R降价演示不显示图 [英] R markdown presentation not displaying plots
问题描述
我在 Windows 上有 Rstudio(下面的sessionInfo())并且我正在尝试使用 Markdown 构建一个 r 演示文稿.当我尝试编写 HTML 或 PDF 时，它似乎没有保留应从中生成绘图的文件夹，因此我的演示文稿缺少绘图.我已经确认它确实适用于基本的 html_document.
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.
有人对如何解决有任何想法吗?
MWE(rstudio 默认带有幻灯片标题)
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.
这是使用 knit html 命令生成的，但是将 html_document 更改为 ioslides_presentation 并且它不会拾取绘图
会话信息
> 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
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
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()
推荐答案
我发现 RStudio-0.98.983 和 R-3.1.1-win 存在同样的问题.卸载并重新安装并没有解决我的问题.我已经尝试过 RStudio-0.98.994，但它也不起作用......
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...
更新:已报告此问题(请参阅下面评论中的链接)，并且 RStudio 团队找到了解决方案.看来这是 ioslides 中使用的 Windows 上的 Lua base64 编码器的问题.解决方案是安装软件包 httpuv 或 catools.重新启动 RStudio 后，问题应该得到解决(至少对我来说是这样！).
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!).
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