk_data_tree
155: vars_select_eval
152: eval_select_impl
151: tidyselect::vars_select
149: gather.data.frame
148: tidyr::gather
147: %>%
146: edges_in_dag [R/edge.R#45]
145: edge_points [R/edge.R#70]
144: <reactive:arrows> [R/module/clickpad.R#102]
128: arrows
127: layout.plotly
126: layout
125: %||%
122: modify_list
121: config
120: %||%
119: shiny_defaults_set
118: shiny_event_add
117: plotly::event_register
116: %||%
115: shiny_defaults_set
114: shiny_event_add
113: plotly::event_register
112: %||%
111: shiny_defaults_set
110: shiny_event_add
109: plotly::event_register
108: %||%
107: shiny_defaults_set
106: shiny_event_add
105: plotly::event_register
104: addHook
103: htmlwidgets::onRender
102: %>%
101: renderPlotly [R/module/clickpad.R#224]
100: func
97: shinyRenderWidget
96: func
83: renderFunc
82: output$clickpad-plot
1: runApp
Warning: Error in tidyr::gather: Can't select columns that don't exist.
✖ Column `from` doesn't exist.
134: <Anonymous>
133: signalCondition
132: signal_abort
131: cnd_signal
130: <Anonymous>
129: signalCondition
128: signal_abort
127: abort
126: stop_subscript
125: stop_subscript_oob
124: <Anonymous>
123: vctrs::vec_as_location
122: chr_as_locations
121: as_indices_impl
120: as_indices_sel_impl
119: walk_data_tree
118: eval_colon
117: walk_data_tree
116: reduce_sels
115: eval_c
114: walk_data_tree
113: vars_select_eval
110: eval_select_impl
109: tidyselect::vars_select
107: gather.data.frame
106: tidyr::gather
105: %>%
104: edges_in_dag [C:\Users\brianod\OneDrive - Universitetet i Oslo\Documents\projects\msc_thesis\ShinyDAG\R\edge.R#45]
97: renderUI [C:\Users\brianod\OneDrive - Universitetet i Oslo\Documents\projects\msc_thesis\ShinyDAG/server.R#653]
96: func
83: renderFunc
82: output$dagExposureOutcomeDiagnositcs
1: runApp
Removing session tempdir: www/6863e16d0c3cb9e83746eafe89e62f7c
> sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=en_US.UTF-8 LC_CTYPE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_NUMERIC=C
[5] LC_TIME=en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plotly_4.10.4 ggplot2_3.5.0 shinyThings_0.4.0 shinycssloaders_1.0.0 shinyjs_2.1.0
[6] shinyWidgets_0.8.6 ggdag_0.2.12 dplyr_1.1.4 shinyBS_0.61.1 shinyAce_0.4.2
[11] texPreview_2.1.0 igraph_2.0.3 dagitty_0.3-4 DiagrammeR_1.0.11 shinydashboard_0.7.2
[16] shiny_1.8.1.1
loaded via a namespace (and not attached):
[1] gtable_0.3.4 xfun_0.43 bslib_0.7.0 htmlwidgets_1.6.4 visNetwork_2.1.2 crosstalk_1.2.1
[7] vctrs_0.6.5 tools_4.3.3 generics_0.1.3 curl_5.2.1 tibble_3.2.1 fansi_1.0.6
[13] pkgconfig_2.0.3 data.table_1.15.4 RColorBrewer_1.1-3 desc_1.4.3 lifecycle_1.0.4 compiler_4.3.3
[19] munsell_0.5.1 tinytex_0.50 fontawesome_0.5.2 httpuv_1.6.15 htmltools_0.5.8.1 sass_0.4.9
[25] lazyeval_0.2.2 yaml_2.3.8 crayon_1.5.2 jquerylib_0.1.4 later_1.3.2 pillar_1.9.0
[31] whisker_0.4.1 tidyr_1.3.1 MASS_7.3-60.0.1 openssl_2.1.1 rsconnect_1.3.1 cachem_1.1.0
[37] details_0.3.0 magick_2.8.3 boot_1.3-30 mime_0.12 tidyselect_1.2.1 digest_0.6.35
[43] purrr_1.0.2 rematch2_2.1.2 fastmap_1.2.0 grid_4.3.3 colorspace_2.1-0 cli_3.6.2
[49] magrittr_2.0.3 base64enc_0.1-3 tidygraph_1.3.1 utf8_1.2.4 svgPanZoom_0.3.4 clipr_0.8.0
[55] withr_3.0.0 scales_1.3.0 promises_1.3.0 httr_1.4.7 askpass_1.2.0 png_0.1-8
[61] memoise_2.0.1 knitr_1.46 V8_4.4.2 viridisLite_0.4.2 rlang_1.1.4 Rcpp_1.0.12
[67] xtable_1.8-4 glue_1.7.0 xml2_1.3.6 rstudioapi_0.16.0 jsonlite_1.8.8 R6_2.5.1
[73] fs_1.6.4
