Rstudio的knit按钮无法对包含rJava包的rmarkdown(Rmd)文件进行编织。但是,如果我使用rmarkdown :: render()
,同样的Rmd文件可以轻松地呈现为html。
我可以通过以下代码重现错误:
test.Rmd的内容:
---
title: "test"
output: html_document
---
```{r}
library(rJava)
```
点击Knit按钮将返回以下内容:
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
使用 rmarkdown::render("test.Rmd")
没问题。同时,在 RStudio 中正常运行 library(rJava)
也没有问题。
使用的软件版本为:RStudio 1.0.136,knitr 1.15.1,rmarkdown 1.3,rJava 0.9-8,R 3.3.2,macOS Sierra 10.12。
更新:根据 @r2evans 的要求添加了 Sys.getenv()
的输出结果。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
在使用
rmarkdown::render()
后生成的文件中:## __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 根据@r2evans的评论
在.Rmd
中包含来自render()
的DYLD_FALLBACK_LIBRARY_PATH
如预期地更改了Sys.getenv()
的结果,但是使用knit按钮时出现错误(与上述相同的错误消息),而在render()
中没有错误。新的.Rmd
内容如下:
---
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,在此 test2.Rmd
文件中使用 render()
,并包括 Sys.getenv()
,现在输出了两个新变量,这些变量之前不存在,并且使用 knit 按钮也不存在:
## DYLD_LIBRARY_PATH /Library/Java/JavaVirtualMachines/jdk1.8.0_101.jdk/Contents/Home/jre/lib/server
## LD_LIBRARY_PATH :@JAVA_LD@
我不知道这是否有意义,但我尝试了一个新的.Rmd
文件(如下),仍然出现相同的错误。
---
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)
```
render
和knit
中运行Sys.getenv()
可能会很有启发性。寻找差异,特别是在PATH
和任何LIB
相关变量中。 - r2evanslibjvm.dylib
的位置吗?我建议在额外的DYLD_FALLBACK_LIBRARY_PATH
路径中寻找(从第二个列表开始)。如果你在那里找到了它,请尝试使用附加路径更新该变量(很可能在.Rmd
文件中)。 - r2evans/Library/Frameworks/R.framework/Resources/lib
)中的DYLD_FALLBACK_LIBRARY_PATH
中没有libjvm.dylib
文件,但是在render()
的路径之一中有(/usr/local/lib
)。我应该将此文件(它是别名)复制到/Library/Frameworks/R.framework/Resources/lib
中吗?还是在.Rmd
文件中写点什么?这个问题是否与这些软件包有关,还是我的机器配置错误?我尝试在加载rJava
之前添加Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH="/usr/local/lib")
,但在编织时出现错误。 - JG11235.Rmd
中分配完整的路径集(而不仅仅是一个)就足够了。您可以尝试使用完整值的DYLD_...
,并更新您的问题,其中包含仍然触发相同错误的示例Rmarkdown。 - r2evans