BiocCheck 功能附加参数使用失败 [R]

Question

我正在尝试使用 BiocCheck package 中的 BiocCheck 函数检查一个包是否符合 Bioconductor 包指南。我在小插图编译方面遇到问题，所以我正要跳过检查的那一部分，我想将更多参数传递给此函数。我正在按照 BiocCheck 函数手册中的说明进行操作，其中有一个句子

...
Run usage() to see the available options. When running BiocCheck interactively, options can be passed like so: BiocCheck(package, `no-check-vignettes`=TRUE)

但我失败了，出现这样的错误：

有人知道如何解决这个问题吗？

> usage()
Usage: R CMD BiocCheck [options] package


Options:
    --no-check-vignettes
        disable vignette checks

    --new-package
        enable checks specific to new packages

    --no-check-bioc-views
        disable biocViews-specific checks (for non-BioC packages)

    -h, --help
        Show this help message and exit


When running interactively, options can be passed like so:
BiocCheck(package, `no-check-vignettes`=TRUE)
> BiocCheck(package = getwd(), `no-check-vignettes`=TRUE)
* This is BiocCheck, version 1.4.0.
* BiocCheck is a work in progress. Output and severity of issues
  may change.
* Installing package...
    * CONSIDER: Clarifying how objects ‘., ., ., .’ (used in
      availableDates, read.mutations, read.rnaseq,
      whichDateToUse) were initialized. Maybe they are part of a
      data set loaded with data(), or perhaps part of an object
      referenced in with() or within().
Error in dots[["no-check-vignettes"]] : subscript out of bounds
> BiocCheck(package = getwd(), "no-check-vignettes"=TRUE)
* This is BiocCheck, version 1.4.0.
* BiocCheck is a work in progress. Output and severity of issues
  may change.
* Installing package...
    * CONSIDER: Clarifying how objects ‘., ., ., .’ (used in
      availableDates, read.mutations, read.rnaseq,
      whichDateToUse) were initialized. Maybe they are part of a
      data set loaded with data(), or perhaps part of an object
      referenced in with() or within().
Error in dots[["no-check-vignettes"]] : subscript out of bounds

我的会话信息是：

> session_info()
Session info -----------------------------------------------------------------------
 setting  value                       
 version  R version 3.2.1 (2015-06-18)
 system   x86_64, mingw32             
 ui       RStudio (0.99.441)          
 language (EN)                        
 collate  Polish_Poland.1250          
 tz       Europe/Warsaw               

Packages ---------------------------------------------------------------------------
 package        * version  date       source                                   
 assertthat       0.1      2013-12-06 CRAN (R 3.2.1)                           
 Biobase          2.28.0   2015-04-17 Bioconductor                             
 BiocCheck      * 1.4.0    2015-04-17 Bioconductor                             
 BiocGenerics     0.14.0   2015-04-17 Bioconductor                             
 BiocInstaller  * 1.18.4   2015-07-22 Bioconductor                             
 biocViews        1.36.2   2015-06-19 Bioconductor                             
 bitops           1.0-6    2013-08-17 CRAN (R 3.2.1)                           
 chron            2.3-47   2015-06-24 CRAN (R 3.2.1)                           
 codetools        0.2-14   2015-07-15 CRAN (R 3.2.1)                           
 curl             0.9.1    2015-07-04 CRAN (R 3.2.1)                           
 data.table     * 1.9.4    2014-10-02 CRAN (R 3.2.1)                           
 devtools       * 1.8.0    2015-05-09 CRAN (R 3.2.1)                           
 digest           0.6.8    2014-12-31 CRAN (R 3.2.1)                           
 getopt           1.20.0   2013-08-30 CRAN (R 3.2.1)                           
 git2r            0.10.1   2015-05-07 CRAN (R 3.2.1)                           
 graph            1.46.0   2015-04-17 Bioconductor                             
 htmltools        0.2.6    2014-09-08 CRAN (R 3.2.1)                           
 httr             1.0.0    2015-06-25 CRAN (R 3.2.1)                           
 knitr            1.10.5   2015-05-06 CRAN (R 3.2.1)                           
 knitrBootstrap   1.0.0    2015-08-05 Github (jimhester/knitrBootstrap@cdaa4a9)
 magrittr         1.5      2014-11-22 CRAN (R 3.2.1)                           
 markdown         0.7.7    2015-04-22 CRAN (R 3.2.1)                           
 memoise          0.2.1    2014-04-22 CRAN (R 3.2.1)                           
 optparse         1.3.0    2014-12-11 CRAN (R 3.2.1)                           
 plyr             1.8.3    2015-06-12 CRAN (R 3.2.1)                           
 R6               2.1.0    2015-07-04 CRAN (R 3.2.1)                           
 RBGL             1.44.0   2015-04-17 Bioconductor                             
 Rcpp             0.12.0   2015-07-25 CRAN (R 3.2.1)                           
 RCurl            1.95-4.7 2015-06-30 CRAN (R 3.2.1)                           
 reshape2         1.4.1    2014-12-06 CRAN (R 3.2.1)                           
 rmarkdown        0.7.3    2015-08-05 Github (rstudio/rmarkdown@88afb8d)       
 RTCGA          * 0.99.0   2015-08-05 Bioconductor (R 3.2.1)                   
 RUnit            0.4.28   2015-01-06 CRAN (R 3.2.1)                           
 rversions        1.0.2    2015-07-13 CRAN (R 3.2.1)                           
 rvest          * 0.2.0    2015-01-01 CRAN (R 3.2.1)                           
 stringi          0.5-5    2015-06-29 CRAN (R 3.2.1)                           
 stringr          1.0.0    2015-04-30 CRAN (R 3.2.1)                           
 XML              3.98-1.3 2015-06-30 CRAN (R 3.2.1)                           
 xml2             0.1.1    2015-06-02 CRAN (R 3.2.1)                           
 yaml             2.1.13   2014-06-12 CRAN (R 3.2.1)

Answer 1

正如@Dan 建议的那样，应该添加 VignetteBuilder: knitr 和 Suggests: knitr

BiocCheck 功能附加参数使用失败 [R]

BiocCheck function additional parameters usage fail [R]

r

package

bioconductor