覆盖另一个包继承的包函数

Question

I am trying to override the tidy.source function of the knitr package. The problem is that tidy.source is defined in the formatR package, which is imported by the knitr package. If I run:

get("tidy.source", envir=asNamespace("knitr"))

I get the original code. So I am tempted to override tidy.source with:

assignInNamespace ("tidy.source", function()print("My tidy.source"), "knitr") ,

but I get:

Error in bindingIsLocked(x, ns) : no binding for "tidy.source" .

In fact tidy.source is defined in formatR and inherited by knitr . With:

assignInNamespace ("tidy.source", function()print("My tidy.source"), "formatR")

everything is apparently smooth, but checking again get("tidy.source", envir=asNamespace("knitr")) shows that inside knitr nothing has changed.

Any help?

EDIT:

This question is partly obsolete due to the new development release of knitr/formatR . Many thanks to Yihui for noticing this discussion and for deciding to update his package. See:

https://github.com/yihui/formatR/commit/6f70360f359caa8d2bb33190a1c89530defb0e98

I can definitely switch from Sweave to knitr .

The general question concerning the overriding of an imported package function remains anyway open. Since it is not related to knitr/formatR package anymore, I restate it in more general terms.

Suppose you have a package main importing the package imp . If you load the former, "package:main" shows in the list of the attached packages and both "main" and "sub" show among the names of the loaded namespaces.

Assume that main imports the exported sub function exp.sub.func , which calls in turns the non-exported sub function prv.sub.func . If you want to change/customise exp.sub.func with your exp.sub.func.mod , you may think of using:

assign("exp.sub.func", exp.sub.func.mod, asNamespace ("sub"))

As a result, by running sub::exp.sub.func you will get your patched version (that is exp.sub.func.mod ).
Unfortunately, as far as your exp.sub.func.mod keeps on relying on prv.sub.func , you get the error:

Error in [...] : object 'prv.sub.func' not found

In fact:

environment(sub::exp.sub.func) 

returns now: <environment: R_GlobalEnv> while it was <environment: namespace:sub> before patching.

The question is: how to move the patched function to the proper namespace ?

To implement the problem above you can use whatever packages of course; in my case I used knitr and formatR as main and imported namespace and tidy.source() as patched function.

Answer 1

Changing the function in the formatR namespace doesn't change what knitr uses because knitr is already loaded. So, you could unload and reload it.

assignInNamespace("tidy.source", function()print("My tidy.source"), "formatR")
detach('package:knitr', unload=TRUE)
library(knitr)
get("tidy.source", envir=asNamespace("knitr"))
#function()print("My tidy.source")

Answer 2

If all you want is comments after function arguments, I have added the support in the development version , and you can install it from Github .

Normally it is a bad idea to modify packages using assignInNamespace() , as its documentation shows.

Answer 3

I am perhaps close to a solution but I have to deal with non-exported formatR functions. In fact the original tidy.source code, and therefore the patched version, has calls to non-exported package functions, eg reflow_comments .

To illustrate the problem and the step I followed, let's start with a test patched tidy.source calling a private formatR function.

### Listing 1 - Modified tidy.source             

tidy.source.mod=function (source, output, text){ 
  #Print body first line of reflow_comments      
  head(reflow_comments,1)                        
}                                                

source, output, text parameters are necessary as passed by knit used ahead.

Now I can patch the tidy.source with tidy.source.mod :

### Listing 2 - Patch tidy.source                       

## General clean up                                     
if("knitr" %in% loadedNamespaces() ) detach('package:knitr', unload=TRUE)
if("formatR" %in% loadedNamespaces() ) detach('package:formatR', unload=TRUE)
if(exists("tidy.source"))rm(tidy.source)                
library("formatR")                                      

## Info                                                 
environment(tidy.source )                               
# <environment: namespace:formatR>                      
environment(formatR::tidy.source )                      
# <environment: namespace:formatR>                      

## Change tidy.source with tidy.source.mod              
unlockBinding("tidy.source", env=as.environment("package:formatR"))
assign("tidy.source", tidy.source.mod, envir=as.environment("package:formatR"))
lockBinding("tidy.source", env=as.environment("package:formatR"))
unlockBinding("tidy.source", env=asNamespace ("formatR"))
assign("tidy.source", tidy.source.mod, asNamespace ("formatR") )
environment(tidy.source)= asNamespace( "formatR" )      
lockBinding("tidy.source", env=asNamespace ("formatR")) 

We can check the results:

### Listing 3 - Check results                                                  

getAnywhere(tidy.source)                                                       
# A single object matching 'tidy.source' was found                             
# It was found in the following places                                         
#   .GlobalEnv                                                                 
#   package:formatR                                                            
#   namespace:formatR                                                          
# with value                                                                   

# function (){                                                                 
#   head(reflow_comments,1)                                                    
# }                                                                            
# <environment: namespace:formatR>                                             

tidy.source()                                                                  
# 1 function (text, idx = grepl("^\\\\s*#+", text), width = getOption("width"))

Apparently tidy.source was correctly substituted with tidy.source.mod ; namespaces were updated so tidy.source has access to (the first line of) non-exported reflow_comments function.

To deal with knitr we need also a file to knit, here I use a text string for simplicity.

### Listing 4 - Sample file/text to knit

library("knitr") 

text="           
\\documentclass{article}
\\begin{document}

<<comme, include=TRUE>>=
print('hello')   
@                

\\end{document}  
"                

Is knitr able to see the patched tidy.source ? We can check this with the help of R debug .

debug(knit)                                   
knit(text=text) #will enter debug session (prompt s'd be like 'Browse[2]>')
# debugging in: knit(text = text)             
# debug: {                                    
# knit body, very long, omitted               
# }                                           
tidy.source #command given inside the debug session
# function (){                                
#   head(reflow_comments,1)                   
# }                                           
tidy.source() # :-( reflow_comments is not accessible
Q  #quit debug session                        

undebug(knit)                                 

Unfortunately from knit the patched tidy.source is visible, but it can't access non-exported formatR functions, which for knit is normally possible via the non-patched tidy.source .

Here some hints may be that formatR::tidy.source() doesn't work either:

formatR::tidy.source()
# Error in head(reflow_comments, 1) (from #2) : object 'reflow_comments' not found

The environment of namespace:formatR is:

environment(formatR::tidy.source )
# <environment: R_GlobalEnv>

That was <environment: namespace:formatR> before patching (see info in Listing 2). While environment(tidy.source ) was easily reset when patching, for namespace:formatR we get an error:

environment(formatR::tidy.source )=asNamespace( "formatR" )
# Error in environment(formatR::tidy.source) = asNamespace("formatR") :
#  object 'formatR' not found 

I am still searching....

Answer 4

This is a possible buggy attempt to allow inline comments after function arguments by tidy.source function included in the formatR package.

## ============ Possible (wrong?) ideas on inline comments ============

  tidy.source.mod=  function (source = "clipboard", keep.comment = getOption("keep.comment",
    TRUE), keep.blank.line = getOption("keep.blank.line", TRUE),
    keep.space = getOption("keep.space", FALSE), replace.assign = getOption("replace.assign",
        FALSE), left.brace.newline = getOption("left.brace.newline",
        FALSE), reindent.spaces = getOption("reindent.spaces",
        4), output = TRUE, text = NULL, width.cutoff = getOption("width"),
    ...)
{     
    if (is.null(text)) {
        if (source == "clipboard" && Sys.info()["sysname"] ==
            "Darwin") {
            source = pipe("pbpaste")
        }
        text = readLines(source, warn = FALSE)
    } 
    if (length(text) == 0L || all(grepl("^\\s*$", text))) {
        if (output)
            cat("\n", ...)
        return(list(text.tidy = "", text.mask = ""))
    } 
    text.lines = text
    if (keep.comment) {
        if (!keep.space)
            text.lines = gsub("^[[:space:]]+|[[:space:]]+$",
                "", text.lines)
        head.comment = grepl("^[[:space:]]*#", text.lines)
        if (any(head.comment)) {
            text.lines[head.comment] = gsub("\"", "'", text.lines[head.comment])
        }
        if (!keep.space) {
            head.comment = head.comment & !grepl("^\\s*#+'",
                text.lines)
            text.lines = reflow_comments(text.lines, head.comment,
                width.cutoff)
            head.comment = grepl("^[[:space:]]*#", text.lines)
        }
        text.lines[head.comment] = sprintf("invisible(\"%s%s%s\")",
            begin.comment, text.lines[head.comment], end.comment)
        blank.line = grepl("^[[:space:]]*$", text.lines)
        if (any(blank.line) && keep.blank.line) {
            else.line = grep("^[[:space:]]*else(\\W|)", text.lines)
            for (i in else.line) {
                j = i - 1
                while (blank.line[j]) {
                  blank.line[j] = FALSE
                  j = j - 1
                  warning("removed blank line ", j, " (you should not put an 'else' in a separate line!)")
                }
            }
            text.lines[blank.line] = sprintf("invisible(\"%s%s\")",
                begin.comment, end.comment)
        }
        text.lines = mask_inline(text.lines)
    } 
    #modified code
    ic=grepl( "%InLiNe_IdEnTiFiEr%", text.lines)
    text.lines[ic]=substr(text.lines[ic], 1, nchar(text.lines[ic])-1)
    text.lines[ic]=  paste0(text.lines[ic], "%InLiNe_IdEnTiFiEr_mod%\"")
    #end modified code
    text.mask = tidy_block(text.lines, width.cutoff, replace.assign)
    text.tidy = if (keep.comment)
        unmask.source(text.mask)
    else text.mask
    text.tidy = reindent_lines(text.tidy, reindent.spaces)
    if (left.brace.newline)
        text.tidy = move_leftbrace(text.tidy, reindent.spaces)
    #modified code
    text.tidy= unlist(sapply(text.tidy, strsplit, "%InLiNe_IdEnTiFiEr_mod%", USE.NAMES=FALSE))
    #end modified code
    if (output)
        cat(paste(text.tidy, collapse = "\n"), "\n", ...)
    invisible(list(text.tidy = text.tidy, text.mask = text.mask))
}     
## ====================================================


## ============ Implementation ============

## Clean-up
if("formatR" %in% loadedNamespaces() ) detach('package:formatR', unload=TRUE)
if(exists("tidy.source"))rm(tidy.source)
library("formatR")


## String with inline comments after arguments
text.input="paste(1 # comm
   ,7)
"     
## The same in vector format
text.input=strsplit(text.input, "\n")[[1]]

## Implementation without patch
tidy.source(text=text.input) #newline removed with  wrong result!
# paste(1  # comm, 7) 


# Tentative patch
unlockBinding("tidy.source", as.environment("package:formatR") )
assign("tidy.source", tidy.source.mod, pos="package:formatR")
environment(tidy.source)= asNamespace( "formatR" )

## Implementation with patch
tidy.source(text=text.input) # apparently ok:
# paste(1  # comm
# , 7)