[R-pkg-devel] (no subject)

[Michael Dewey]

Your documentation files do not match the functions and you have some 
files R was not expecting. See inline below for more detail

On 19/11/2018 10:53, Oloyede Isiaq wrote:
>   I am developing a package in R, but I encountered the below problems,
> kindly assist.
> 
> 
> Updating relrisks documentation
> Loading relrisksWarning: The existing 'NAMESPACE' file was not
> generated by roxygen2, and will not be overwritten.-- Building
> ------------------------------------------------------------- relrisks
> --Setting env vars:
> * CFLAGS    : -Wall -pedantic -fdiagnostics-color=always
> * CXXFLAGS  : -Wall -pedantic -fdiagnostics-color=always
> * CXX11FLAGS: -Wall -pedantic
> -fdiagnostics-color=always-------------------------------------------------------------------------------------v
>   checking for file
> 'C:\Users\DrIOloyede\Documents\relrisks/DESCRIPTION' (1.6s)-
> preparing 'relrisks': (3.1s)v  checking DESCRIPTION meta-information-
> checking for LF line-endings in source and make files and shell
> scripts (845ms)-  checking for empty or unneeded directories-
> building 'relrisks_0.1.0.tar.gz'
>     -- Checking -------------------------------------------------------------
> relrisks --Setting env vars:
> * _R_CHECK_CRAN_INCOMING_REMOTE_: FALSE
> * _R_CHECK_CRAN_INCOMING_       : FALSE
> * _R_CHECK_FORCE_SUGGESTS_      : FALSE-- R CMD check
> ------------------------------------------------------------------
> using log directory 'C:/Users/DrIOloyede/Documents/relrisks.Rcheck'
> (2.3s)-  using R version 3.5.1 (2018-07-02)-  using platform:
> x86_64-w64-mingw32 (64-bit)-  using session charset: ISO8859-1-  using
> options '--no-manual --as-cran' (1.3s)v  checking for file
> 'relrisks/DESCRIPTION'-  checking extension type ... Package-  this is
> package 'relrisks' version '0.1.0'-  package encoding: UTF-8v
> checking package namespace information ...v  checking package
> dependencies (3m 54.2s)v  checking if this is a source package ...v
> checking if there is a namespacev  checking for executable files
> (982ms)v  checking for hidden files and directoriesv  checking for
> portable file names ...v  checking serialization versionsv  checking
> whether package 'relrisks' can be installed (7.8s)v  checking
> installed package size (533ms)v  checking package directoryv  checking
> DESCRIPTION meta-information (1s)N  checking top-level files ...
>     Non-standard files/directories found at top level:
>       'rrisks.Rmd' 'rrisks.html'v  checking for left-over filesv
> checking index informationv  checking package subdirectories (517ms)v
> checking R files for non-ASCII characters (482ms)v  checking R files
> for syntax errors (460ms)v  checking whether the package can be loaded
> (967ms)v  checking whether the package can be loaded with stated
> dependencies (342ms)v  checking whether the package can be unloaded
> cleanly (451ms)v  checking whether the namespace can be loaded with
> stated dependencies (455ms)v  checking whether the namespace can be
> unloaded cleanly (563ms)v  checking loading without being on the
> library search path (705ms)v  checking dependencies in R code (352ms)v
>   checking S3 generic/method consistency (1.2s)v  checking replacement
> functions (335ms)v  checking foreign function calls (469ms)v  checking
> R code for possible problems (8.9s)v  checking Rd files (582ms)v
> checking Rd metadata (370ms)v  checking Rd line widths (359ms)v
> checking Rd cross-references (2.2s)v  checking for missing
> documentation entries (674ms)v  checking for code/documentation
> mismatches (2.1s)W  checking Rd \usage sections (907ms)

So here, for example, you have not documented coefs, se and df

>     Undocumented arguments in documentation object 'rrci'
>       'coefs' 'se' 'df'

But you have documented arguments which do not exist in the function in 
the code.

>     Documented arguments not in \usage in documentation object 'rrci':
>       'coefficients'
> 
>     Undocumented arguments in documentation object 'rrcip'
>       'coefs' 'se' 'df'
>     Documented arguments not in \usage in documentation object 'rrcip':
>       'coefficients'
> 
>     Undocumented arguments in documentation object 'rrciqr'
>       'coefs' 'se' 'iqr' 'df'
>     Documented arguments not in \usage in documentation object 'rrciqr':
>       'coefficients'
> 
>     Undocumented arguments in documentation object 'rrciqrp'
>       'coefs' 'se' 'iqr' 'df'
>     Documented arguments not in \usage in documentation object 'rrciqrp':
>       'coefficients'
> 
>     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.v  checking Rd contents (2.5s)v  checking for
> unstated dependencies in examples (453ms)-  checking examples ... NONE
> (841ms)
> 
>     See
>       'C:/Users/DrIOloyede/Documents/relrisks.Rcheck/00check.log'
>     for details.
> 
>     -- R CMD check results -------------------------------------
> relrisks 0.1.0 ----
> Duration: 4m 36.5s
>> checking Rd \usage sections ... WARNING
>    Undocumented arguments in documentation object 'rrci'
>      'coefs' 'se' 'df'
>    Documented arguments not in \usage in documentation object 'rrci':
>      'coefficients'
> 
>    Undocumented arguments in documentation object 'rrcip'
>      'coefs' 'se' 'df'
>    Documented arguments not in \usage in documentation object 'rrcip':
>      'coefficients'
> 
>    Undocumented arguments in documentation object 'rrciqr'
>      'coefs' 'se' 'iqr' 'df'
>    Documented arguments not in \usage in documentation object 'rrciqr':
>      'coefficients'
> 
>    Undocumented arguments in documentation object 'rrciqrp'
>      'coefs' 'se' 'iqr' 'df'
>    Documented arguments not in \usage in documentation object 'rrciqrp':
>      'coefficients'
> 
>    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 top-level files ... NOTE
>    Non-standard files/directories found at top level:
>      'rrisks.Rmd' 'rrisks.html'

These files are in the wrong place.

> 0 errors v | 1 warning x | 1 note xError: R CMD check found
> WARNINGsExecution halted
> Exited with status 1.
> 
> #' @title Computing Relative Risks, Confidence Interval & P-Values.
> #'
> #' @param   coefs Numeric value of the coefficients of GAM and GLM.
> #' @param   se    Numeric value of the standard errors of GAM and GLM.
> #' @param   df    Numeric value of the different between the number of
> rows and columns of explanatory variables.
> #' @return The sequence of the RR,CI & P-values.
> #' @export
> ###RR & Ci
> 

-- 
Michael
http://www.dewey.myzen.co.uk/home.html