CentOS Question posted in
The official documentation can be found here.

skimr(iris) generates error in check_dots_used when printing in linux RStudio console – CentOS

When I run the default skimr command in the console on a linux RStudio server I get the following partial output and error:

library(skimr)
skim(iris)

── Data Summary ────────────────────────
Values
Name iris
Number of rows 150
Number of columns 5

Column type frequency:
factor 1
numeric 4

Group variables None
Error in check_dots_used(action = warn) : unused argument (action = warn)

However, the same code will run just fine when I knit it in an RMarkdown document.

RMarkdown Output

The same code will also run fine on my Mac OSX laptop instance of RStudio, both in the console and an RMarkdown document.

I can assign the output of the skimr command and View the assigned output object just fine on the server instance:

out <- skim(iris)
View(out)
class(out)
1 "skim_df" "tbl_df" "tbl" "data.frame"

but print(out) generates the same error again

Here’s the sessionInfo.

sessionInfo()

R version 3.5.1 (2018-07-02)

Platform: x86_64-redhat-linux-gnu (64-bit)

Running under: CentOS Linux 7 (Core)

Matrix products: default

BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
1 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

1 stats graphics grDevices utils datasets methods base

other attached packages:
1 skimr_2.1.2

loaded via a namespace (and not attached):

1 Rcpp_1.0.2 rstudioapi_0.13 knitr_1.31 magrittr_1.5 tidyselect_1.1.0 R6_2.3.0 rlang_0.4.10 fansi_0.4.0 stringr_1.4.0
[10] dplyr_1.0.4 tools_3.5.1 xfun_0.20 utf8_1.1.4 cli_2.3.0 DBI_1.0.0 withr_2.4.1 htmltools_0.3.6 ellipsis_0.2.0.1
[19] yaml_2.2.0 rprojroot_1.3-2 assertthat_0.2.0 digest_0.6.18 tibble_3.0.6 lifecycle_0.2.0 crayon_1.3.4 tidyr_1.1.2 purrr_0.3.4
[28] repr_1.1.3 base64enc_0.1-3 vctrs_0.3.6 evaluate_0.12 glue_1.4.2 rmarkdown_1.10 stringi_1.2.4 compiler_3.5.1 pillar_1.4.7
[37] backports_1.1.2 generics_0.1.0 jsonlite_1.6 pkgconfig_2.0.2

Tags:

2

Answers


  1. 0

    You need to use options(skimr_strip_metadata = FALSE). It’s due to something related to the {pilar} package.
    https://github.com/ropensci/skimr/issues/641

    Also please update the ellipsis package. See this answer.
    Basic dyplr functions give an error: "check_dots_used"

    I don’t know why doing it in rmarkdown would work when the console doesn’t, unless somehow a different version of the package is loading.

    Login or Signup to reply.
  2. 0

    I used to have a similar situation where skim_without_chart will return an error could not find function "skim_without_charts".

    The solution I used is to first call skimr before calling skimm_without_charts like skimr::skim_without_charts(penguins) enter image description here
    That solves the problem for me.

    Login or Signup to reply.
Please signup or login to give your own answer.

Back To Top
Search