Rstudio Knit 按钮无法加载 rJava

Question

Rstudio 的编织按钮无法编织包含 rJava 包的 rmarkdown (Rmd) 文件。但是，如果我使用 rmarkdown::render() ，相同的 Rmd 文件渲染成 html 没有问题。

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 Knit 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

和 rmarkdown::render("test.Rmd")工作正常。此外，运行 library(rJava)通常(不是针织)也可以正常工作(在 RStudio 中)。

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:添加 Sys.getenv() 的输出根据@r2evans 的要求。 DYLD_FALLBACK_LIBRARY_PATH 的值是有区别的，但是不知道这个有没有意义。我用 XXX 替换了一些私有(private)信息。

在由 Knit 按钮生成的 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

在由 rmarkdown::render() 生成的文件中:

## __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:/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

更新2 关注@r2evans 的评论

包括来自 render() 的 DYLD_FALLBACK_LIBRARY_PATH在 .Rmd更改 Sys.getenv() 的结果正如预期的那样，但是 knit 按钮的错误行为(与上面相同的错误消息)并且 render() 中没有错误持续存在。新 .Rmd内容是:

---
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，使用 render()在这个 test2.Rmd就在上面，包括 Sys.getenv()现在输出两个新变量，以前不存在，也没有使用 knit 按钮存在:

## DYLD_LIBRARY_PATH     /Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home/jre/lib/server
## LD_LIBRARY_PATH       :@JAVA_LD@

我不知道它是否有意义，但我尝试了一个新的 .Rmd (下)，仍然给出相同的错误

---
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)
```

Answer 1

在命令行上运行以下命令为我解决了这个问题:

sudo R CMD javareconf