Question

在构建R包之后，当键入任何包的函数名称时，我收到此错误：

Error in gzfile(file, "rb") : cannot open the connection

Screenshot of the problem.

当R试图显示函数提示时（弹出显示函数接受哪些参数），这个错误显然会发生。奇怪的是，使用devtool的document（）函数后错误就消失了。此外，在键入＆＃34;？function_name＆＃34;后，帮助屏幕不会显示。（使用document（）后的工作原理）

即使出现此错误，该程序包也能正常运行，问题是每次构建后，或者甚至在重新初始化R后再次加载程序包时，都会返回此错误，强制用户使用document（）来清除它，这很烦人。

我尝试重新安装R，甚至在不同的系统上运行（起初我使用的是Windows机器，但是现在，使用ubuntu，问题仍然存在）。还尝试创建其他几个测试包以查看错误是否特定于此包，但始终在创建的测试项目中首次使用document（）之后，此错误开始发生。

我搜索了很多，最接近我找到一个类似问题的是以下帖子，这似乎是同样的问题，但没有得到解决：

https://community.rstudio.com/t/error-connecting-to-help-documenation/881

以下是我如何使用roxygen2编写documentatin的示例。

//'@title title...
//'
//'@description description...
//'@param params...
//'@export
// [[Rcpp::export]]
Rcpp::DataFrame test(Rcpp::DataFrame arg1, Rcpp::DataFrame arg2) {

    //code

}

有人能解决这个问题吗？

编辑：

似乎问题不会发生在一个没有使用Rcpp的项目中，所以错误可能与使用roxygen2的Rcpp文档有关。

这是github上的一个包的链接，它给了我这个错误，万一有人想安装它并测试：

https://github.com/GoldenSushi/helpeR

Answer 1

简而言之，您没有按正确的顺序执行正确的命令。

你回购本身很好（但需要工作）。

第1步：获取回购

edd@rob:~$ mkdir /tmp/goldensushi
edd@rob:~$ cd /tmp/goldensushi/
edd@rob:/tmp/goldensushi$ git clone git@github.com:GoldenSushi/helpeR.git
Cloning into 'helpeR'...
remote: Counting objects: 186, done.
remote: Compressing objects: 100% (134/134), done.
remote: Total 186 (delta 42), reused 180 (delta 39), pack-reused 0
Receiving objects: 100% (186/186), 66.03 KiB | 1.54 MiB/s, done.
Resolving deltas: 100% (42/42), done.
edd@rob:/tmp/goldensushi$

第2步：compileAttributes和roxygenize

您必须先运行compileAttributes()才能从C ++获取Roxygen标记到R，然后调用roxygenize来创建Rd个文件。我使用更小的脚本;其他人可能喜欢devtools。不要紧。您仍然必须调用正确的底层R函数。

edd@rob:/tmp/goldensushi$ cd helpeR/
edd@rob:/tmp/goldensushi/helpeR(master)$ compAttr.r    # script: compileAttributes
edd@rob:/tmp/goldensushi/helpeR(master)$ roxy.r        # script: roxygenize()
Loading required package: Rcpp
Warning: @export [RcppExports.R#10]: unknown tag
Warning: @export [RcppExports.R#18]: unknown tag
Warning: @export [RcppExports.R#32]: unknown tag
Warning: @useDynLib [_roxyTags.R#2]: unknown tag
Warning: @importFrom [_roxyTags.R#3]: unknown tag
Warning: @export [file_readers.R#8]: unknown tag
Warning: @export [tablemanip.R#6]: unknown tag
Warning message:
Version of roxygen2 last used with this package is 6.0.1.9000. \
       You only have version 6.0.1 
edd@rob:/tmp/goldensushi/helpeR(master)$

您似乎在使用roxygen方面存在一些问题。

第3步：构建包

同样，我使用了我编写的帮助脚本（并在littler中发布）。不要紧。您需要调用正确的R脚本。

edd@rob:/tmp/goldensushi/helpeR(master)$ build.r       # convenience script for R CMD build .
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘helpeR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* excluding invalid files
Subdirectory 'R' contains invalid file names:
  ‘_roxyTags.R’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘helpeR_1.0.tar.gz’

edd@rob:/tmp/goldensushi/helpeR(master)$

第4步：检查包

同样，我使用了一个助手，这次是围绕着Gabor的rcmdcheck()。您也可以致电R CMD check ...

edd@rob:/tmp/goldensushi/helpeR(master)$ rcc.r helpeR_1.0.tar.gz   # convenience script for R CMD check
────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/file107a2d75f173/helpeR.Rcheck’
─  using R version 3.4.4 (2018-03-15)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
✔  checking for file ‘helpeR/DESCRIPTION’
─  checking extension type ... Package
─  this is package ‘helpeR’ version ‘1.0’
✔  checking package namespace information
✔  checking package dependencies
W  checking if this is a source package
   Subdirectory ‘src’ contains:
     environment_calls.hpp table.hpp valid.hpp
   These are unlikely file names for src files.
✔  checking if there is a namespace
✔  checking for executable files
✔  checking for hidden files and directories
✔  checking for portable file names
✔  checking for sufficient/correct file permissions
─  checking whether package ‘helpeR’ can be installed ... [20s/17s] OK
✔  checking installed package size
✔  checking package directory
N  checking DESCRIPTION meta-information
   Malformed Title field: should not end in a period.
N  checking top-level files
   File
     LICENSE
   is not mentioned in the DESCRIPTION file.
✔  checking for left-over files
✔  checking index information
✔  checking package subdirectories
✔  checking R files for non-ASCII characters
✔  checking R files for syntax errors
✔  checking whether the package can be loaded
✔  checking whether the package can be loaded with stated dependencies
✔  checking whether the package can be unloaded cleanly
✔  checking whether the namespace can be loaded with stated dependencies
✔  checking whether the namespace can be unloaded cleanly
✔  checking loading without being on the library search path
✔  checking dependencies in R code
✔  checking S3 generic/method consistency
✔  checking replacement functions
✔  checking foreign function calls
N  checking R code for possible problems
   hread_table: no visible global function definition for ‘read.table’
   Undefined global functions or variables:
     read.table
   Consider adding
     importFrom("utils", "read.table")
   to your NAMESPACE file.
✔  checking Rd files
✔  checking Rd metadata
✔  checking Rd cross-references
✔  checking for missing documentation entries
✔  checking for code/documentation mismatches
W  checking Rd \usage sections
   Undocumented arguments in documentation object 'neural.arrange'
     ‘x’

   Functions with \usage entries need to have the appropriate \alias
   entries, and all their arguments documented.
   The \usage entries must correspond to syntactically valid R code.
   See chapter ‘Writing R documentation files’ in the ‘Writing R
   Extensions’ manual.
✔  checking Rd contents
✔  checking for unstated dependencies in examples
✔  checking line endings in C/C++/Fortran sources/headers
✔  checking compiled code
✔  checking examples
✔  checking PDF version of manual

   See
     ‘/tmp/file107a2d75f173/helpeR.Rcheck/00check.log’
   for details.



── 0 errors ✔ | 2 warnings ✖ | 3 notes ✖
edd@rob:/tmp/goldensushi/helpeR(master)$

所以简而言之：没有问题，当然没有Rcpp。你只是缺乏一些这些工具的经验，所以我建议你尝试更多地了解它们。

Postscriptum

您可以使用这些不依赖于小号的备用命令：

edd@rob:/tmp/goldensushi/helpeR(master)$ Rscript -e 'Rcpp::compileAttributes()'
edd@rob:/tmp/goldensushi/helpeR(master)$ Rscript -e 'roxygen2::roxygenize()'
Loading required package: Rcpp
Warning message:
Version of roxygen2 last used with this package is 6.0.1.9000.  You only have version 6.0.1 
edd@rob:/tmp/goldensushi/helpeR(master)$ R CMD build .
* checking for file ‘./DESCRIPTION’ ... OK
[...]
* building ‘helpeR_1.0.tar.gz’

edd@rob:/tmp/goldensushi/helpeR(master)$ R CMD check helpeR_1.0.tar.gz
* using log directory ‘/tmp/goldensushi/helpeR/helpeR.Rcheck’
* using R version 3.4.4 (2018-03-15)
[...]
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  ‘/tmp/goldensushi/helpeR/helpeR.Rcheck/00check.log’
for details.


edd@rob:/tmp/goldensushi/helpeR(master)$

使用roxygen2

1 个答案:

第1步：获取回购

第2步：compileAttributes和roxygenize

第3步：构建包

第4步：检查包

Postscriptum