Local images in DT call not being written to _site directory - r

Question
How can I get each local image that is only referenced in a DT call to render to the _site directory so that it shows up in the site? Any suggestions or guidance would be much appreciated.
I reviewed this and this SO question.
Context
I am working in a Quarto website, but I get similar results from R Markdown.
I have a large number of image files in a series of sub-directories. These files correspond to records in a data frame (location, material, etc). Using the DT library, I would like to display the table and include the image files.
Problem
After rendering the website, local images only referenced within the DT call are not written out to the _site directory. However, if I reference an image using html that I pull directly from a data frame cell (i.e. df$imagefile[1]), the image is written to the _site directory and thus shows both in the html and the DT.
Without html chunk.
With html chunk.
Repro
Create a new Quarto website and add the code below to the index.qmd file.
First render the document without the final html chunk and no images will show.
Delete the _site directory and restart R.
Re-render the document including the html chunk and the first table image will show along with another copy below the table.
Note, sometimes once an image is knit is seems to remain in memory even if deleted. I've found it useful to both delete _site and restart R.
#| echo: false
knitr::opts_chunk$set(
echo = FALSE,
message = FALSE
)
#| label: libraries
library(dplyr)
library(DT)
#| label: create-dirs
main_dir <- here::here()
sub_dir <- "data"
sub_dir2 <- "data/Images"
# Check first dir
if (file.exists(sub_dir)){
} else {
dir.create(file.path(main_dir, sub_dir))
}
# Check second dir
if (file.exists(sub_dir2)){
} else {
dir.create(file.path(main_dir, sub_dir2))
}
#| label: make-images
jpeg(filename = "data/Images/2347.jpg")
plot(rnorm(25))
jpeg(filename = "data/Images/2348.jpg")
plot(rnorm(25))
jpeg(filename = "data/Images/2349.jpg")
plot(rnorm(25))
dev.off()
#| label: generate-list-make-df
image_list <- list.files("data/Images", full.names = TRUE)
df <- data.frame(imagefile = image_list)
df <- df |>
mutate(imagefile = paste0("<a href='",
imagefile,
"' target = 'blank'>",
"<img src='",
imagefile,
"' width = '125'></a></img>"))
datatable(df, escape = FALSE)
Final html chunk
Render first without and then again with the following chunk.
<a href='/data/Images/2347.jpg' target = 'blank'><img src='/data/Images/2347.jpg' width = '125'></a></img>
Session Info
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
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
attached base packages:
1 stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
1 compiler_4.2.1 here_1.0.1 fastmap_1.1.0 cli_3.4.1 rprojroot_2.0.3 htmltools_0.5.2 tools_4.2.1
[8] yaml_2.3.6 rmarkdown_2.17 knitr_1.40 xfun_0.33 digest_0.6.30 rlang_1.0.6 renv_0.15.5
[15] evaluate_0.16

Related

knitr cannot find pdflatex when creating pdf from shiny app

I am trying to create a shiny App that offers users a choice of canned reports from a database that renders reactively, and then offers users the option to download a pdf of their desired report. I am running into trouble getting knitr to discover pdflatex to make the pdf. I originally tried using MikTex, but on advice of other posts removed MikTex and instead used tinytex. I followed the guidance here: https://yihui.org/tinytex/r/#debugging. The shiny app works fine, but when I click the download button, R initially starts the process of compiling, but once I click save when the dialog button launches, R throws this error (I include the verbose output as suggested by Yuhui Xie - the tinytex package author):
processing file: Reports.Rmd
|.................. | 25%
ordinary text without R code
|.................................... | 50%
label: unnamed-chunk-1
|...................................................... | 75%
ordinary text without R code
|........................................................................| 100%
label: unnamed-chunk-2
output file: Reports.knit.md
"C:/Program Files/RStudio/bin/pandoc/pandoc" +RTS -K512m -RTS Reports.utf8.md --to latex --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc5ac42d2964ee.tex --lua-filter "C:\Users\SCMCKENZIE\Documents\R\win-library\4.0\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\SCMCKENZIE\Documents\R\win-library\4.0\rmarkdown\rmarkdown\lua\latex-div.lua" --self-contained --highlight-style tango --pdf-engine xelatex --variable graphics --variable "geometry:margin=1in"
Warning: Error in : LaTeX failed to compile C:\Users\SCMCKE~1\AppData\Local\Temp\Rtmp0a6jRk\file5ac45df413ce.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
[No stack trace available]
Here is my SessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plyr_1.8.6 rmarkdown_2.6 knitr_1.29
[4] tmap_3.3 rgeos_0.5-3 sp_1.4-1
[7] sf_0.9-7 xtable_1.8-4 readr_1.4.0
[10] shinydashboard_0.7.1 odbc_1.2.3 DBI_1.1.0
[13] shiny_1.5.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 lattice_0.20-41 png_0.1-7 class_7.3-17
[5] digest_0.6.25 mime_0.9 R6_2.4.1 evaluate_0.14
[9] e1071_1.7-3 pillar_1.4.6 rlang_0.4.7 rstudioapi_0.11
[13] raster_3.3-13 blob_1.2.1 stringr_1.4.0 htmlwidgets_1.5.1
[17] bit_1.1-15.2 tinytex_0.29 compiler_4.0.2 httpuv_1.5.4
[21] xfun_0.20 pkgconfig_2.0.3 tmaptools_3.1-1 base64enc_0.1-3
[25] htmltools_0.5.0 tidyselect_1.1.0 tibble_3.0.3 codetools_0.2-16
[29] XML_3.99-0.4 viridisLite_0.3.0 crayon_1.3.4 dplyr_1.0.0
[33] later_1.1.0.1 grid_4.0.2 jsonlite_1.7.0 lwgeom_0.2-5
[37] lifecycle_0.2.0 magrittr_1.5 units_0.6-7 KernSmooth_2.23-17
[41] stringi_1.4.6 promises_1.1.1 leafsync_0.1.0 leaflet_2.0.4.1
[45] ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2 RColorBrewer_1.1-2
[49] tools_4.0.2 dichromat_2.0-0 bit64_0.9-7 leafem_0.1.3
[53] glue_1.4.1 purrr_0.3.4 hms_0.5.3 crosstalk_1.1.0.1
[57] abind_1.4-5 parallel_4.0.2 fastmap_1.0.1 yaml_2.2.1
[61] stars_0.5-1 classInt_0.4-3
I have ensured that I have selected my Global Options in RStudio to use knitr and pdflatex. Sys.which('pdflatex') gives me:
pdflatex
"C:\\Users\\SCMCKE~1\\AppData\\Roaming\\TinyTeX\\bin\\win32\\pdflatex.exe"
And tinytex::tlmgr_conf() gives me:
tlmgr conf
=========================== version information ==========================
tlmgr revision 57424 (2021-01-15 03:30:58 +0100)
tlmgr using installation: C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX
TeX Live (https://tug.org/texlive) version 2020
==================== executables found by searching PATH =================
PATH: C:\Users\SCMCKE~1\AppData\Roaming\TinyTeX\tlpkg\tlperl\bin;C:\Users\SCMCKE~1\AppData\Roaming\TinyTeX\bin\win32;C:\rtools40\usr\bin;C:\Program Files\R\R-4.0.3\bin\x64;C:\Program Files\Common Files\Oracle\Java\javapath;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Program Files\Microsoft MPI\Bin\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Windows\System32\OpenSSH\;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files (x86)\Microsoft SQL Server\150\DTS\Binn\;C:\Program Files (x86)\Microsoft SQL Server\150\Tools\Binn\;C:\Program Files\Microsoft SQL Server\150\Tools\Binn\;C:\Program Files\Microsoft SQL Server\150\DTS\Binn\;C:\Program Files\Microsoft SQL Server\Client SDK\ODBC\170\Tools\Binn\;C:\Program Files\Microsoft SQL Server\130\Tools\Binn\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Users\SCMCKENZIE\AppData\Roaming\TinyTeX\bin\win32;C:\Users\SCMCKENZIE\AppData\Local\Microsoft\WindowsApps;C:\Users\SCMCKENZIE\AppData\Local\Programs\MiKTeX\miktex\bin\x64
dvipdfmx: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/dvipdfmx.EXE
dvips: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/dvips.EXE
fmtutil: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/fmtutil.EXE
kpsewhich: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/kpsewhich.EXE
luatex: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/luatex.EXE
mktexpk: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/mktexpk.EXE
pdftex: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/pdftex.EXE
tex: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/tex.EXE
tlmgr: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/tlmgr.BAT
updmap: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/updmap.EXE
xetex: C:/Users/SCMCKE~1/AppData/Roaming/TinyTeX/bin/win32/xetex.EXE
=========================== active config files ==========================
config.ps: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist/dvips/config/config.ps
fmtutil.cnf: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist/web2c/fmtutil.cnf
mktex.cnf: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist/web2c/mktex.cnf
pdftexconfig.tex: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist/tex/generic/tex-ini-files/pdftexconfig.tex
texmf.cnf: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf.cnf
texmf.cnf: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist/web2c/texmf.cnf
updmap.cfg: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist/web2c/updmap.cfg
============================= font map files =============================
kanjix.map: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var/fonts/map/dvipdfmx/updmap/kanjix.map
pdftex.map: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var/fonts/map/pdftex/updmap/pdftex.map
ps2pk.map: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var/fonts/map/dvips/updmap/ps2pk.map
psfonts.map: c:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var/fonts/map/dvips/updmap/psfonts.map
=========================== kpathsea variables ===========================
ENCFONTS=.;{C:/PROGRA~1/R/R-40~1.2/share/texmf,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}/fonts/enc//
SYSTEXMF=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var;C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local;C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist
TEXCONFIG={C:/PROGRA~1/R/R-40~1.2/share/texmf,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}/dvips//
TEXFONTMAPS=.;{C:/PROGRA~1/R/R-40~1.2/share/texmf,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}/fonts/map/{kpsewhich,pdftex,dvips,}//
TEXMF={C:/PROGRA~1/R/R-40~1.2/share/texmf,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}
TEXMFCONFIG=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config
TEXMFDBS={!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}
TEXMFDIST=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist
TEXMFHOME=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local
TEXMFLOCAL=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local
TEXMFMAIN=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist
TEXMFSYSCONFIG=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config
TEXMFSYSVAR=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var
TEXMFVAR=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var
TEXPSHEADERS=.;{C:/PROGRA~1/R/R-40~1.2/share/texmf,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}/{dvips,fonts/{enc,type1,type42,type3}}//
VARTEXFONTS=C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var/fonts
WEB2C={C:/PROGRA~1/R/R-40~1.2/share/texmf,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-local,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-config,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-var,!!C:/Users/SCMCKENZIE/AppData/Roaming/TinyTeX/texmf-dist}/web2c
==== kpathsea variables from environment only (ok if no output here) ====
In case it is a matter of my coding, below is a reproducible R script:
##Loading Necessary Packages
library(shiny)
library(shinydashboard)
library(rmarkdown)
library(knitr)
library(plyr)
##Getting data for reproducibility
data("iris")
data("airquality")
names(airquality)[5]<-"Species"#To allow for using the same plyr code in server function on both data sets
####Creating Shiny App####
##User Interface
ui<-dashboardPage(
dashboardHeader(title="FAKE SHINY APPLICATION"),
dashboardSidebar(
sidebarMenu(tabName="REPORTS",
menuItem("OPTIONS", tabName = "SOME MENU OPTIONS",
radioButtons(inputId = "REPORT", label = "Select Something", choices = c("Iris", "AQ")),
downloadButton(outputId = "DWNLD", "Download Report")
)
)
),
dashboardBody(
tableOutput(outputId = "TABLE"),
plotOutput(outputId = "PLOT")
)
)
##Server Function##
server<-function(input, output){
##Reactive Plot##
output$PLOT<-renderPlot({
RPT<-list(Iris = iris, AQ = airquality)
DF<-RPT[[input$REPORT]]
pairs(DF[,c(1:4)])})
##Reactive Table##
output$TABLE<-renderTable({
RPT<-list(Iris = iris, AQ = airquality)
DF<-RPT[[input$REPORT]]
rpt_tbl<-ddply(DF, "Species", colwise(mean))
xtable(rpt_tbl)
})
##Download As PDF##
output$DWNLD<-downloadHandler(
filename=paste(input$REPORT, "pdf", sep="."),
content<-function(file){
RPT<-list(iris, airquality)
names(RPT)<-c("Iris", "AQ")
tmp<-file.path(tempdir(), "Reports.Rmd")
file.copy(paste(getwd(),"Reports.Rmd", sep="/"), tmp, overwrite=TRUE)
params<-list(DF
rmarkdown::render(tmp, output_file = file,
params = params,
envir = new.env(parent = globalenv()
))#End render
}
)
}
##Launch Shiny App##
shinyApp(ui=ui, server = server)
And here is the script for the Rmarkdown document saved as Reports.Rmd:
---
title: "FAKE REPORT"
output: pdf_document
params:
DF: NA
---
Fake Report Output
```{R}
rpt_tbl<-ddply(params$DF, "Species", colwise(mean))
xtable(rpt_tbl)
```
More Fake Output
```{R}
pairs(params$DF[,c(1:4)])
```
I have scoured Stack Overflow and RStudio answers, but haven't found any that seem to be my problem. Part of me is wondering if this is a platform issue. Any help would be much appreciated. Thanks so much.
Take Care,
-Sean
After much searching and testing, I found out that the problem was not with tinytex or pdflatex, but rather my call to rmarkdown::render() That led me to this answer on GitHub https://github.com/rstudio/shiny/issues/1831. Apparently, when rmarkdown::render() is called within downloadHandler(), you should NOT specify the output_file argument in render() Instead you need to rename the file AFTER rendering.
Here is the correct code (simply replace the call to downloadHandler() in the script from my original question.
output$DWNLD<-downloadHandler(
filename=paste0(input$REPORT, ".pdf"),
content<-function(file){
RPT<-list(iris, airquality)
names(RPT)<-c("Iris", "AQ")
tmp <- file.path(tempdir(), "Reports.Rmd", fsep="\\")
file.copy("F:/Apps/DNR_TRIS/Shiny_report_scripts/SQL_SCRIPTS/Reports.Rmd", tmp, overwrite = TRUE)
out<-RPT[[input$REPORT]]
params<-list(out)
names(params)<-"DF"
out<-rmarkdown::render(tmp,
params = params,
envir = new.env(parent = globalenv()
))#End render
file.rename(out, file)
}
)

defining operator doesn't work anymore (Error in UseMethod("%op%"): no applicable method for '%op%' applied to an object of class "character")

In my toy package, I have defined %+% operator as an alias to paste0(). Trying to reduce interference with other packages, I realized it the following way:
`%+%` <- function(...) UseMethod("%+%")
`%+%.character` <- paste0
`%+%.numeric` <- paste0
`%+%.default` <- function (arg1, arg2){
e <- parent.env(getEnvByName(.GlobalEnv,'package:mypackagename'));
if (exists('%+%', envir = e)) get('%+%',envir = e)(arg1,arg2);
}
i.e. I override it only for character and numeric arguments, otherwise it tries to find if the method was previously defined.
It was working just fine until recently when it started giving an error:
'a' %+% 'b'
# Error in UseMethod("%+%") :
# no applicable method for '%+%' applied to an object of class "character"
It only fails when called outside of the package. If I define a function within the package, it works correctly:
# testab2() is defined in R file as a part of the package:
testab2 <- function(inpA, inpB){
print (inpA %+% inpB)
}
# when called outside of the package:
testab2('a','b')
# ab
I am pretty sure I didn't change anything in my code, so I'm wondering if it could be caused by R update. What could have changed and how to make it work back?
P.S. getEnvByName() is my helper function that searches for an object in parent environments:
getEnvByName <- function(inpEnv=.GlobalEnv, lookFor){
e <- inpEnv;
while (environmentName(e) != 'R_EmptyEnv' & environmentName(e)!=lookFor) e <- parent.env(e);
if (environmentName(e) != lookFor) return(NULL);
return(e);
}
And the exporting was done by the following lines in the NAMESPACE file:
exportPattern("^[[:alpha:]]+")
exportPattern("%.*%")
export("%+%.default")
export("%+%.character")
P.P.S. sessionInfo:
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
system code page: 1251
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] vautils_0.1.1.105 magrittr_1.5 data.table_1.13.0
loaded via a namespace (and not attached):
[1] dplyr_1.0.2 crayon_1.3.4 grid_4.0.2 R6_2.4.1 lifecycle_0.2.0 gtable_0.3.0
[7] scales_1.1.1 ggplot2_3.3.2 pillar_1.4.6 rlang_0.4.7 rstudioapi_0.11 generics_0.0.2
[13] vctrs_0.3.4 ellipsis_0.3.1 tools_4.0.2 glue_1.4.2 purrr_0.3.4 munsell_0.5.0
[19] compiler_4.0.2 pkgconfig_2.0.3 colorspace_1.4-1 tidyselect_1.1.0 tibble_3.0.3
To export S3 methods, your NAMESPACE file needs to (in your case) contain the following declarations:
export(`%+%`)
S3method(`%+%`, default)
S3method(`%+%`, character)
S3method(`%+%`, numeric)
That is, export the %+% generic, and declare S3 methods for the methods.
Better yet, instead of manually editing the NAMESPACE file use ‘roxygen2’, which generates the correct declarations for you based on the #export documentation tag.

RStudio Server on linux: how to create a shiny app that immediately returns user input text if button OK pressed, or FALSE if button CANCEL pressed

I want my function to implement a dialog with an editable text box using a shiny app.
I.e. calling the function should open a shiny app displaying some text for the user to edit, then press the 'Ok' button to close the app and return the edited text or the 'Cancel' button to close the app and return an empty character vector.
My code runs fine on Windows (Rstudio desktop).
However on Linux (Rstudio Server Pro) the shiny page is displayed but the interface seems to be greyed, the text can be edited but the buttons are not responsive. Why?
--EDIT--
The unresponsiveness problem occurs with Internet Explorer and Microsoft Edge, not Chrome. Although the page in Chrome is greyed too, and opening Chrome's 'Inspect' tool shows 2 errors:
(1) shinyapp.js:83 WebSocket connection to 'wss://XXXXXXXXXXXXXXX/websocket/' failed: Error during WebSocket handshake: net::ERR_CONNECTION_RESET
(2) Uncaught TypeError: Cannot read property 'readyState' of null
at ShinyApp.$sendMsg (shiny.min.js:3)
at ShinyApp.sendInput (shiny.min.js:3)
at InputBatchSender.$sendNow (shiny.min.js:3)
[where XXXXXXXXXXXXXXX stands for my Rstudio Server's URL]
library(shiny)
getMyText <- function(default = "This is my input\n- Anonymous") {
require(stringr)
ui <- fluidPage(
textAreaInput("myTextBox", "Edit text", paste(default, collapse="\n"),
width = "600px", height = "400px"),
actionButton("okBtn", "Ok"),
actionButton("cancelBtn", "Cancel")
)
server <- function(input, output) {
observe({
if(input$cancelBtn > 0){
stopApp(character(0))
}
});
observe({
if(input$okBtn > 0){
stopApp(unlist(str_split(input$myTextBox, "\n")))
}
});
}
return(runApp(list(ui = ui, server = server)))
}
args <- getMyText()
sessionInfo:
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.4 (Maipo)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] stringr_1.3.1 shiny_1.4.0.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4 digest_0.6.18 later_1.0.0 mime_0.6 R6_2.4.1 xtable_1.8-3 magrittr_1.5 rlang_0.4.5
[9] stringi_1.1.7 promises_1.1.0 tools_3.5.0 httpuv_1.5.2 yaml_2.2.0 fastmap_1.0.1 compiler_3.5.0 htmltools_0.4.0
>
The greyed out screen to me sounds like your observe block is firing before all inputs are set up. This can be remedied in two ways:
observe({
req(input$cancelBtn)
if (input$cancelBtn > 0) {
stopApp(character(0))
}
})
observeEvent(input$cancelBtn, {
if (input$cancelBtn > 0) {
stopApp(character(0))
}
}, ignoreNULL = TRUE) # which is the default, including it for clarity
FYI: win10, R-3.5.3, shiny-1.4.0
It turns out this problem was due to a server (mis)configuration.
Interestingly, I found out that setting option shiny.host to the IP address of the server (instead of the default 127.0.0.1) enabled interaction with the shiny app, e.g.:
options(shiny.host = '10.1.2.3')
The following code could be used to set this option dynamically on a Linux host, useful in case load balancing gets the user connected to one of several Rstudio servers:
if (Sys.info()["sysname"] == 'Linux') {
hostIP <- system("hostname -I | awk '{print $1}'", intern = TRUE)
options(shiny.host = hostIP)
}

RMarkdown and knitting in Armenian

Thanks in advance for the help. I am trying to parametrically knit an RMD file into PDFs and HTMLs of different languages; one of them is Armenian. Knitting the Armenian version to any kind of format always produces literal UTF entities, like <U+0553><U+0578><U+0580><U+0571><U+0561><U+057C><U+0578>.
The .tex files are rendered as follows: \textless U+0553\textgreater\textless U+0578\textgreater\textless U+0580\textgreater\textless U+0571\textgreater
I have also tried using XeLaTeX and setting the main font to DejaVu Sans (i.e. latex_engine: xelatex and mainfont: DejaVu Sans), but it still knits the Armenian characters as Unicode literals.
I edited the XeTex .tex output and put in Armenian characters, and it worked fine. If Pandoc/RMD/Knitr didn't convert the characters to literals, then everything would work pefectly fine.
Even the .knit.md file already has the Unicode literals, so the problem is high up in the knitting chain, and I am not sure why this might be.
Any help would be appreciated.
Here's my minimal document (LuaLaTeX):
---
title: "Test Doc"
author: "Document"
output:
html_fragment:
section_divs: no
pdf_document:
latex_engine: lualatex
geometry: margin = 2cm
params:
lang: yes
lang: "`r switch(params$lang, CY = 'cy-GB', EN = 'en-GB', HY = 'hy-AM')`"
knit: (function(inputFile, encoding){ files <- c("cv-cy", "cv-en", "cv-hy"); langs <- c(list(lang = "CY"), list(lang = "EN"), list(lang = "HY")); i <- 1; for(f in files){ rmarkdown::render(inputFile, output_format = c("html_fragment", "pdf_document"), encoding = encoding, params = langs[i], output_file = c(paste0(dirname(inputFile), "/", print(f)), paste0(dirname(inputFile), "/", print(f)))); i <- i +1 } })
---
```
{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
lswitch <- function(lang, ...){
switch(lang, ..., stop(""))
}
```
`r lswitch(params$lang,
CY = "# Enw",
EN = "# Name",
HY = "# Անում"
)
`
Here's the pertinent section in the .log for the LuaLaTeX build:
) (d:/texlive/texmf-dist/tex/generic/babel/babel.sty
Package: babel 2019/05/04 3.31 The Babel package
(d:/texlive/texmf-dist/tex/generic/babel/switch.def
File: switch.def 2019/05/04 3.31 Babel switching mechanism
) (d:/texlive/texmf-dist/tex/generic/babel/luababel.def
\l#dumylang=\language2
Package babel Info: Non-standard hyphenation setup on input line 114.
\l#nohyphenation=\language3
\l#german-x-2019-04-04=\language4
\l#ngerman-x-2019-04-04=\language5
\l#afrikaans=\language6
\l#ancientgreek=\language7
\l#ibycus=\language8
\l#arabic=\language9
\l#armenian=\language10
\l#basque=\language11
\l#belarusian=\language12
\l#bulgarian=\language13
\l#catalan=\language14
\l#pinyin=\language15
\l#churchslavonic=\language16
\l#coptic=\language17
\l#croatian=\language18
\l#czech=\language19
\l#danish=\language20
\l#dutch=\language21
\l#ukenglish=\language22
\l#usenglishmax=\language23
\l#esperanto=\language24
\l#estonian=\language25
\l#ethiopic=\language26
\l#farsi=\language27
\l#finnish=\language28
\l#french=\language29
\l#friulan=\language30
\l#galician=\language31
\l#georgian=\language32
\l#german=\language33
\l#ngerman=\language34
\l#swissgerman=\language35
\l#monogreek=\language36
\l#greek=\language37
\l#hungarian=\language38
\l#icelandic=\language39
\l#assamese=\language40
\l#bengali=\language41
\l#gujarati=\language42
\l#hindi=\language43
\l#kannada=\language44
\l#malayalam=\language45
\l#marathi=\language46
\l#oriya=\language47
\l#panjabi=\language48
\l#pali=\language49
\l#tamil=\language50
\l#telugu=\language51
\l#indonesian=\language52
\l#interlingua=\language53
\l#irish=\language54
\l#italian=\language55
\l#kurmanji=\language56
\l#latin=\language57
\l#classiclatin=\language58
\l#liturgicallatin=\language59
\l#latvian=\language60
\l#lithuanian=\language61
\l#mongolian=\language62
\l#mongolianlmc=\language63
\l#bokmal=\language64
\l#nynorsk=\language65
\l#occitan=\language66
\l#piedmontese=\language67
\l#polish=\language68
\l#portuguese=\language69
\l#romanian=\language70
\l#romansh=\language71
\l#russian=\language72
\l#sanskrit=\language73
\l#serbian=\language74
\l#serbianc=\language75
\l#slovak=\language76
\l#slovenian=\language77
\l#spanish=\language78
\l#swedish=\language79
\l#thai=\language80
\l#turkish=\language81
\l#turkmen=\language82
\l#ukrainian=\language83
\l#uppersorbian=\language84
\l#welsh=\language85
)
! Package babel Error: Unknown option `armenian'. Either you misspelled it
(babel) or the language definition file armenian.ldf was not fou
nd.
See the babel package documentation for explanation.
Type H <return> for immediate help.
...
l.533 \ExecuteOptions{\bbl#opt#main}
Session info:
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363), RStudio 1.2.5019
Locale:
LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
LC_TIME=English_United Kingdom.1252
Package version:
base64enc_0.1.3 digest_0.6.23 evaluate_0.14 glue_1.3.1 graphics_3.6.1 grDevices_3.6.1 highr_0.8
htmltools_0.4.0 jsonlite_1.6 knitr_1.26 magrittr_1.5 markdown_1.1 methods_3.6.1 mime_0.7
Rcpp_1.0.3 rlang_0.4.2 rmarkdown_1.18 stats_3.6.1 stringi_1.4.3 stringr_1.4.0 tinytex_0.17
tools_3.6.1 utils_3.6.1 xfun_0.11 yaml_2.2.0
Pandoc version: 2.7.2

Error in getMetricsFromLatex(TeXMetrics, verbose = verbose)

When compiling R code within a child, I get the following error.
Error in getMetricsFromLatex(TeXMetrics, verbose = verbose) :
TeX was unable to calculate metrics for the following string
or character:
m
Common reasons for failure include:
* The string contains a character which is special to LaTeX unless
escaped properly, such as % or $.
* The string makes use of LaTeX commands provided by a package and
the tikzDevice was not told to load the package.
The file worked flawlessly until I changed one tiny detail that I cannot recall. The tikzDictionary is in the directory of the first child containing R-code. I removed the tikZDictionary to no avail. The file created is empty (0 Bytes). Taking the code and compiling it in a file with the appropriate headers works fine. I tried copying the contents of the whole thesis to a new folder and recompile it there, but the same problems occur there.
> sessionInfo()
> R version 3.4.0 (2017-04-21) Platform: x86_64-apple-darwin16.5.0 (64-bit) Running under: macOS Sierra 10.12.4
>
> Matrix products: default BLAS:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK:
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
>
> locale: [1]
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages: [1] stats graphics grDevices utils
> datasets methods base
>
> other attached packages: [1] tikzDevice_0.10-1 plyr_1.8.4
> xtable_1.8-2 knitr_1.15.1
>
> loaded via a namespace (and not attached): [1] compiler_3.4.0
> magrittr_1.5 tools_3.4.0 Rcpp_0.12.10 [5]
> codetools_0.2-15 filehash_2.4-1 stringi_1.1.5 highr_0.6
> [9] grid_3.4.0 digest_0.6.12 stringr_1.2.0 evaluate_0.10
Copying all relevant files to a new directory and trying to compile it throws the same error.
1) Can one try to force the tikZdevice to recalculate the metrics?!
2) Can I get the correct metrics from elsewhere?
Thank you so much for your help.
I got it to work after a total of about 6 hours. I put all the R-Code in the main file, it compiles flawlessly. The ´main-tikzDirectory´ is in the same directory as the ´main´.
However, it is about 1000 lines of R code (we're talking about the results party of my whole thesis...), which I would rather have in a separate file.
As soon as I place anything in a child I get the same error. Also, while the error had been thrown in the ´R´ console before and no tex file is produced, when using the minimal example below the error message is written to the tex-file.
I provide a minimal example:
\documentclass[10pt,a4paper]{book}
\usepackage{geometry} % Titelseite braucht eigene Margins.
%\usepackage[ngerman]{babel} % Trennungsregeln, Datumsangabe etc. in Deutsch
\usepackage[T1]{fontenc} % europäischer Zeichensatz (Sonderzeichen, etc.)
%\usepackage[bitstream-charter]{mathdesign} % Moderne, serifenbetonte und sachliche Schriftart
\usepackage[utf8]{inputenc} % utf8 Eingabezeichensatz
\usepackage{xstring} % Testen/Vergleichen von (Sub)Strings
\usepackage{totcount} % Zähle Seitenzahlen, Abbildungen etc.
\usepackage{siunitx} % SI Einheiten
\DeclareSIUnit{\molar}{M}
%\usepackage{natbib} % Naturwissenschaftliche Zitierungen
\usepackage[sorting=none, citestyle=nature, maxnames=99, minnames=99, backend=biber]{biblatex}
\addbibresource{bibliography/bibliography.bib}
\renewcommand*{\bibfont}{\small}
\usepackage[version=3]{mhchem} % chemische Summen- und Strukturformeln
\usepackage{eurosym} % Euro-Zeichen
\usepackage{hyperref} %
\usepackage[xindy,acronym,nonumberlist,nomain]{glossaries} % Abkürzung + Abkürzungsverzeichnis
\makeglossaries %
\usepackage{multicol}
% Grafiken
\usepackage{tikz}
\usepackage{epsfig}
\usepackage{graphics}
\usepackage{graphicx}
% Tabellen
\usepackage{booktabs}
\usepackage{tabularx}
\usepackage{tabu}
\usepackage{array}
\usepackage{rotating}
\usepackage{bigdelim}
\usepackage{multirow}
\usepackage{float}
\usepackage{colortbl}
\usepackage{xcolor}
\def\TReg{\textsuperscript{\textregistered}}
\def\TCop{\textsuperscript{\textcopyright}}
\def\TTra{\textsuperscript{\texttrademark}}
%% Nummerierung
\setcounter{secnumdepth}{4}
%% Eigene Makros
\input{config/config}
\input{macros/InOderAm}
\input{macros/HideIfZero}
\input{macros/citenumCounter}
\input{macros/totalfiguresCounter}
\input{macros/totalappendixCounter}
%% Floats erst ab 80% auf eigene Seite
\renewcommand{\floatpagefraction}{.8}%
%% Dokument
\begin{document}
%% Knitr-optionen
<<setup, echo = FALSE, results= 'hide', message = FALSE>>=
library(xtable)
library(plyr)
opts_chunk$set(fig.path='figure/graphics-', cache.path='cache/graphics-', fig.align='center', dev='tikz', external=TRUE, fig.width=5, fig.height=5, fig.show='hold', cache=TRUE, global.par=FALSE)
knit_hooks$set(par=function(before, options, envir){
if (before && options$fig.show!='none') par(mar=c(4,4,.1,.1),cex=1,cex.lab=.9,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3)
}, crop=hook_pdfcrop)
#
<<results, child="content/main/results/results2.Rnw">>=
#
\end{document}
The child is located some folders below.
<<corruption>>=
plot(runif(100,0,1)^2)
#

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