>>>>> wolski writes:
> 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?
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
> 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.
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