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Error when rendering plotly with tidyverse 1.3.2 in shiny #2190

Open Mailinnia opened 1 year ago

Mailinnia commented 1 year ago

I've run into issues with displaying a simple plotly output in shiny when I install the latest tidyverse (1.3.2). The issue does not appear with tidyverse 1.3.1, or if I do not install tidyverse.

I also reported it to the tidyverse repo: https://github.com/tidyverse/tidyverse/issues/303

I've only installed plotly, shiny, and tidyverse. I get the following error:

Warning: Error in vec_as_location: `...` must be empty.
✖ Problematic argument:
• call = call
  119: <Anonymous>
  118: signalCondition
  117: signal_abort
  116: action
  114: action_dots
  113: ellipsis::check_dots_empty
  112: vec_as_location
  109: vectbl_as_col_location
  108: [.tbl_df
  105: <Anonymous>
  104: mapply
  103: Map
  102: plotly_build.plotly
   98: getFromNamespace("prepareWidget", "plotly")
   97: shinyRenderWidget
   96: func
   83: renderFunc
   82: output$test_graph
    1: shiny::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.

when running this simple script:

library(shiny)
library(plotly)

ui <- fluidPage(plotlyOutput('test_graph'))

server <- function(input, output, session){

  output$test_graph <- renderPlotly({
    x <- c(1:100)
    random_y <- rnorm(100, mean = 0)
    data <- data.frame(x, random_y)

    fig <- plot_ly(data, x = ~x, y = ~random_y, type = 'scatter', mode = 'lines')

    fig
  })
}

shinyApp(ui = ui, server = server)
I have the following R version and packages installed: R version
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 1.1
year 2021
month 08
day 10
svn rev 80725
language R
version.string R version 4.1.1 (2021-08-10)
nickname Kick Things
Packages Package Version Package Version Package Version
AnnotationDbi 1.54.1 fs 1.5.0 ps 1.6.0
AnnotationFilter 1.16.0 futile.logger 1.4.3 purrr 0.3.4
askpass 1.1 futile.options 1.0.1 R6 2.5.1
assertthat 0.2.1 gargle 1.2.0 rappdirs 0.3.3
backports 1.2.1 generics 0.1.0 RColorBrewer 1.1-2
bamsignals 1.24.0 GenomeInfoDb 1.28.4 Rcpp 1.0.7
base64enc 0.1-3 GenomeInfoDbData 1.2.6 RCurl 1.98-1.5
bezier 1.1.2 GenomicAlignments 1.28.0 readr 2.1.2
BH 1.75.0-0 GenomicFeatures 1.44.2 readxl 1.3.1
Biobase 2.52.0 GenomicRanges 1.44.0 regioneR 1.24.0
BiocFileCache 2.0.0 getopt 1.20.3 rematch 1.0.1
BiocGenerics 0.38.0 ggplot2 3.3.5 rematch2 2.1.2
BiocIO 1.2.0 glue 1.6.2 reprex 2.0.1
BiocManager 1.30.16 googledrive 2.0.0 restfulr 0.0.13
BiocParallel 1.26.2 googlesheets4 1.0.0 Rhtslib 1.24.0
BiocVersion 3.13.1 gridExtra 2.3 rjson 0.2.20
biomaRt 2.48.3 gtable 0.3.0 rlang 1.0.4
Biostrings 2.60.2 haven 2.4.3 Rsamtools 2.8.0
biovizBase 1.40.0 highr 0.9 RSQLite 2.2.8
bit 4.0.4 Hmisc 4.5-0 rstudioapi 0.13
bit64 4.0.5 hms 1.1.1 rtracklayer 1.52.1
bitops 1.0-7 htmlTable 2.2.1 rvest 1.0.2
blob 1.2.2 htmltools 0.5.2 S4Vectors 0.30.1
broom 1.0.0 htmlwidgets 1.5.4 sass 0.4.2
BSgenome 1.60.0 httpuv 1.6.5 scales 1.1.1
bslib 0.4.0 httr 1.4.2 selectr 0.4-2
cachem 1.0.6 ids 1.0.1 shiny 1.7.2
callr 3.7.0 IRanges 2.26.0 snow 0.4-3
cellranger 1.1.0 isoband 0.2.5 sourcetools 0.1.7
checkmate 2.0.0 jpeg 0.1-9 stringi 1.7.4
cli 3.3.0 jquerylib 0.1.4 stringr 1.4.0
clipr 0.8.0 jsonlite 1.7.2 SummarizedExperiment 1.22.0
colorout 1.2-2 karyoploteR 1.18.0 sys 3.4
colorspace 2.0-2 KEGGREST 1.32.0 tibble 3.1.8
commonmark 1.8.0 labeling 0.4.2 tidyr 1.1.4
cpp11 0.4.0 lambda.r 1.2.4 tidyselect 1.1.1
crayon 1.5.1 later 1.3.0 tidyverse 1.3.2
crosstalk 1.2.0 latticeExtra 0.6-29 tinytex 0.34
curl 4.3.2 lazyeval 0.2.2 tzdb 0.1.2
data.table 1.14.2 lifecycle 1.0.1 utf8 1.2.2
DBI 1.1.1 lubridate 1.8.0 uuid 0.1-4
dbplyr 2.1.1 magrittr 2.0.1 VariantAnnotation 1.38.0
DelayedArray 0.18.0 MatrixGenerics 1.4.3 vctrs 0.3.8
dichromat 2.0-0 matrixStats 0.61.0 viridis 0.6.1
digest 0.6.28 memoise 2.0.0 viridisLite 0.4.0
docopt 0.7.1 mime 0.12 vroom 1.5.7
dplyr 1.0.7 modelr 0.1.8 withr 2.4.2
dtplyr 1.2.1 munsell 0.5.0 xfun 0.26
ellipsis 0.3.2 openssl 1.4.5 XML 3.99-0.8
ensembldb 2.16.4 pillar 1.8.0 xml2 1.3.3
evaluate 0.14 pkgconfig 2.0.3 xtable 1.8-4
fansi 0.5.0 plogr 0.2.0 XVector 0.32.0
farver 2.1.0 plotly 4.10.0 yaml 2.2.1
fastmap 1.1.0 png 0.1-7 zlibbioc 1.38.0
filelock 1.0.2 prettyunits 1.1.1 littler 0.3.12
fontawesome 0.3.0 processx 3.5.2
forcats 0.5.1 progress 1.2.2
formatR 1.11 promises 1.2.0.1
Formula 1.2-4 ProtGenerics 1.24.0

I've identified these differences in installed packages when I install install.packages('tidyverse', repos='https://cloud.r-project.org/') vs install.packages('https://cran.r-project.org/src/contrib/Archive/tidyverse/tidyverse_1.3.1.tar.gz', repos=NULL, type='source'):

Packages v1.3.2 v1.3.1
broom 1.0.0 0.7.9
cli 3.3.0 3.0.1
clipr 0.8.0 not installed
crayon 1.5.1 1.4.1
dtplyr 1.2.1 1.1.0
glue 1.6.2 1.4.2
lubridate 1.8.0 1.7.10
pillar 1.8.0 1.6.3
readr 2.1.2 2.0.2
rlang 1.0.4 0.4.11
rvest 1.0.2 1.0.1
tibble 3.1.8 3.1.5
tidyverse 1.3.2 1.3.1
vroom 1.5.7 1.5.5
xml2 1.3.3 1.3.2

But I haven't looked further into this.

cpsievert commented 1 year ago

Hmm, for some reason I'm not able to replicate this with tidyverse v1.3.2 (as well as recent CRAN versions of other packages). It'd be great if you could pinpoint exactly what package version introduces the problem