browseVignettes找不到实际存在的晕影

Question

我在github存储库上有一个包,vignettes/目录中有2个晕影.

我试着用这样的devtools包下载

> if (!require(devtools)) {
+     install.packages("devtools")
+     require(devtools)
+ }
> install_github("MarcinKosinski/RTCGA", build_vignettes=TRUE)
Downloading github repo MarcinKosinski/RTCGA@master
Installing RTCGA
"D:/R-32~1.2/bin/x64/R" --no-site-file --no-environ --no-save --no-restore CMD INSTALL  \
  "C:/Users/Marcin/AppData/Local/Temp/Rtmpg1Kbfy/devtools3cf47f1f6731/MarcinKosinski-RTCGA-0d91d7c"  \
  --library="C:/Users/Marcin/Documents/R/win-library/3.2" --install-tests 

* installing *source* package 'RTCGA' ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RTCGA)
Reloading installed RTCGA
Welcome to the RTCGA (version: 0.99.6).

但是当我尝试浏览Vignettes时,似乎它们不是构建的.

> library(RTCGA)
> browseVignettes("RTCGA")
No vignettes found by browseVignettes("RTCGA")

我已经看到人们建议使用的一些旧问题build_vignettes=TRUE,但是你看到它没有帮助OR添加移动Vignettes inst/doc/从.Rbuildignore文件中删除目录.但这一定是老问题,因为在安装软件包后我没有在二进制源中看到这样的目录.

我也在类似的问题上看到了这个答案,但是当我构建源代码然后从源代码安装软件包时,它看起来有同样的问题:No vignettes found by browseVignettes("RTCGA").

有关如何使这项工作的任何想法？

编辑

根据马丁的回答,我已经将这段代码添加到了小插曲的YAML中

vignette: >
  %\VignetteIndexEntry{Integrating TCGA Data - RTCGA Tutorial}
  %\VignetteEngine{knitr::rmarkdown}

我已经编辑过2个我的小插曲的YAML

• 我已经为YAML的开头添加了代码 - 这个文件
• 以防我曾经在YAML的末尾添加新信息 - 这个文件

但是从github安装后仍然没有可用的晕影

    > devtools::install_github("MarcinKosinski/RTCGA")
    Downloading github repo MarcinKosinski/RTCGA@master
    Installing RTCGA
    '/usr/lib/R/bin/R' --vanilla CMD INSTALL  \
      '/tmp/Rtmpk34Zbr/devtools531845716f54/MarcinKosinski-RTCGA-5571117'  \
      --library='/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

    * installing *source* package ‘RTCGA’ ...
    ** R
    ** tests
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
    * DONE (RTCGA)
    > library(RTCGA)
    Welcome to the RTCGA (version: 0.99.6).
    > browseVignettes("RTCGA")
    No vignettes found by browseVignettes("RTCGA")

编辑2

当然我忘了添加参数buildVignettes = TRUE但在此之后它看起来像是晕影但是在构建期间它们的编译存在一些问题:

devtools::install_github("MarcinKosinski/RTCGA", build_vignettes=TRUE)
Downloading github repo MarcinKosinski/RTCGA@master
Installing RTCGA
'/usr/lib/R/bin/R' --vanilla CMD build  \
  '/tmp/RtmpA7il1Q/devtools5fc871b48f57/MarcinKosinski-RTCGA-e47bdf6'  \
  --no-resave-data --no-manual 

* checking for file ‘/tmp/RtmpA7il1Q/devtools5fc871b48f57/MarcinKosinski-RTCGA-e47bdf6/DESCRIPTION’ ... OK
* preparing ‘RTCGA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory ‘RTCGA/ghPage’
Removed empty directory ‘RTCGA/inst’
* building ‘RTCGA_0.99.6.tar.gz’

'/usr/lib/R/bin/R' --vanilla CMD INSTALL  \
  '/tmp/RtmpA7il1Q/RTCGA_0.99.6.tar.gz'  \
  --library='/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2'  \
  --install-tests 

* installing *source* package ‘RTCGA’ ...
** R
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
Warning in file(con, "w") :
  cannot open file '/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2/RTCGA/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing ‘/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2/RTCGA’
* restoring previous ‘/home/mkosinski/R/x86_64-pc-linux-gnu-library/3.2/RTCGA’
Error: Command failed (1)

Answer 1

从编写R扩展,第1.4.2节,您的插图需要有一条线

%\VignetteEngine{knitr::knitr}

在他们中; 一个常见的范例是将以下内容添加到小插图顶部的yaml中

vignette: >
  %\VignetteIndexEntry{Integrating TCGA Data}
  %\VignetteEngine{knitr::rmarkdown}

VignetteIndexEntry为R的帮助系统提供了方便的标题.请记住BiocStyle包,用于创建具有一致外观的晕影.