Skip to content

R CMD check does not checks for superfluous documentation (PR#7231)

2 messages · Wolski, Kurt Hornik

Original
Wolski
# 
Hi!

Due to package maintenance I have removed some functions but forgot to update the coresponding Rd files. 
If R CMD check is checking for missing documentation entries why it does not check for documentation entries which tell the user about nonexisting funcitons?

In my opinion checking for documentation entries that document non-existing functions is much more important than the other way around.
To type by accident the name of an undocumented functions is not really a danger especially if it is not exported.
But to tell the user that there is a function if there are non ...

By looking on the tools::undoc function and at the check(.pl) file it seems to me that all info is available to output also 

all_doc_topics %w/o% code_objs 


Yours Eryk.
Kurt Hornik
# 
It can do all these things, but we can have topics which do not have
corresponding functions, nor even R objects.

You can use

library(tools)

classifyRdTopics <-
function(package = "base", lib.loc = NULL)
{
    ## Classify Rd topics in an installed package according to whether
    ## they correspond to an object in the code or not.

    ## Useful output via
    ##   summary(classifyRdTopics())
    
    dir <- .find.package(package, lib.loc)
    isBase <- basename(dir) == "base"
    if(!isBase) tools:::.loadPackageQuietly(package, lib.loc)
    codeEnv <-
        as.environment(paste("package", package, sep = ":"))
    contents <- .readRDS(file.path(dir, "Meta", "Rd.rds"))
    keywords <- contents[ , "Keywords"]
    ## Disregard data sets docs.
    idx <- keywords != "datasets"
    ## Also, just to make sure, disregard everything marked as internal.
    idx <- idx & is.na(sapply(keywords,
                              function(x) match("internal", x)))
    ## Should really also ignore defunct and maybe also deprecated stuff
    ## when computing on base.
    contents <- contents[idx, , drop = FALSE]
    aliases <- unlist(contents$Aliases)
    topicIsAnObject <-
        aliases %in% objects(envir = codeEnv, all.names = TRUE)
    x <- list(aliases = aliases,
              topicIsAnObject = topicIsAnObject)
    class(x) <- "classifyRdTopics"
    x
}

summary.classifyRdTopics <- function(x) {
    x <- list(table(x$topicIsAnObject),
              x$aliases[!x$topicIsAnObject])
    class(x) <- "summary.classifyRdTopics"
    x
}
print.summary.classifyRdTopics <- function(x, ...) {
    writeLines("Numbers of topics which are objects (or not):")
    print(c(x[[1]]), ...)
    writeLines(c("", "Topics which are not objects:"))
    print(x[[2]], ...)
    invisible(x)
}

and then e.g. get

R> summary(classifyRdTopics("base"))
Numbers of topics which are objects (or not):
FALSE  TRUE 
   90   980 

Topics which are not objects:
 [1] "Arithmetic"         "AsIs"               "bessel"            
 [4] "Bessel"             "Comparison"         "Control"           
 [7] "else"               "DateTimeClasses"    "POSIXct"           
[10] "POSIXlt"            "POSIXt"             "Math.POSIXlt"      
[13] "Date"               "Dates"              "Defunct"           
[16] "Deprecated"         "Extract"            "Subscript"         
[19] "Foreign"            "Logic"              "Memory-limits"     
[22] "Memory"             "NA"                 "NULL"              
[25] "Paren"              "Random.user"        ".Random.seed"      
[28] "RNG"                "Rdconv"             "Rd2txt"            
[31] "Rd2dvi"             "Sd2Rd"              "Special"           
[34] "Startup"            "Rprofile"           ".Rprofile"         
[37] "Rprofile.site"      "Renviron.site"      ".Renviron"         
[40] ".First"             "Syntax"             "Trig"              
[43] "S3Methods"          "fuzzy matching"     "->"                
[46] "->>"                ".Autoloaded"        "base-deprecated"   
[49] "connections"        "connection"         "copyright"         
[52] "copyrights"         "files"              ".Method"           
[55] ".Generic"           ".Group"             ".Class"            
[58] "Math"               "Ops"                "Summary"           
[61] "Arith"              "Compare"            "Complex"           
[64] "Math2"              "group generic"      "Inf"               
[67] "NaN"                "R_LIBS"             ".First.lib"        
[70] ".Last.lib"          "localeconv"         "locales"           
[73] "TRUE"               "FALSE"              "matmult"           
[76] "name"               "NotYetImplemented"  "NotYetUsed"        
[79] ".onLoad"            ".onUnload"          ".onAttach"         
[82] "print.htest"        ".Last"              "regex"             
[85] "regexp"             "regular expression" "tilde"             
[88] ".Traceback"         "InternalMethods"    "Signals"           

to assess the magnitude of the issue at hand: about 10% of the base
topics do *not* corresponding to R objects.

Admittedly, some of these are perhaps not quite right, or better made
into \concept entries, but e.g. for a documentation object explaining R
CMD stuff, there will most likely never be an R object to use as topic.

More long term, I am planning to include ways to report "possible"
problems such as the above, perhaps alongside with us integrating Luke's
code analysis tools which face a similar issue.  But I don't think we
can peruse R CMD check to generate warnings about possible problems by
default.

[It detects enough real problems these days which package maintainers
are not always quick to fix ...]

-k