rpresentation vs mathjax & preview pane

Publishing Your Results
1

I'm trying to embed math in an Rpresentation, then show it in the Rstudio PRESENTATION pane.

Code sample...

solve() for systems of equations
========================================================
author: Mark Niemann-Ross
date: 
autosize: true


Solve a system of equations
===
As an example, start with this system of equations:

$$
2x_1 - 3x_2 - 1x_3 = 2\\
1x_1 + 2x_2 + 3x_3 = 15\\
5x_1 + 1x_2 - 1x_3 = 4\\
$$

Then I click on the Preview tab. The presentation (not the viewer) pane correctly shows the title slide. Then the second slide shows the latex instead of the rendered formula. i.e.

As an example, start with this system of equations:

[ 2x_1 - 3x_2 - 1x_3 = 2\ 1x_1 + 2x_2 + 3x_3 = 15\ 5x_1 + 1x_2 - 1x_3 = 4\ ]

…when converted to a matrix…

[ \begin{pmatrix} 2 & -3 & -1\ 1 & 2 & 3\ 5 & 1 & -1\ \end{pmatrix} \begin{pmatrix} x_1\ x_2\ x_3\ \end{pmatrix} = \begin{pmatrix} 2\ 15\ 4\ \end{pmatrix} ]

If I open the intermediate .md file (created from the .Rpres file) then knit, the equations and math are rendered correctly in the VIEWER pane (but not the presentation pane)

Here is a screen shot showing the presentation pane and the viewer pane. Note the equation is rendered in the viewer - but not the presentation..

Screenshot (25)
Screenshot (25)1045×1053 50.8 KB

It is rendered correctly when I open the file in a system browser such as Chrome.

I'm using windows 10, Rstudio 1.3.959, R version 4.0.0 (2020-04-24) -- "Arbor Day"

Sys.getenv() returns (abbreviated)...
RMARKDOWN_MATHJAX_PATH C:/Program Files/RStudio/resources/mathjax-27. All files in that directory appear to be intact.

This was working as expected before I updated R & Rstudio. It continues to work on my older linux machine with Rstudio 1.1.456/R 3.6.3

I'm not sure where to start troubleshooting - can anyone help with some debugging guidance?

Thanks!
Mark Niemann-Ross

2

Here is the diagnostics report:

RStudio Diagnostics Report

WARNING: This report may contain sensitive security information and / or
personally identifiable information. Please audit the below and redact any
sensitive information before submitting your diagnostics report.

Generated: Wed Jun 03 18:47:46 2020

RStudio Version

1.3.959

Session Information

R version 4.0.0 (2020-04-24)
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
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_4.0.0 htmltools_0.4.0 tools_4.0.0 yaml_2.2.1
[5] Rcpp_1.0.4.6 rmarkdown_2.2 knitr_1.28 xfun_0.14
[9] digest_0.6.25 packrat_0.5.0 rlang_0.4.6 evaluate_0.14

System Information

sysname : Windows
release : 10 x64
version : build 18363
nodename : OOPSKAYAK
machine : x86-64
login : mnr
user : mnr
effective_user : mnr

Platform Information

OS.type : windows
file.sep : /
dynlib.ext : .dll
GUI : RStudio
endian : little
pkgType : win.binary
path.sep : ;
r_arch : x64

Environment Variables

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R_PACKRAT_SYSTEM_LIBRARY : C:/Users/mnr/DOCUME~1/R/R-40~1.0/library
R_USER : C:/Users/mnr/Documents
RMARKDOWN_MATHJAX_PATH : C:/Program Files/RStudio/resources/mathjax-27
RS_LOCAL_PEER : \.\pipe\41824-rsession
RS_RPOSTBACK_PATH : C:/Program Files/RStudio/bin/rpostback
RS_SHARED_SECRET : *** redacted ***
RSTUDIO : 1
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RTOOLS40_HOME : C:\rtools40
SESSIONNAME : Console
SystemDrive : C:
SystemRoot : C:\WINDOWS
TEMP : C:\Users\mnr\AppData\Local\Temp
TERM : xterm-256color
TMP : C:\Users\mnr\AppData\Local\Temp
USERDOMAIN : OOPSKAYAK
USERDOMAIN_ROAMINGPROFILE : OOPSKAYAK
USERNAME : *** redacted ***
USERPROFILE : C:\Users\mnr
windir : C:\WINDOWS

R Version

platform : x86_64-w64-mingw32
arch : x86_64
os : mingw32
system : x86_64, mingw32
status :
major : 4
minor : 0.0
year : 2020
month : 04
day : 24
svn rev : 78286
language : R
version.string : R version 4.0.0 (2020-04-24)
nickname : Arbor Day

R Home

C:/Users/mnr/DOCUME~1/R/R-40~1.0

R Search Path

.GlobalEnv
tools:rstudio
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package:graphics
package:grDevices
package:utils
package:datasets
package:methods
Autoloads
package:base

R Library Paths

C:/Users/mnr/Documents/R/R-4.0.0/library

Loaded Packages

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compiler : C:/Users/mnr/Documents/R/R-4.0.0/library/compiler
datasets : C:/Users/mnr/Documents/R/R-4.0.0/library/datasets
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yaml : C:/Users/mnr/Documents/R/R-4.0.0/library/yaml

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R System Profile: C:/Users/mnr/DOCUME~1/R/R-40~1.0/library/base/R/Rprofile

This is the system Rprofile file. It is always run on startup.

Additional commands can be placed in site or user Rprofile files

(see ?Rprofile).

Copyright (C) 1995-2015 The R Core Team

Notice that it is a bad idea to use this file as a template for

personal startup files, since things will be executed twice and in

the wrong environment (user profiles are run in .GlobalEnv).

.GlobalEnv <- globalenv()
attach(NULL, name = "Autoloads")
.AutoloadEnv <- as.environment(2)
assign(".Autoloaded", NULL, envir = .AutoloadEnv)
T <- TRUE
F <- FALSE
R.version <- structure(R.Version(), class = "simple.list")
version <- R.version # for S compatibility

for backwards compatibility only

R.version.string <- R.version$version.string

NOTA BENE: options() for non-base package functionality are in places like

--------- ../utils/R/zzz.R

options(keep.source = interactive())
options(warn = 0)

options(repos = c(CRAN="@CRAN@"))

options(BIOC = "http://www.bioconductor.org")

options(timeout = 60)
options(encoding = "native.enc")
options(show.error.messages = TRUE)

keep in sync with PrintDefaults() in ../../main/print.c :

options(scipen = 0)
options(max.print = 99999)# max. #{entries} in internal printMatrix()
options(add.smooth = TRUE)# currently only used in 'plot.lm'

if(isFALSE(as.logical(Sys.getenv("R_OPTIONS_STRINGS_AS_FACTORS",
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options(stringsAsFactors = FALSE)
} else {
options(stringsAsFactors = TRUE)
}

if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)

local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, "")) ## it fact methods is done first
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
else if(identical(dp, "NULL")) dp <- character(0)
else dp <- strsplit(dp, ",")[[1]]
dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\1", dp) # strip whitespace
options(defaultPackages = dp)
})

Expand R_LIBS_* environment variables.

Sys.setenv(R_LIBS_SITE =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))

local({
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_CPU")))
setSessionTimeLimit(cpu = tl)
if(nzchar(tl <- Sys.getenv("R_SESSION_TIME_LIMIT_ELAPSED")))
setSessionTimeLimit(elapsed = tl)
})

.First.sys <- function()
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
call. = FALSE, domain = NA)
}
}

called at C level in the startup process prior to .First.sys

.OptRequireMethods <- function()
{
pkg <- "methods" # done this way to avoid R CMD check warning
if(pkg %in% getOption("defaultPackages"))
if(!require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE))
warning('package "methods" in options("defaultPackages") was not found',
call. = FALSE)
}

if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
print(proc.time())
}
## avoid passing on to spawned R processes
## A system has been reported without Sys.unsetenv, so try this
try(Sys.setenv(R_BATCH=""))
}

local({
if(nzchar(rv <- Sys.getenv("R_RNG_VERSION")))
suppressWarnings(RNGversion(rv))
})
###-- R --

this will break if R is on a network share

.Library <- file.path(chartr("\", "/", R.home()), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ";"))
.Library.site <- .Library.site[file.exists(.Library.site)]

if(!nzchar(Sys.getenv("R_LIBS_USER")))
Sys.setenv(R_LIBS_USER=
file.path(Sys.getenv("R_USER"), "R",
"win-library",
paste(R.version$major,
sub("\..*$", "", R.version$minor),
sep=".")
))

invisible(.libPaths(c(unlist(strsplit(Sys.getenv("R_LIBS"), ";")),
unlist(strsplit(Sys.getenv("R_LIBS_USER"), ";"))
)))

local({
popath <- Sys.getenv("R_TRANSLATIONS", "")
if(!nzchar(popath)) {
paths <- file.path(.libPaths(), "translations", "DESCRIPTION")
popath <- dirname(paths[file.exists(paths)][1])
}
bindtextdomain("R", popath)
bindtextdomain("R-base", popath)
bindtextdomain("RGui", popath)
assign(".popath", popath, .BaseNamespaceEnv)
})

if(nzchar(Sys.getenv("R_PAPERSIZE"))) {
options(papersize = Sys.getenv("R_PAPERSIZE"))
} else {
if(grepl("(canada|united.states)", Sys.getlocale("LC_MONETARY"),
ignore.case = TRUE)) options(papersize = "letter")
else options(papersize = "a4")
}

options(pager = if(length(grep("--ess", commandArgs()))) "console" else "internal",
useFancyQuotes = (.Platform$GUI == "Rgui"),
pdfviewer = Sys.getenv("R_PDFVIEWER", file.path(R.home("bin"), "open.exe")))

if(.Platform$GUI == "Rgui")
Sys.setenv(GFORTRAN_STDOUT_UNIT = "-1", GFORTRAN_STDERR_UNIT = "-1")

local({
br <- Sys.getenv("R_BROWSER", NA_character_)
if(!is.na(br)) options(browser = br)
tests_startup <- Sys.getenv("R_TESTS")
if(nzchar(tests_startup)) source(tests_startup)
ca_cert <- Sys.getenv("CURL_CA_BUNDLE", NA_character_)
if(!is.na(ca_cert) &&
file.exists(ca_path <- file.path(R.home("etc"), "curl-ca-bundle.crt")))
Sys.setenv(CURL_CA_BUNDLE = ca_path)
})

R Site Profile: C:/Users/mnr/DOCUME~1/R/R-40~1.0/etc/Rprofile.site

Things you might want to change

options(papersize="a4")

options(editor="notepad")

options(pager="internal")

set the default help type

options(help_type="text")

options(help_type="html")

set a site library

.Library.site <- file.path(chartr("\", "/", R.home()), "site-library")

set a CRAN mirror

local({r <- getOption("repos")

r["CRAN"] <- "http://my.local.cran"

options(repos=r)})

Give a fortune cookie, but only to interactive sessions

(This would need the fortunes package to be installed.)

if (interactive())

fortunes::fortune()

R User Profile: C:/Users/mnr/Documents/.Rprofile

(File does not exist)

R Site Environ: C:/Users/mnr/DOCUME~1/R/R-40~1.0/etc/Renviron.site

(File does not exist)

R User Environ: C:/Users/mnr/Documents/.Renviron

(File does not exist)

R Temporary Directory

C:\Users\mnr\AppData\Local\Temp\RtmpUPjWrr

Files in R Temporary Directory

rs-graphics-9ede047b-4aae-4a84-a890-07d110d49411
view2570197d2ea8.dir

Log file: C:/Users/mnr/AppData/Local/RStudio-Desktop/log/rdesktop.log

13 Apr 2020 20:32:00 [rdesktop] ERROR generic error -2147023174 (Unknown error); OCCURRED AT: class rstudio::core::Error __cdecl rstudio::desktop::OfficeViewer::getItemFromPath(const class std::basic_string<wchar_t,struct std::char_traits<wchar_t>,class std::allocator<wchar_t> > &,struct IDispatch **) C:\jenkins\workspace\IDE\windows-v1.2\src\cpp\desktop\DesktopOfficeViewer.cpp:192; LOGGED FROM: void __cdecl rstudio::desktop::GwtCallback::prepareShowWordDoc(void) C:\jenkins\workspace\IDE\windows-v1.2\src\cpp\desktop\DesktopGwtCallback.cpp:648
13 Apr 2020 20:40:32 [rdesktop] ERROR generic error -2147023174 (Unknown error); OCCURRED AT: class rstudio::core::Error __cdecl rstudio::desktop::OfficeViewer::getItemFromPath(const class std::basic_string<wchar_t,struct std::char_traits<wchar_t>,class std::allocator<wchar_t> > &,struct IDispatch **) C:\jenkins\workspace\IDE\windows-v1.2\src\cpp\desktop\DesktopOfficeViewer.cpp:192; LOGGED FROM: void __cdecl rstudio::desktop::GwtCallback::prepareShowWordDoc(void) C:\jenkins\workspace\IDE\windows-v1.2\src\cpp\desktop\DesktopGwtCallback.cpp:648
27 Apr 2020 17:46:22 [rdesktop] ERROR generic error -2147023174 (Unknown error); OCCURRED AT: class rstudio::core::Error __cdecl rstudio::desktop::OfficeViewer::getItemFromPath(const class std::basic_string<wchar_t,struct std::char_traits<wchar_t>,class std::allocator<wchar_t> > &,struct IDispatch **) C:\jenkins\workspace\IDE\windows-v1.2\src\cpp\desktop\DesktopOfficeViewer.cpp:192; LOGGED FROM: void __cdecl rstudio::desktop::GwtCallback::prepareShowPptPresentation(void) C:\jenkins\workspace\IDE\windows-v1.2\src\cpp\desktop\DesktopGwtCallback.cpp:659

Log file: C:/Users/mnr/AppData/Local/RStudio-Desktop/log/rsession-mnr.log

04 Jun 2020 01:47:47 [rstudio-diagnostics] ERROR system error 32 (The process cannot access the file because it is being used by another process) [path: C:/Users/mnr/AppData/Local/RStudio-Desktop/log/rsession-mnr.log]; OCCURRED AT auto __cdecl rstudio::core::FilePath::openForRead::<lambda_08754985928f41bffddcf4ccb546a6bb>::operator ()(void) const src/cpp/shared_core/FilePath.cpp:1134; LOGGED FROM: void __cdecl `anonymous-namespace'::writeFile(const class std::basic_string<char,struct std::char_traits,class std::allocator > &,const class rstudio::core::FilePath &,class std::basic_ostream<char,struct std::char_traits > &) src/cpp/diagnostics/DiagnosticsMain.cpp:63
(Empty)

User prefs: C:/Users/mnr/AppData/Roaming/RStudio/rstudio-prefs.json

{
"show_margin": false,
"font_size_points": 14,
"default_project_location": "~",
"document_author": "Mark Niemann-Ross",
"rmd_preferred_template_path": "C:/Users/mnr/Documents/R/R-4.0.0/library/learnr/rmarkdown/templates/tutorial",
"wrap_tab_navigation": false,
"reuse_sessions_for_project_links": true,
"jobs_tab_visibility": "shown"
}

System prefs: C:/ProgramData/RStudio/rstudio-prefs.json

(Not Found)

User state: C:/Users/mnr/AppData/Local/RStudio/rstudio-desktop.json

{
"context_id": "E5B0E511",
"document_outline_width": 193,
"error_handler_type": "traceback"
}

3

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