Cairo pdf由于“内存不足”而无法正常工作。在R中 [英] Cairo pdf doesn't work properly due to "out of memory" in R
问题描述
我正在尝试生成一个具有一些R函数创建的图形的pdf文档，例如 plot（）或 ggplot（）。由于我使用的是Windows计算机，因此需要调用 cairo_pdf 来更改绘图的字体系列并嵌入我指定的其他字体。
I'm trying to produce a pdf document with a graphic created with some R functions, like plot() or ggplot(). Since I use a Windows machine, I need to call cairo_pdf to change the font-family of the plot and to embed another fonts I specify.
我已经成功地在Windows 10上编织了用cairo创建的图的pdf文档。但是，当我尝试在Windows 8.1上编织文档时，我总是收到以下错误消息：
I have successfully knit the pdf document with plots created with cairo on my Windows 10. However, when I try to knit the document on my Windows 8.1, I always receive the following error message:
Quitting from lines 22-23 (test.Rmd)
Error in (function (filename = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf", :
unable to start device 'cairo_pdf'
Calls: <Anonymous> ... block_exec -> chunk_device -> dev_new -> do.call -> <Anonymous>
In addition: Warning messages:
1: In strsplit(info, "\n") : input string 3 is invalid in this locale
2: In strsplit(info, "\n") : input string 3 is invalid in this locale
3: In (function (filename = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf", :
cairo error 'out of memory'
Execution halted
我想知道为什么 cairo_pdf 导致-内存问题，即使在编织文档时 RStudio R Session 并不会消耗太多内存（我检查了 RStudio R Session的内存在任务管理器中在我的系统中是稳定的）。另外，我完全不确定为什么 R 寻找 Rplots.pdf 或 Rplot％ 03d.pdf ，尽管它们都不存在于当前目录或系统中...这是特定于OS的问题吗？还是我无法设置 cairo_pdf 的路径？
I'm wondering why cairo_pdf causes out-of-memory problem, even though RStudio R Session doesn't consume much memory when I knit the document (I checked the memory RStudio R Session occupied is stable in my system by Task Manager). Also, I'm totally not sure why R looks for Rplots.pdf or Rplot%03d.pdf, though both of them do not exist in my current directory nor in my system... Is this OS-specific problem? Or do I fail to set a path of cairo_pdf?
---
output:
bookdown::pdf_book:
base_format: "function(..., number_sections)
rmarkdown::beamer_presentation(...)"
number_sections: false
keep_tex: yes
latex_engine: lualatex
theme: "AnnArbor"
colortheme: "dolphin"
fonttheme: "structurebold"
slide_level: 1
toc: false
fig_caption: TRUE
dev: cairo_pdf
citation_package: natbib
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
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 cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE, dev.args = list(family = "Garamond")}
plot(pressure, main = "A plot whose characters are Garamond")
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
会话信息
Session Information
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8.1 x64 (build 9600)
Matrix products: default
locale:
[1] LC_COLLATE=Japanese_Japan.932 LC_CTYPE=Japanese_Japan.932 LC_MONETARY=Japanese_Japan.932
[4] LC_NUMERIC=C LC_TIME=Japanese_Japan.932
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] jpndistrict_0.3.2 numDeriv_2016.8-1 optimx_2018-7.10 lemon_0.4.3
[5] DiagrammeR_1.0.0 ggsci_2.9 kableExtra_1.0.1 pbkrtest_0.4-7
[9] effects_4.1-0 car_3.0-2 carData_3.0-2 languageR_1.5.0
[13] coefplot_1.2.6 ggrepel_0.8.0 lmerTest_3.1-0 lme4_1.1-20
[17] Matrix_1.2-15 data.table_1.12.0 reshape_0.8.8 formattable_0.2.0.1
[21] knitr_1.21 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.0.1
[25] readr_1.3.1 tidyr_0.8.2 tibble_2.0.1 tidyverse_1.2.1
[29] ggspatial_1.0.3 purrr_0.3.0 sf_0.7-2 xtable_1.8-3
[33] jpmesh_1.1.1 gdata_2.18.0 ggjoy_0.4.1 ggridges_0.5.1
[37] gridExtra_2.3 ggplot2_3.1.0 magrittr_1.5 nnet_7.3-12
[41] MASS_7.3-51.1 lattice_0.20-38 needs_0.0.3
loaded via a namespace (and not attached):
[1] useful_1.2.6 minqa_1.2.4 colorspace_1.4-0 class_7.3-14
[5] rio_0.5.16 leaflet_2.0.2 rstudioapi_0.9.0 lubridate_1.7.4
[9] xml2_1.2.0 splines_3.5.2 jsonlite_1.6 nloptr_1.2.1
[13] broom_0.5.1 shiny_1.2.0 compiler_3.5.2 httr_1.4.0
[17] backports_1.1.3 assertthat_0.2.0 lazyeval_0.2.1 survey_3.35-1
[21] cli_1.0.1 later_0.8.0 visNetwork_2.0.5 htmltools_0.3.6
[25] tools_3.5.2 igraph_1.2.4 gtable_0.2.0 glue_1.3.0
[29] reshape2_1.4.3 Rcpp_1.0.0 rgexf_0.15.3 cellranger_1.1.0
[33] nlme_3.1-137 crosstalk_1.0.0 xfun_0.5 openxlsx_4.1.0
[37] rvest_0.3.2 mime_0.6 miniUI_0.1.1.1 gtools_3.8.1
[41] XML_3.98-1.17 scales_1.0.0 hms_0.4.2 promises_1.0.1
[45] parallel_3.5.2 RColorBrewer_1.1-2 yaml_2.2.0 curl_3.3
[49] downloader_0.4 stringi_1.3.1 Rook_1.1-1 e1071_1.7-0.1
[53] zip_1.0.0 rlang_0.3.1 pkgconfig_2.0.2 evaluate_0.13
[57] htmlwidgets_1.3 tidyselect_0.2.5 plyr_1.8.4 bookdown_0.9
[61] R6_2.4.0 generics_0.0.2 DBI_1.0.0 pillar_1.3.1
[65] haven_2.1.0 foreign_0.8-71 withr_2.1.2 units_0.6-2
[69] survival_2.43-3 abind_1.4-5 modelr_0.1.4 crayon_1.3.4
[73] rmarkdown_1.11 viridis_0.5.1 readxl_1.3.0 influenceR_0.1.0
[77] webshot_0.5.1 digest_0.6.18 classInt_0.3-1 httpuv_1.4.5.1
[81] brew_1.0-6 munsell_0.5.0 viridisLite_0.3.0
>RStudio.Version()$version
[1] ‘1.2.1280’
另外，我还安装了 Cairo 和 cairoDevice 软件包。
Also I've installed Cairo and cairoDevice package.
推荐答案
我不确定，但是通过安装最新的R（ R 3.6.0 （对于我来说），并在中添加 ... dev = cairo_pdf knitr :: opts_chunk $ set（）
I'm not sure, but somehow the problem was solved by installing the latest R (R 3.6.0 in my case) and by adding dev = "cairo_pdf" to knitr::opts_chunk$set()...
---
title: "The definitive MWE"
subtitle: "Oh, yeah"
author: "CLR"
institute: "CLR's office"
abstract: "This should work!"
output:
bookdown::pdf_document2:
number_sections: true
latex_engine: xelatex
keep_tex: true
toc: false
fig_caption: TRUE
dev: cairo_pdf #Cairo_pdf <- cairoDevice, CairoPDF <- Cairo
citation_package: natbib
documentclass: bxjsarticle #Replace this with the document class you use
classoption: pandoc,everyparhook=compat #These options are suitable for bxjsarticle
indent: true
fontsize: 10pt
geometry: "left=2cm,right=2cm,top=2cm,bottom=3cm"
always_allow_html: yes
link-citations: yes
---
```{r}
knitr::opts_chunk$set(fig.path = "somewhere/you/want/to/store/your/awesome/figs",
fig.height=6,
fig.width=8,
fig.align="center",
echo=FALSE,
message = FALSE,
warning = FALSE,
#Select the same device as the one you specified in YAML section
dev = "cairo_pdf",
#Put the name of your favorite font into ""
dev.args = list(family = "Source Han Sans JP Normal")
)
```
```{r cars}
library(ggplot2)
a=ggplot(cars, aes(x=speed, y=dist))+
geom_point()+
xlab("速度")
a
```
这篇关于Cairo pdf由于“内存不足”而无法正常工作。在R中的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！
