R markdown presentation not displaying plots

Question

I have Rstudio on Windows (sessionInfo() below) and am trying to build an r presentation using markdown. When I try to knit HTML or PDF it does not seem to be retaining the folder where plots should be generated from and as a result my presentations are missing plots. I have confirmed that it does work with a basic html_document though.

Does anyone have any ideas on how to resolve?

MWE (rstudio default with headers for slides)

---
title: "plottest2"
author: "AN Other"
date: "Monday, June 30, 2014"
output: html_document
---
## Area 1 ##
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r}
summary(cars)
```

## Area 2 ##
You can also embed plots, for example:

```{r, echo=FALSE}
plot(cars)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

This generates using the knit html command, but change html_document to ioslides_presentation and it won't pick up the plot

SessionInfo

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] lattice_0.20-29 ggplot2_1.0.0  

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4 digest_0.6.4     evaluate_0.5.5   formatR_0.10     grid_3.1.0       gtable_0.1.2     htmltools_0.2.4  knitr_1.6        labeling_0.2     MASS_7.3-31     
[11] munsell_0.4.2    plyr_1.8.1       proto_0.3-10     Rcpp_0.11.2      reshape2_1.4     rmarkdown_0.2.49 scales_0.2.4     stringr_0.6.2    tools_3.1.0      yaml_2.1.13

C:\Program Files\R\R-3.1.0\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
#
#  Copyright (C) 1995-2012 The R Core Team
### (see ?Rprofile).

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

local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
       if(identical(dp, "")) # marginally faster to do methods last
           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")))

.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)
    }
}

.OptRequireMethods <- function()
{
      if("methods" %in% getOption("defaultPackages")) {
        res <- require("methods", quietly = TRUE, warn.conflicts = FALSE,
                       character.only = TRUE)
        if(!res)
            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=""))
}
###-*- 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)
})

C:\Program Files\R\R-3.1.0\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()

Solution 1

I have found the same issue with RStudio-0.98.983 and R-3.1.1-win. Uninstalling both and reinstalling did NOT solve the issue for me. I have tried with RStudio-0.98.994 and it did not work either...

Update: This was reported (see link in the comments below) and a solution was found by the RStudio team. It seems it is an issue with the Lua base64 encoder on Windows, which is used in ioslides. The solution is to install the packages httpuv or catools. After restarting RStudio, the issue should be fixed (at least it was for me!).

Solution 2

I had a similar problem with a chart not being displayed. It turned out that the problem was that the name of the .Rpres file I was using had spaces in it. Once I replaced the spaces with underscores the plot appeared again.

Use "Example_File_Name.Rpres" not "Example File Name.Rpres".

Solution 3

I had the same problem, and a different solution worked for me. - don't save the rmarkdown with any numbers in the document name, - and also don't inlcude the .html in the document name, to the markdown file you wish to save

Using just a name without the two above should create one rmd-file and one html-file in your designated folder. The rmd-file will not include plots, the html-File however should inlcude them in its presentation.

Comments

[Steph Locke]

Hi @Alfonso, might be worth adding a new Q, mentioning this one, & adding you're own sessionInfo(). Have you uninstalled everything and removed previous R folders also before reinstalling?

[Alfonso]

Thanks for the answer. I'm not sure I uninstalled the package library before reinstalling, I might try that later. What I did is to report it as a bug in their github project and they are looking into it. If they find a cause and/or fix, I will update here!

[Alfonso]

They managed to reproduce the issue so hopefully there comes a fix soon. The link: github.com/rstudio/rmarkdown/issues/210

[Alfonso]

They found a solution: install httpuv or catools packages. Edited answer text accordingly...

[Andrie]

This didn't work for me, but the solution posted by @justinmeyer did: Remove spaces from the file name.

[David Jorquera]

Funny how this one worked for me, kill me if I have to uninstall and reinstall all of R and RStudio