[R] R CMD check package "mypkg-Ex.R" failed

[Berend Hasselman]

On 01-06-2013, at 02:56, Justin <dlyzxl at yahoo.com> wrote:

> I build a test package in order to publish my own package to bioconductor.
> 
> I am using package.skeleton
> Step 1. create test package "mypkg"
>   f <- function(x,y) x+y
>   package.skeleton(list=c("f"), name="mypkg")
> 
> Step 2. build tar.gz file
> 
> {mars:/local/workspace01/zhangju/R_autopackage_Elbow}../bin/R CMD build mypkg
> * checking for file ‘mypkg/DESCRIPTION’ ... OK
> * preparing ‘mypkg’:
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building ‘mypkg_1.0.tar.gz’
> 
> Step 3. check compressed package file
> 
> {mars:/local/workspace01/zhangju/R_autopackage_Elbow}../bin/R CMD check mypkg_1.0.tar.gz 
> * using log directory ‘/local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck’
> *
> using R version 2.14.0 (2011-10-31)
> * using platform: x86_64-unknown-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘mypkg/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘mypkg’ version ‘1.0’
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking whether package ‘mypkg’ can be installed ... ERROR
> Installation failed.
> See ‘/local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00install.out’ for details.
> 
> Step 4. check error 
> 
> {mars:/local/workspace01/zhangju/R_autopackage_Elbow}head mypkg.Rcheck/00install.out 
> * installing *source* package ‘mypkg’ ...
> ** R
> ** preparing package for lazy loading
> ** help
> Warning:
> 
> 
> /local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00_pkg_src/mypkg/man/mypkg-package.Rd:33:
> All text must be in a section
> Warning: 
> /local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00_pkg_src/mypkg/man/mypkg-package.Rd:34:
> All text must be in a section
> *** installing help indices
> Error in Rd_info(db[[i]]) : 
>   missing/empty \title field in '/local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00_pkg_src/mypkg/man/f.Rd'
> Rd files must have a non-empty \title.
> 
> Step 5. add "test package" to the title of f.Rd
> Step 6. build again
> 
> {mars:/local/workspace01/zhangju/R_autopackage_Elbow}../bin/R CMD build mypkg
> * checking for file ‘mypkg/DESCRIPTION’ ... OK
> * preparing ‘mypkg’:
> * checking DESCRIPTION meta-information ... OK
> * checking for LF line-endings in source and make files
> * checking for empty or unneeded directories
> * building ‘mypkg_1.0.tar.gz’
> 
> Step 7.
> check compressed package again
> 
> {mars:/local/workspace01/zhangju/R_autopackage_Elbow}../bin/R CMD check mypkg_1.0.tar.gz 
> * using log directory ‘/local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck’
> * using R version 2.14.0 (2011-10-31)
> * using platform: x86_64-unknown-linux-gnu (64-bit)
> * using session charset: UTF-8
> * checking for file ‘mypkg/DESCRIPTION’ ... OK
> * checking extension type ... Package
> * this is package ‘mypkg’ version ‘1.0’
> * checking package namespace information ... OK
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking if there is a namespace ... OK
> * checking for executable files ... OK
> * checking whether package ‘mypkg’ can be installed ... WARNING
> Found the following significant warnings:
>   Warning: /local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00_pkg_src/mypkg/man/mypkg-package.Rd:33: All
> text must be in a section
>   Warning: 
> /local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00_pkg_src/mypkg/man/mypkg-package.Rd:34:
> All text must be in a section
> See ‘/local/workspace01/zhangju/R_autopackage_Elbow/mypkg.Rcheck/00install.out’ for details.
> * checking installed package size ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking for sufficient/correct file permissions ... OK
> * checking DESCRIPTION meta-information ... WARNING
> Non-standard license specification:
>   What license is it under?
> Standardizable: FALSE
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for non-ASCII characters ... OK
> * checking R files for syntax errors ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated
> dependencies ... OK
> * checking whether the package can be unloaded cleanly ... OK
> * checking whether the namespace can be loaded with stated dependencies ... OK
> * checking whether the namespace can be unloaded cleanly ... OK
> * checking for unstated dependencies in R code ... OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... WARNING
> prepare_Rd: f.Rd:7-9: Dropping empty section \description
> prepare_Rd: f.Rd:22-24: Dropping empty section \details
> prepare_Rd: f.Rd:25-31: Dropping empty section \value
> prepare_Rd: f.Rd:38-40: Dropping empty section \note
> prepare_Rd: f.Rd:35-37: Dropping empty section \author
> prepare_Rd: f.Rd:32-34: Dropping empty section \references
> prepare_Rd: f.Rd:44-46: Dropping empty section \seealso
> checkRd: (5) f.Rd:0-60: Must have a
> \description
> prepare_Rd: mypkg-package.Rd:33: All text must be in a section
> prepare_Rd: mypkg-package.Rd:34: All text must be in a section
> * checking Rd metadata ... OK
> * checking Rd cross-references ... WARNING
> Unknown package(s) ‘<pkg>’ in Rd xrefs
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * checking Rd contents ... OK
> * checking for unstated dependencies in examples ... NOTE
> Warning: parse error in file ‘mypkg-Ex.R’:
> 11: unexpected symbol
> 42: 
> 43: " ~~ simple examples
>               ^
> * checking examples ... ERROR
> Running examples in ‘mypkg-Ex.R’ failed
> The error most likely occurred in:
> 
>> ### Name: mypkg-package
>> ### Title: What the package does (short line) ~~ package title ~~
>> ### Aliases:
> mypkg-package mypkg
>> ### Keywords: package
>> 
>> ### ** Examples
>> 
>> ~~ simple examples of the most important functions ~~
> Error: unexpected symbol in "~~ simple examples"
> Execution halted
> 
> 
> My question: How to correct the above error?
> 

How about making a working example replacing " ~~ simple examples"?
Have you tried entering the text " ~~ simple examples" (without the quotes) in R and looked at the error message you get?

Berend