I have Rstudio on Windows ( sessionInfo()below) and I'm trying to create an r-presentation using markdowns. When I try to knit HTML or PDF, it does not seem to save the folder in which the graphics should be created, and as a result, there are no graphics in my presentations. I confirmed that it really works with basic html_document.
Does anyone have any ideas on how to resolve this?
MWE (rstudio by default with titles for slides)
---
title: "plottest2"
author: "AN Other"
date: "Monday, June 30, 2014"
output: html_document
---
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)
```
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 changes the html_document to ioslides_presentation and will not display the graph
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
.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
R.version.string <- R.version$version.string
options(keep.source = interactive())
options(warn = 0)
options(timeout = 60)
options(encoding = "native.enc")
options(show.error.messages = TRUE)
options(scipen = 0)
options(max.print = 99999)
options(add.smooth = TRUE)
options(stringsAsFactors = TRUE)
if(!interactive() && is.null(getOption("showErrorCalls")))
options(showErrorCalls = TRUE)
local({dp <- Sys.getenv("R_DEFAULT_PACKAGES")
if(identical(dp, ""))
dp <- c("datasets", "utils", "grDevices", "graphics",
"stats", "methods")
else if(identical(dp, "NULL")) dp <- character(0)
else dp <- strsplit(dp, ",")[[1]]
dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp)
options(defaultPackages = dp)
})
Sys.setenv(R_LIBS_SITE =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_SITE")))
Sys.setenv(R_LIBS_USER =
.expand_R_libs_env_var(Sys.getenv("R_LIBS_USER")))
.First.sys <- function()
{
for(pkg in getOption("defaultPackages")) {
res <- require(pkg, quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning(gettextf('package %s in options("defaultPackages") was not found', sQuote(pkg)),
call.=FALSE, domain = NA)
}
}
.OptRequireMethods <- function()
{
if("methods" %in% getOption("defaultPackages")) {
res <- require("methods", quietly = TRUE, warn.conflicts = FALSE,
character.only = TRUE)
if(!res)
warning('package "methods" in options("defaultPackages") was not found', call.=FALSE)
}
}
if(nzchar(Sys.getenv("R_BATCH"))) {
.Last.sys <- function()
{
cat("> proc.time()\n")
print(proc.time())
}
try(Sys.setenv(R_BATCH=""))
}
.Library <- file.path(chartr("\\", "/", R.home()), "library")
.Library.site <- Sys.getenv("R_LIBS_SITE")
.Library.site <- if(!nchar(.Library.site)) file.path(R.home(), "site-library") else unlist(strsplit(.Library.site, ";"))
.Library.site <- .Library.site[file.exists(.Library.site)]
if(!nzchar(Sys.getenv("R_LIBS_USER")))
Sys.setenv(R_LIBS_USER=
file.path(Sys.getenv("R_USER"), "R",
"win-library",
paste(R.version$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()