Rstudio的编织按钮无法编写包含rJava包的rmarkdown(Rmd)文件。但是,如果我使用rmarkdown::render()
,相同的Rmd文件会呈现为html而不会出现问题。
我可以使用以下代码重现错误:
test.Rmd:
的内容---
title: "test"
output: html_document
---
```{r}
library(rJava)
```
单击编织按钮按钮将返回:
processing file: test.Rmd
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava/libs/rJava.so
Reason: image not found
Quitting from lines 7-8 (test.Rmd)
Error: package or namespace load failed for 'rJava'
Execution halted
rmarkdown::render("test.Rmd")
工作正常。此外,正常运行library(rJava)
(非编织)也可以正常运行(在RStudio内)。
在macOS Sierra 10.12中使用RStudio版本1.0.136,knitr 1.15.1,rmarkdown 1.3,rJava 0.9-8,R 3.3.2。
更新:根据@ r2evans的要求添加Sys.getenv()
的输出。 DYLD_FALLBACK_LIBRARY_PATH的值有所不同,但我不知道这是否重要。我用XXX替换了一些私人信息。
在Knit按钮产生的html文件中:
## __CF_USER_TEXT_ENCODING
## 0x1F5:0x0:0x52
## Apple_PubSub_Socket_Render
## /private/tmp/com.apple.launchd.HvKScioyGU/Render
## DISPLAY :0
## DYLD_FALLBACK_LIBRARY_PATH
## /Library/Frameworks/R.framework/Resources/lib
## EDITOR vi
## GIT_ASKPASS rpostback-askpass
## HOME XXX
## LANG en_CA.UTF-8
## LC_CTYPE en_CA.UTF-8
## LN_S ln -s
## LOGNAME XXX
## MAKE make
## NOT_CRAN true
## PAGER /usr/bin/less
## PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin
## PWD XXX
## R_ARCH
## R_BROWSER /usr/bin/open
## R_BZIPCMD /usr/bin/bzip2
## R_DOC_DIR /Library/Frameworks/R.framework/Resources/doc
## R_GZIPCMD /usr/bin/gzip
## R_HOME /Library/Frameworks/R.framework/Resources
## R_INCLUDE_DIR /Library/Frameworks/R.framework/Resources/include
## R_LIBS /Library/Frameworks/R.framework/Versions/3.3/Resources/library
## R_LIBS_SITE
## R_LIBS_USER ~/Library/R/3.3/library
## R_PAPERSIZE a4
## R_PAPERSIZE_USER a4
## R_PDFVIEWER /usr/bin/open
## R_PLATFORM x86_64-apple-darwin13.4.0
## R_PRINTCMD lpr
## R_QPDF /Library/Frameworks/R.framework/Resources/bin/qpdf
## R_RD4PDF times,inconsolata,hyper
## R_SESSION_TMPDIR /var/folders/15/vdvn4fvx0zn0gc93_5krp6h00000gn/T//RtmpiYlwpU
## R_SHARE_DIR /Library/Frameworks/R.framework/Resources/share
## R_SYSTEM_ABI osx,gcc,gxx,gfortran,?
## R_TEXI2DVICMD /usr/local/bin/texi2dvi
## R_UNZIPCMD /usr/bin/unzip
## R_ZIPCMD /usr/bin/zip
## RMARKDOWN_MATHJAX_PATH
## /Applications/RStudio.app/Contents/Resources/resources/mathjax-26
## RMARKDOWN_PREVIEW_DIR
## /var/folders/15/vdvn4fvx0zn0gc93_5krp6h00000gn/T//RtmpLe3D9z
## RS_RPOSTBACK_PATH /Applications/RStudio.app/Contents/MacOS/rpostback
## RS_SHARED_SECRET XXX
## RSTUDIO 1
## RSTUDIO_PANDOC /Applications/RStudio.app/Contents/MacOS/pandoc
## RSTUDIO_SESSION_PORT
## XXX
## RSTUDIO_USER_IDENTITY
## XXX
## RSTUDIO_WINUTILS bin/winutils
## SED /usr/bin/sed
## SHELL /bin/bash
## SHLVL 0
## SSH_AUTH_SOCK XXX
## TAR /usr/bin/tar
## TMPDIR /var/folders/15/vdvn4fvx0zn0gc93_5krp6h00000gn/T/
## USER XXX
## XPC_FLAGS 0x0
## XPC_SERVICE_NAME 0
在rmarkdown::render()
:
## __CF_USER_TEXT_ENCODING
## 0x1F5:0x0:0x52
## Apple_PubSub_Socket_Render
## /private/tmp/com.apple.launchd.HvKScioyGU/Render
## DISPLAY :0
## DYLD_FALLBACK_LIBRARY_PATH
## /Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Users/Jayme/lib:/usr/local/lib:/usr/lib::::::::
## EDITOR vi
## GIT_ASKPASS rpostback-askpass
## HOME XXX
## LANG en_CA.UTF-8
## LC_CTYPE en_CA.UTF-8
## LN_S ln -s
## LOGNAME XXX
## MAKE make
## PAGER /usr/bin/less
## PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin
## R_BROWSER /usr/bin/open
## R_BZIPCMD /usr/bin/bzip2
## R_DOC_DIR /Library/Frameworks/R.framework/Resources/doc
## R_GZIPCMD /usr/bin/gzip
## R_HOME /Library/Frameworks/R.framework/Resources
## R_INCLUDE_DIR /Library/Frameworks/R.framework/Resources/include
## R_LIBS_SITE
## R_LIBS_USER ~/Library/R/3.3/library
## R_PAPERSIZE a4
## R_PDFVIEWER /usr/bin/open
## R_PLATFORM x86_64-apple-darwin13.4.0
## R_PRINTCMD lpr
## R_QPDF /Library/Frameworks/R.framework/Resources/bin/qpdf
## R_RD4PDF times,inconsolata,hyper
## R_SESSION_TMPDIR /var/folders/15/vdvn4fvx0zn0gc93_5krp6h00000gn/T//RtmpLe3D9z
## R_SHARE_DIR /Library/Frameworks/R.framework/Resources/share
## R_SYSTEM_ABI osx,gcc,gxx,gfortran,?
## R_TEXI2DVICMD /usr/local/bin/texi2dvi
## R_UNZIPCMD /usr/bin/unzip
## R_ZIPCMD /usr/bin/zip
## RMARKDOWN_MATHJAX_PATH
## /Applications/RStudio.app/Contents/Resources/resources/mathjax-26
## RS_RPOSTBACK_PATH /Applications/RStudio.app/Contents/MacOS/rpostback
## RS_SHARED_SECRET XXX
## RSTUDIO 1
## RSTUDIO_PANDOC /Applications/RStudio.app/Contents/MacOS/pandoc
## RSTUDIO_SESSION_PORT
## XXX
## RSTUDIO_USER_IDENTITY
## XXX
## RSTUDIO_WINUTILS bin/winutils
## SED /usr/bin/sed
## SHELL /bin/bash
## SSH_AUTH_SOCK XXX
## TAR /usr/bin/tar
## TMPDIR /var/folders/15/vdvn4fvx0zn0gc93_5krp6h00000gn/T/
## USER XXX
## XPC_FLAGS 0x0
## XPC_SERVICE_NAME 0
Update2 以下来自@ r2evans的评论
在render()
中包含来自.Rmd
的DYLD_FALLBACK_LIBRARY_PATH按预期更改Sys.getenv()
的结果,但是使用编织按钮的错误行为(与上面相同的错误消息)并且没有错误render()
仍然存在。新的.Rmd
内容为:
---
title: "test2"
output: html_document
---
```{r}
Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH="/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Users/Jayme/lib:/usr/local/lib:/usr/lib::::::::")
library(rJava)
```
有趣的是,在上面render()
中使用test2.Rmd
,包括Sys.getenv()
现在输出两个新变量,使用编织按钮之前不存在且不存在:
## DYLD_LIBRARY_PATH /Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home/jre/lib/server
## LD_LIBRARY_PATH :@JAVA_LD@
我不知道是否有意义,但我尝试了一个新的.Rmd
(下方),仍然会出现同样的错误
---
title: "test3"
output: html_document
---
```{r}
Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH="/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Users/Jayme/lib:/usr/local/lib:/usr/lib::::::::")
Sys.setenv(DYLD_LIBRARY_PATH="/Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home/jre/lib/server")
Sys.setenv(LD_LIBRARY_PATH= ":@JAVA_LD@")
library(rJava)
```
答案 0 :(得分:8)
在命令行上运行以下内容为我解决了这个问题:
sudo R CMD javareconf
答案 1 :(得分:1)
我和你有同样的问题。在Rstudio R控制台中加载rJava没有问题,但在编织HTML文件时遇到加载失败。和你一样,我也可以使用render()命令在“knit”上加载rJava。我没有做过你所进行的大量测试,但是我最终可以通过跟踪neilfws提交给你的链接在“knit”中成功加载rJava -
然后我按照元(https://stackoverflow.com/users/5697305/yuan)的建议,使用以下命令直接在R中加载库:
dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0[YOURVERSIONHERE].jdk/Contents/Home/jre/lib/server/libjvm.dylib')
在RMarkdown文件中插入此行不会影响正常的控制台行为,但允许使用“编织”按钮进行编织。从来没有想出原因,但解决方案有效。
答案 2 :(得分:0)
你知道你正在使用哪种Java吗?我不太了解Java以了解我的经验是否有帮助,但是,当我尝试重现您的错误时,我被指向了这个网站:
https://support.apple.com/kb/DL1572?locale=en_US
我下载并安装了适用于OS X 10.11 El Capitan,OS X 10.10 Yosemite,OS X 10.9 Mavericks,OS X 10.8 Mountain Lion和OS X 10.7 Lion的旧版Java 6运行时。这样做是否可以解决您的错误?
我正在使用Sierra 10.12.3,RStudio 1.0.136,rJava_0.9-8在MacBook Pro上工作。