Open OskaratOmni opened 4 months ago
Posting the video here for reference: https://muse.ai/e/4m6kV17
@OskaratOmni could you send me the code used to create this error? Or, better yet, could you create a simple, reproducible example that I can run to recreate this?
Hey @dgkeyes , you bet. I did find that using option = 'gt' made the issue go away.
Github doesn't allow attaching rmd files but here's the code:
---
title: "Odd omni table issue"
subtitle: "minimal working example"
author: "Oskar "
date: "`r Sys.Date()`"
output:
omni::omni_html_report:
hypothesis: false
editor_options:
chunk_output_type: console
markdown:
wrap: 72
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(fig.path='figs/',
echo=FALSE, # change to TRUE if most code chunks should knit to report
warning=FALSE,
message=FALSE)
library(tidyverse)
library(omni)
library(flextable)
mtcars %>%
slice(1:5) %>%
omni_table(caption = "Caption", option = "gt")
Second table
mtcars %>%
slice(1:5) %>%
omni_table(caption = "Caption")
On my end the first table looks fine and the second has the weird table caption and stuff, like in the video.
Weird. This looks totally fine on my end.
I assume you've updated the omni
package to the latest version?
Can you also run `sessionInfo()' in the console and paste in what you get? Here's what I get, for example:
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flextable_0.9.6 omni_1.0.2023 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[7] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] gtable_0.3.5 xfun_0.44 ggrepel_0.9.5 tzdb_0.4.0
[5] vctrs_0.6.5 tools_4.3.3 generics_0.1.3 curl_5.2.1
[9] fansi_1.0.6 pkgconfig_2.0.3 data.table_1.15.4 uuid_1.2-0
[13] gt_0.10.1 lifecycle_1.0.4 compiler_4.3.3 textshaping_0.4.0
[17] munsell_0.5.1 httpuv_1.6.15 fontquiver_0.2.1 fontLiberation_0.1.0
[21] htmltools_0.5.8.1 yaml_2.3.8 later_1.3.2 pillar_1.9.0
[25] crayon_1.5.2 gfonts_0.2.0 openssl_2.2.0 rsconnect_1.2.0
[29] mime_0.12 fontBitstreamVera_0.1.1 tidyselect_1.2.1 zip_2.3.1
[33] digest_0.6.35 stringi_1.8.4 fastmap_1.2.0 grid_4.3.3
[37] colorspace_2.1-0 cli_3.6.2 magrittr_2.0.3 crul_1.4.2
[41] utf8_1.2.4 withr_3.0.0 gdtools_0.3.7 scales_1.3.0.9000
[45] promises_1.3.0 timechange_0.3.0 rmarkdown_2.27 officer_0.6.6
[49] ggtext_0.1.2 hms_1.1.3 askpass_1.2.0 ragg_1.3.2
[53] shiny_1.8.1.1 evaluate_0.23 knitr_1.45 rlang_1.1.3
[57] gridtext_0.1.5 Rcpp_1.0.12 xtable_1.8-4 glue_1.7.0
[61] httpcode_0.3.0 xml2_1.3.6 rstudioapi_0.16.0 jsonlite_1.8.8
[65] R6_2.5.1 systemfonts_1.1.0 fs_1.6.4
Hey @dgkeyes Sorry for slow response. We are in peak reporting and I was out of office for a few days on top of that.
I just did a bunch of updating hoping it would resolve the issue but I'm still getting it on my end.
Here's my session info:
sessionInfo() R version 4.4.0 (2024-04-24 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Denver tzcode source: internal
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flextable_0.9.6 omni_1.0.2023 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.0.2
[8] readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] gtable_0.3.5 xfun_0.44 ggrepel_0.9.5 tzdb_0.4.0
[5] vctrs_0.6.5 tools_4.4.0 generics_0.1.3 curl_5.2.1
[9] fansi_1.0.6 pkgconfig_2.0.3 data.table_1.15.4 gt_0.10.1
[13] uuid_1.2-0 lifecycle_1.0.4 farver_2.1.2 compiler_4.4.0
[17] textshaping_0.4.0 munsell_0.5.1 httpuv_1.6.15 fontquiver_0.2.1
[21] fontLiberation_0.1.0 sass_0.4.9 htmltools_0.5.8.1 yaml_2.3.8
[25] pillar_1.9.0 later_1.3.2 crayon_1.5.2 gfonts_0.2.0
[29] openssl_2.2.0 mime_0.12 fontBitstreamVera_0.1.1 tidyselect_1.2.1
[33] zip_2.3.1 digest_0.6.35 stringi_1.8.4 labeling_0.4.3
[37] fastmap_1.2.0 grid_4.4.0 colorspace_2.1-0 cli_3.6.2
[41] magrittr_2.0.3 crul_1.4.2 utf8_1.2.4 withr_3.0.0
[45] gdtools_0.3.7 scales_1.3.0 promises_1.3.0 timechange_0.3.0
[49] rmarkdown_2.27 officer_0.6.6 ggtext_0.1.2 askpass_1.2.0
[53] ragg_1.3.2 hms_1.1.3 evaluate_0.24.0 shiny_1.8.1.1
[57] knitr_1.47 rlang_1.1.4 gridtext_0.1.5 Rcpp_1.0.12
[61] xtable_1.8-4 glue_1.7.0 httpcode_0.3.0 xml2_1.3.6
[65] rstudioapi_0.16.0 jsonlite_1.8.8 R6_2.5.1 fs_1.6.4
[69] systemfonts_1.1.0
Restarting R session...
Would you try to install the dev version of flextable
with devtools::install_github("davidgohel/flextable")
(according to https://github.com/davidgohel/flextable/issues/621 this is supposed to work, even if on my side this doesn't).
If you remove the caption this works, it's a matter of knitr
blocks that changed
Thanks @tvroylandt ,
I tried this and verified that the dev version installed.
It didn't work on my end either. We still get the
`
{=html}`
characters in both pdf and html with flextable.
@tvroylandt are you getting these too? @dgkeyes does not get them but we weren't able to identify a difference in our setups that could be behind the difference in behavior.
I have them too bur wasn't able yet to solve that
Hey @dgkeyes I just sent you a video describing an issue we have been having when knitting tables with the omni_table() function.
You can see here that it does something weird where the lower part of the code chunk, the ```, displays and it messes up the figure caption too. Any ideas?