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Diff of /pkg/inlinedocs/R/parsers.R

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revision 105, Tue May 18 17:32:43 2010 UTC revision 352, Mon Apr 9 12:43:46 2012 UTC
# Line 1  Line 1 
1    do.not.generate <- structure(function
2    ### Make a Parser Function used to indicate that certain Rd files
3    ### should not be generated.
4    (...
5    ### Character strings indicating Rd files without the .Rd suffix.
6     ){
7      filenames <- c(...)
8      function(docs,...){
9        for(fn in filenames){
10          docs[[fn]] <- list()
11        }
12        docs$.overwrite <- TRUE
13        docs
14      }
15    ### A Parser Function that will delete items from the outer
16    ### Documentation List.
17    },ex=function(){
18      silly.pkg <- system.file("silly",package="inlinedocs")
19      owd <- setwd(tempdir())
20      file.copy(silly.pkg,".",recursive=TRUE)
21    
22      ## define a custom Parser Function that will not generate some Rd
23      ## files
24      custom <- do.not.generate("silly-package","Silly-class")
25      parsers <- c(default.parsers,list(exclude=custom))
26    
27      ## At first, no Rd files in the man subdirectory.
28      man.dir <- file.path("silly","man")
29      dir(man.dir)
30    
31      ## Running package.skeleton.dx will generate bare-bones files for
32      ## those specified in do.not.generate, if they do not exist.
33      package.skeleton.dx("silly",parsers)
34      Rd.files <- c("silly-package.Rd","Silly-class.Rd","silly.example.Rd")
35      Rd.paths <- file.path(man.dir,Rd.files)
36      stopifnot(all(file.exists(Rd.paths)))
37    
38      ## Save the modification times of the Rd files
39      old <- file.info(Rd.paths)$mtime
40      Sys.sleep(1/60) ## to make sure there is at least 1 second elapsed
41    
42      ## However, it will NOT generate Rd for files specified in
43      ## do.not.generate, if they DO exist already.
44      package.skeleton.dx("silly",parsers)
45      mtimes <- data.frame(old,new=file.info(Rd.paths)$mtime)
46      rownames(mtimes) <- Rd.files
47      mtimes$changed <- mtimes$old != mtimes$new
48      print(mtimes)
49      stopifnot(mtimes["silly-package.Rd","changed"]==FALSE)
50      stopifnot(mtimes["Silly-class.Rd","changed"]==FALSE)
51      stopifnot(mtimes["silly.example.Rd","changed"]==TRUE)
52    
53      unlink("silly",recursive=TRUE)
54      setwd(owd)
55    })
56    
57    ### combine lists or character strings
58    combine <- function(x,y)UseMethod("combine")
59    
60    ### combine character strings by pasting them together
61    combine.character <- function(x,y)
62        paste(x,y,sep="\n")
63    
64    ### combine lists by adding elements or adding to existing elements
65    combine.list <- function(x,y){
66      toadd <- if(".overwrite"%in%names(y)){
67        y <- y[names(y)!=".overwrite"]
68        rep(TRUE,length(y))
69      }else{
70        !names(y)%in%names(x)
71      }
72      toup <- names(y)[!toadd]
73      x[names(y)[toadd]] <- y[toadd]
74      for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
75      x
76    ### A list, same type as x, but with added elements from y.
77    }
78    
79    
80    getSource <- function
81    ### Extract a function's source code.
82    (fun.obj
83    ### A function.
84     ) {
85          srcref <- attr(fun.obj, "srcref")
86          if (!is.null(srcref)) {
87            ##unlist(strsplit(as.character(srcref), "\n"))
88            as.character(srcref)
89          }
90          else attr(fun.obj, "source")
91    ### Source code lines as a character vector.
92    }
93    
94    ### Prefix for code comments used with grep and gsub.
95    prefix <- "^[ \t]*###[ \t]*"
96    
97    decomment <- function
98    ### Remove comment prefix and join lines of code to form a
99    ### documentation string.
100    (comments
101    ### Character vector of prefixed comment lines.
102     ){
103      gsub(prefix,"",comments)
104    ### String without prefixes or newlines.
105    }
106    
107    forall <- function
108  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
109  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
110  ### documentation list.  ### documentation list.
 forall <- function  
111  (FUN,  (FUN,
112  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
113   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 9  Line 115 
115  ### is.function. subfun(x)==TRUE means FUN will be applied to x and  ### is.function. subfun(x)==TRUE means FUN will be applied to x and
116  ### the result will be returned.  ### the result will be returned.
117   ){   ){
118    function(objs,docs,...){    FUN <- FUN
119      f <- function(objs,docs,...){
120        if(length(objs)==0)return(list())
121      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
122      L <- list()      L <- list()
123      for(N in names(docs)){      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
124        for(N in union(names(docs),names(objs))){
125        o <- objs[[N]]        o <- objs[[N]]
126        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
127                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
128      }      }
129        on.exit()## remove warning message
130      L      L
131    }    }
132      class(f) <- c("allfun","function")
133      f
134  ### A Parser Function.  ### A Parser Function.
135  }  }
136    
137  ### For each function in the package, do something.  ### Print method for functions constructed using forall.
138  forfun <- function(FUN)forall(FUN,is.function)  print.allfun <- function(x,...){
139      e <- environment(x)
140  ### Parsers for each object/function that are constructed    cat("Function to apply to every element.\nselector:")
141  ### automatically. This is a named list, each element is a list of 2    print(e$subfun)
142  ### elements: forfun/forall, then a parser function for an individual    cat("processor:")
143  ### object.    print(e$FUN)
 forall.parsers <-  
   list(## Extract lots of info from normal functions.  
        parsefun=list(forfun,function(src,name,...){  
          extract.docs.fun(src,name)  
        }),  
        ## Fill in author from DESCRIPTION and titles.  
        author.from.description=list(forall,function(desc,...){  
          list(author=desc[,"Maintainer"])  
        }),  
        ## The format section sometimes causes problems, so erase it.  
        erase.format=list(forall,function(...){  
          list(format="")  
        }),  
        ## Convert the function name to a title.  
        title.from.name=list(forall,function(name,doc,...){  
          if("title"%in%names(doc))list() else  
          list(title=gsub("[._]"," ",name))  
        }),  
        ## Get examples for FUN from the file test/FUN.R  
        examples.from.testfile=list(forfun,function(name,...){  
          tfile <- file.path("..","tests",paste(name,".R",sep=""))  
          if(file.exists(tfile))  
            list(examples=paste(readLines(tfile),collapse="\n"))  
          else list()  
        }),  
        ## Get examples from inline definitions after return()  
        examples.after.return=list(forfun,function(name,src,...){  
          coll <- paste(src,collapse="\n")  
          thispre <- gsub("^[\\^]","",prefix)  
          FIND <- paste("(return|UseMethod)[(][^\\n]*\\n",thispre,sep="")  
          m <- regexpr(FIND,coll)  
          if(m[1]==-1)return(list())  
          after <- substr(coll,m[1],nchar(coll))  
          FIND <-  
            paste("[^\\n]*",# rest of the return line  
                  "((?:\\n###[^\\n]*)+)",#comment value lines \\1  
                  "([\\w\\W]*)[}]",#examples \\2  
                  sep="")  
          SEP <- "-/-/-/-/-=====-----"  
          REP <- paste("\\1",SEP,"\\2",sep="")  
          r <- strsplit(gsub(FIND,REP,after,perl=TRUE),split=SEP)[[1]]  
          l <- strsplit(r,split="\n")  
          excode <- c(l[[2]],"")  
          if(length(l)<2||paste(excode,collapse="")=="")return(list())  
          prefixes <- gsub("(\\s*).*","\\1",excode,perl=TRUE)[grep("\\w",excode)]  
          FIND <- prefixes[which.min(nchar(prefixes))]  
          list(examples=paste(sub(FIND,"",excode),collapse="\n"),  
               value=decomment(l[[1]][-1]))  
        }))  
   
 ### List of parser functions that operate on single objects. This list  
 ### is useful for testing these functions, ie  
 ### lonely$parsefun(attr(extract.docs.file,"source"),"extract.docs.file")  
 lonely <- sapply(forall.parsers,function(L)L[[2]])  
   
 extract.docs.file <- function # Extract documentation from a file  
 ### Parse R code to extract inline documentation from comments around  
 ### each function. These are not able to be retreived simply by  
 ### looking at the "source" attribute. This is a Parser Function that  
 ### can be used in the parser list of package.skeleton.dx().  
 (code,  
 ### Code lines in a character vector containing multiple R objects to  
 ### parse for documentation.  
  objs,  
 ### The objects defined in the code.  
  ...  
 ### ignored  
  ){  
   parsed <- extract.file.parse(code)  
   extract.docs.try <- function(o,on)  
     {  
       ## Note: we could use parsed information here too, but that  
       ## would produce different results for setMethodS3 etc.  
       doc <- list()  
       if ( !is.null(parsed[[on]]) ){  
         if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics  
           doc$definition <- paste(parsed[[on]]@code,collapse="\n")  
         }  
         if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){  
           doc$description <- parsed[[on]]@description  
         }  
         if ( "setMethodS3" == parsed[[on]]@created ){  
           pattern <- "^([^\\.]+)\\.(.*)$"  
           doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),  
               m2 <- gsub(pattern,"\\2",on,perl=TRUE))  
           if ( 0 < length(grep("\\W",m1,perl=TRUE)) ){  
             m1 <- paste("`",m1,"`",sep="")  
           }  
           cat("S3method(",m1,",",m2,")\n",sep="")  
         }  
       }  
       if("title" %in% names(doc) && !"description" %in% names(doc) ){  
         ## For short functions having both would duplicate, but a  
         ## description is required. Therefore automatically copy title  
         ## across to avoid errors at package build time.  
         doc$description <- doc$title  
       }  
       doc  
     }  
   extract.docs <- function(on){  
     res <- try({o <- objs[[on]]  
                 extract.docs.try(o, on)},FALSE)  
     if(class(res)=="try-error"){  
       cat("Failed to extract docs for: ",on,"\n\n")  
       list()  
     } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){  
       NULL  
     } else if(0 == length(res) && "function" %in% class(o)  
               && 1 == length(osource <- attr(o,"source"))  
               && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))  
               ){  
       ## phew - this should only pick up R.oo S3 generic definitions like:  
       ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"  
       NULL  
     } else res  
   }  
   doc.names <- names(objs)  
   res <- sapply(doc.names,extract.docs,simplify=FALSE)  
   ## Special processing for S4 classes as they do not appear in normal ls()  
   for ( nn in names(parsed) ){  
     if ( parsed[[nn]]@created == "setClass" ){  
       S4class.docs <- extract.docs.setClass(parsed[[nn]])  
       docname <- paste(nn,"class",sep="-")  
       if ( is.null(res[[docname]]) ){  
         res[[docname]] <- S4class.docs  
         doc.names <- c(doc.names,docname)  
       } else {  
         stop(nn," appears as both S4 class and some other definition")  
       }  
     }  
   }  
   inherit.docs <- function(on){  
     in.res <- res[[on]]  
     if ( !is.null(parsed[[on]]) ){  
       for ( parent in parsed[[on]]@parent ){  
         if ( !is.na(parent) ){  
           if ( is.null(in.res) ){  
             in.res <- res[[parent]]  
           } else if ( parent %in% names(res) ){  
             parent.docs <- res[[parent]]  
             for ( nn in names(parent.docs) ){  
               if ( !nn %in% names(in.res) ){  
                 in.res[[nn]] <- parent.docs[[nn]]  
               }  
             }  
           }  
         }  
       }  
     }  
     invisible(in.res)  
   }  
   all.done <- FALSE  
   while ( !all.done ){  
     res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)  
     all.done <- identical(res1,res)  
     res <- res1  
   }  
   ## now strip out any generics (which have value NULL in res):  
   res.not.null <- sapply(res,function(x){!is.null(x)})  
   if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){  
     res <- res[res.not.null]  
   }  
   res  
 ### named list of lists, one for each object to document.  
144  }  }
145    
146  ### List of parsers to use by default with package.skeleton.dx.  ### For each function in the package, do something.
147  default.parsers <- c(extract.docs.file=extract.docs.file,  forfun <- function(FUN)forall(FUN,is.function)
                      sapply(forall.parsers,function(L)L[[1]](L[[2]])))  
148    
149  extract.docs.fun <- function # Extract documentation from a function  kill.prefix.whitespace <- function
150  ### Given source code of a function, return a list describing inline  ### Figure out what the whitespace preceding the example code is, and
151  ### documentation in that source code.  ### then delete that from every line.
152  (code,  (ex
153  ### The function to examine.  ### character vector of example code lines.
  name.fun  
 ### The name of the function/chunk to use in warning messages.  
154   ){   ){
155    res <- list()    tlines <- gsub("\\s*","",ex)
156    clines <- grep(prefix,code)    ##tlines <- gsub("#.*","",tlines)
157    if(length(grep("#",code[1]))){    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
158      res$title <- gsub("[^#]*#\\s*(.*)","\\1",code[1],perl=TRUE)    FIND <- prefixes[which.min(nchar(prefixes))]
159    }    ## Eliminate leading tabulations or 2/4 spaces
160    if(length(clines) > 0){    sub(FIND, "", ex)
161      ##details<<  ### Character vector of code lines with preceding whitespace removed.
162      ## The primary mechanism is that consecutive groups of lines matching  }
163      ## the specified prefix regular expression "\code{^### }" (i.e. lines  
164      ## beginning with "\code{### }") are collected  prefixed.lines <- structure(function(src,...){
165      ## as follows into documentation sections:\describe{  ### The primary mechanism of inline documentation is via consecutive
166      ## \item{description}{group starting at line 2 in the code}  ### groups of lines matching the specified prefix regular expression
167      ## \item{arguments}{group following each function argument}  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
168      ## \item{value}{group ending at the penultimate line of the code}}  ### collected as follows into documentation sections:\describe{
169      ## These may be added to by use of the \code{##<<} constructs described  ### \item{description}{group starting at line 2 in the code}
170      ## below.  ### \item{arguments}{group following each function argument}
171    ### \item{value}{group ending at the penultimate line of the code}}
172    ### These may be added to by use of the \code{##<<} constructs
173    ### described below.
174      clines <- grep(prefix,src)
175      if(length(clines)==0)return(list())
176      bounds <- which(diff(clines)!=1)      bounds <- which(diff(clines)!=1)
177      starts <- c(1,bounds+1)      starts <- c(1,bounds+1)
178      ends <- c(bounds,length(clines))      ends <- c(bounds,length(clines))
179      ## detect body of function using paren matching
180      code <- gsub("#.*","",src)
181      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
182      parens <- f("(")-f(")")
183      body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
184      if(length(body.begin)==0)body.begin <- 1 ## rare cases
185      is.arg <- function(){
186        gres <- grep("^\\s*#",src[start-1],perl=TRUE)
187        0 == length(gres) && start<=body.begin
188      }
189      res <- list()
190      for(i in seq_along(starts)){      for(i in seq_along(starts)){
191        start <- clines[starts[i]]        start <- clines[starts[i]]
192        end <- clines[ends[i]]        end <- clines[ends[i]]
193        lab <- if(end+1==length(code))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
194        lab <- if(all(processed==""))"value"
195        else if(start==2)"description"        else if(start==2)"description"
196        else if ( 0 == length(grep("^\\s*#",code[start-1],perl=TRUE)) ){      else if(is.arg()){
197           #arg <- gsub("^[ (]*","",code[start-1])        ##twutz: strip leading white spaces and brackets and ,
198           #arg <- gsub("^([^=,]*)[=,].*","\\1",arg)        arg <- gsub("^[ \t(,]*", "", src[start - 1])
          #arg <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots  
                  arg <- gsub("^[ \t(,]*", "", code[start - 1])  #twutz: strip leading white spaces and brackets and ,  
199                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
200                   arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)   #twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
201                   arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
202          arg <- gsub("...", "\\dots", arg, fixed = TRUE)
203           paste("item{",arg,"}",sep="")           paste("item{",arg,"}",sep="")
204         } else {         } else {
205           next;           next;
206         }         }
207        res[[lab]] <- decomment(code[start:end])      res[[lab]] <- decomment(src[start:end])
     }  
208    }    }
209      res
210    },ex=function(){
211    test <- function
212    ### the description
213    (x,
214    ### the first argument
215     y ##<< another argument
216     ){
217      5
218    ### the return value
219    ##seealso<< foobar
220    }
221    src <- getSource(test)
222    prefixed.lines(src)
223    extract.xxx.chunks(src)
224    })
225    
226    extract.xxx.chunks <- function # Extract documentation from a function
227    ### Given source code of a function, return a list describing inline
228    ### documentation in that source code.
229    (src,
230    ### The source lines of the function to examine, as a character
231    ### vector.
232     name.fun="(unnamed function)",
233    ### The name of the function/chunk to use in warning messages.
234     ...
235    ### ignored.
236     ){
237      res <- list()
238    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
239    ## documented by appending \code{##<<} comments on the same line as the    ## documented by appending \code{##<<} comments on the same line as the
240    ## argument name. Mixing this mechanism with \code{###} comment lines for    ## argument name. Mixing this mechanism with \code{###} comment lines for
# Line 318  Line 307 
307          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
308        }        }
309        chunk.res <- NULL        chunk.res <- NULL
310        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
311          chunk.res <-          chunk.res <-
312            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
313            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
314        invisible(chunk.res)        invisible(chunk.res)
315      }      }
316    while ( k <= length(code) ){    while ( k <= length(src) ){
317      line <- code[k]      line <- src[k]
318      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      ##print(line)
319        ##if(grepl("^$",line))browser()
320        if ( grepl(extra.regexp,line,perl=TRUE) ){
321        ## we have a new extra chunk - first get field name and any payload        ## we have a new extra chunk - first get field name and any payload
322        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
323        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
324          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
325        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
326        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
327        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 339  Line 330 
330        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
331        if ( "describe" == new.field ){        if ( "describe" == new.field ){
332          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
333          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
334          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
335          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
336            ## \code{##describe<<} comments.
337          if ( first.describe ){          if ( first.describe ){
338            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
339          } else {          } else {
# Line 401  Line 393 
393            first.describe <- TRUE;            first.describe <- TRUE;
394          }          }
395        }        }
396      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
397        ## append this line to current chunk        ## append this line to current chunk
398        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
399          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
400          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
401          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 416  Line 408 
408            payload <- stripped            payload <- stripped
409          }          }
410        }        }
411      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
412        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
413        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
414          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 425  Line 417 
417        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
418        in.chunk <- TRUE        in.chunk <- TRUE
419        if ( not.describe ){        if ( not.describe ){
420          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          ## TDH 2010-06-18 For item{}s in the documentation list names,
421            ## we don't need to have a backslash before, so delete it.
422            arg <- gsub("^[\\]+","",arg)
423            cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
424          payload <- comment          payload <- comment
425        } else {        } else {
426          ## this is a describe block, so we need to paste with existing          ## this is a describe block, so we need to paste with existing
# Line 475  Line 470 
470  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
471  }  }
472    
473    leadingS3generic <- function # check whether function name is an S3 generic
474    ### Determines whether a function name looks like an S3 generic function
475    (name,                     ##<< name of function
476     env,                      ##<< environment to search for additional generics
477     ...)                      ##<< ignored here
478    {
479      ##details<< This function is one of the default parsers, but exposed as
480      ## possibly of more general interest. Given a function name of the form
481      ## x.y.z it looks for the generic function x applying to objects of class
482      ## y.z and also for generic function x.y applying to objects of class z.
483      ##
484      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
485      l <- length(parts)
486      if (l > 1) {
487        for (i in 1:(l - 1)) {
488          ## Look for a generic function (known by the system or defined
489          ## in the package) that matches that part of the function name
490          generic <- paste(parts[1:i], collapse = ".")
491          if (any(generic %in% utils:::getKnownS3generics()) ||
492              utils:::findGeneric(generic, env) != "") {
493            object <- paste(parts[(i + 1):l], collapse = ".")
494            ##details<< Assumes that the first name which matches any known
495            ## generics is the target generic function, so if both x and x.y
496            ## are generic functions, will assume generic x applying to objects
497            ## of class y.z
498            ##value<< If a matching generic found returns a list with a single component:
499            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
500          }
501        }
502      }
503      ##value<< If no matching generic functions are found, returns an empty list.
504      list()
505    }
506    
507    ### Parsers for each function that are constructed automatically. This
508    ### is a named list, and each element is a parser function for an
509    ### individual object.
510    forfun.parsers <-
511      list(prefixed.lines=prefixed.lines,
512           extract.xxx.chunks=extract.xxx.chunks,
513           ## title from first line of function def
514           title.from.firstline=function(src,...){
515             first <- src[1]
516             if(!is.character(first))return(list())
517             if(!grepl("#",first))return(list())
518             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
519           },
520           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
521           ## please, let me choose which dir to use for examples!
522           ## Get examples for FUN from the file tests/FUN.R
523           examples.from.testfile=function(name,...){
524             tsubdir <- getOption("inlinedocs.exdir")
525             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
526             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
527             if(file.exists(tfile))
528               list(examples=readLines(tfile))
529             else list()
530           },
531           definition.from.source=function(doc,src,...){
532             def <- doc$definition
533             is.empty <- function(x)is.null(x)||x==""
534             if(is.empty(def) && !is.empty(src))
535               list(definition=src)
536             else list()
537           })
538    
539    ### List of Parser Functions that can be applied to any object.
540    forall.parsers <-
541      list(## Fill in author from DESCRIPTION and titles.
542           author.from.description=function(desc,...){
543             list(author=desc[,"Author"])
544           },
545           ## The format section sometimes causes problems, so erase it.
546           erase.format=function(...){
547             list(format="")
548           },
549           ## Convert the function name to a title.
550           title.from.name=function(name,doc,...){
551             if("title"%in%names(doc))list() else
552             list(title=gsub("[._]"," ",name))
553           },
554           ## PhG: here is what I propose for examples code in the 'ex' attribute
555           examples.in.attr =  function (name, o, ...) {
556             ex <- attr(o, "ex")
557             if (!is.null(ex)) {
558               ## Special case for code contained in a function
559               if (inherits(ex, "function")) {
560                 ## If source is available, start from there
561                 src <- getSource(ex)
562                 if (!is.null(src)) {
563                   ex <- src
564                 } else { ## Use the body of the function
565                   ex <- deparse(body(ex))
566                 }
567                 ## Eliminate leading and trailing code
568                 ex <- ex[-c(1, length(ex))]
569                 if(ex[1]=="{")ex <- ex[-1]
570                 ## all the prefixes
571                 ex <- kill.prefix.whitespace(ex)
572                 ## Add an empty line before and after example
573                 ex <- c("", ex, "")
574               }
575               list(examples = ex)
576             } else list()
577           },collapse=function(doc,...){
578             L <- lapply(doc,paste,collapse="\n")
579             L$.overwrite <- TRUE
580             L
581           },tag.s3methods=leadingS3generic
582           )
583    
584    ### List of parser functions that operate on single objects. This list
585    ### is useful for testing these functions.
586    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
587      f <- function # title
588    ### description
589      (x, ##<< arg x
590       y
591    ### arg y
592       ){
593        ##value<< a list with elements
594        list(x=x, ##<< original x value
595             y=y, ##<< original y value
596             sum=x+y) ##<< their sum
597        ##end<<
598      }
599      src <- getSource(f)
600      lonely$extract.xxx.chunks(src)
601      lonely$prefixed.lines(src)
602    })
603    
604    extra.code.docs <- function # Extract documentation from code chunks
605    ### Parse R code to extract inline documentation from comments around
606    ### each function. These are not able to be retreived simply by
607    ### looking at the "source" attribute. This is a Parser Function that
608    ### can be used in the parser list of package.skeleton.dx(). TODO:
609    ### Modularize this into separate Parsers Functions for S4 classes,
610    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
611    (code,
612    ### Code lines in a character vector containing multiple R objects to
613    ### parse for documentation.
614     objs,
615    ### The objects defined in the code.
616     ...
617    ### ignored
618     ){
619      parsed <- extract.file.parse(code)
620      extract.docs.try <- function(o,on)
621        {
622          ## Note: we could use parsed information here too, but that
623          ## would produce different results for setMethodS3 etc.
624          doc <- list()
625          if ( !is.null(parsed[[on]]) ){
626            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
627              doc$definition <- paste(parsed[[on]]@code)
628            }
629            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
630              doc$description <- parsed[[on]]@description
631            }
632            ## if ( "setMethodS3" == parsed[[on]]@created ){
633            ##   gen <- leadingS3generic(on,topenv())
634            ##   if ( 0 < length(gen) ){
635            ##     doc$.s3method <- gen$.s3method
636            ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
637            ##   }
638            ## }
639          }
640          if("title" %in% names(doc) && !"description" %in% names(doc) ){
641            ## For short functions having both would duplicate, but a
642            ## description is required. Therefore automatically copy title
643            ## across to avoid errors at package build time.
644            doc$description <- doc$title
645          }
646          doc
647        }
648      extract.docs <- function(on){
649        res <- try({o <- objs[[on]]
650                    extract.docs.try(o, on)},FALSE)
651        if(class(res)=="try-error"){
652          cat("Failed to extract docs for: ",on,"\n\n")
653          list()
654        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
655          NULL
656        } else if(0 == length(res) && "function" %in% class(o)
657                  && 1 == length(osource <- getSource(o))
658                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
659                  ){
660          ## phew - this should only pick up R.oo S3 generic definitions like:
661          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
662          NULL
663        } else res
664      }
665      doc.names <- names(objs)
666      res <- sapply(doc.names,extract.docs,simplify=FALSE)
667      ## Special processing for S4 classes as they do not appear in normal ls()
668      for ( nn in names(parsed) ){
669        if ( parsed[[nn]]@created == "setClass" ){
670          S4class.docs <- extract.docs.setClass(parsed[[nn]])
671          docname <- paste(nn,"class",sep="-")
672          if ( is.null(res[[docname]]) ){
673            res[[docname]] <- S4class.docs
674            doc.names <- c(doc.names,docname)
675          } else {
676            stop(nn," appears as both S4 class and some other definition")
677          }
678        }
679      }
680      inherit.docs <- function(on){
681        in.res <- res[[on]]
682        if ( !is.null(parsed[[on]]) ){
683          for ( parent in parsed[[on]]@parent ){
684            if ( !is.na(parent) ){
685              if ( is.null(in.res) ){
686                in.res <- res[[parent]]
687              } else if ( parent %in% names(res) ){
688                parent.docs <- res[[parent]]
689                for ( nn in names(parent.docs) ){
690                  if ( !nn %in% names(in.res) ){
691                    in.res[[nn]] <- parent.docs[[nn]]
692                  }
693                }
694              }
695            }
696          }
697        }
698        invisible(in.res)
699      }
700      all.done <- FALSE
701      while ( !all.done ){
702        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
703        all.done <- identical(res1,res)
704        res <- res1
705      }
706      ## now strip out any generics (which have value NULL in res):
707      res.not.null <- sapply(res,function(x){!is.null(x)})
708      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
709        res <- res[res.not.null]
710      }
711      res
712    ### named list of lists, one for each object to document.
713    }
714    
715    ### List of parsers to use by default with package.skeleton.dx.
716    default.parsers <-
717      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
718        sapply(forfun.parsers,forfun),
719        edit.package.file=function(desc,...){
720          in.details <- setdiff(colnames(desc),"Description")
721          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
722          L <-
723            list(list(title=desc[,"Title"],
724                      description=desc[,"Description"],
725                      `tabular{ll}`=details))
726          names(L) <- paste(desc[,"Package"],"-package",sep="")
727          L
728        },
729        sapply(forall.parsers,forall)
730        )
731    
732  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
733  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
734  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
735  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
736    ### the parent class.
737           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
738                          created="character", ##<< how created                          created="character", ##<< how created
739                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 513  Line 768 
768      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
769      default.description <- NULL      default.description <- NULL
770      while ( start > last.end+1      while ( start > last.end+1
771             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
772        start <- start-1        start <- start-1
773      }      }
774      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 540  Line 795 
795        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
796        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
797        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
798        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
799          parent <- chars[3]          parent <- chars[3]
800        }        }
801        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 572  Line 827 
827        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
828        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
829        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
830        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
831          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
832        }        }
833        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 613  Line 868 
868    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
869    ## following line.    ## following line.
870    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
871    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
872      ## also apply source parsing functions that I separated out into
873      ## separate functions
874      docs <- combine(docs,lonely$prefixed.lines(chunk.source))
875      docs$title <- lonely$title.from.firstline(chunk.source)
876      ##details<<
877      ## If there is no explicit title on the first line of setClass, then
878      ## one is made up from the class name.
879      if ( 0 == length(docs$title) ){
880        docs$title <- list(title=paste(class.name,"S4 class"))
881      }
882    ##details<<    ##details<<
883    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
884    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
# Line 638  Line 903 
903    invisible(docs)    invisible(docs)
904  }  }
905    
906  extract.docs.code <- function  apply.parsers <- function
907  ### Write code to a file and parse it to r objs, then run all the  ### Parse code to r objs, then run all the parsers and return the
908  ### parsers and return the documentation list.  ### documentation list.
909  (code,  (code,
910  ### Character vector of code lines.  ### Character vector of code lines.
911   parsers,   parsers=default.parsers,
912  ### List of Parser Functions.  ### List of Parser Functions.
913   verbose=TRUE,   verbose=FALSE,
914  ### Echo names of Parser Functions?  ### Echo names of Parser Functions?
915   ...   ...
916  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
917   ){   ){
   code.file <- tempfile()  
   writeLines(code,code.file)  
918    e <- new.env()    e <- new.env()
919    old <- options(keep.source.pkgs=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
920    tryCatch(suppressWarnings(sys.source(code.file,e)),error=function(e){    ## Error in assignClassDef(Class, classDef, where) :
921      stop("source ",code.file," failed with error:\n",e)    ##   Class "DocLink" has a locked definition in package "inlinedocs"
922    })    ## Traced to "where" argument in setClassDef which defaults to topenv()
923    options(old)    ## which in turn is inlinedocs when processing inlinedocs package, hence
924      ## the clash. The following works (under R 2.12.2), so that the topenv()
925      ## now finds e before finding the inlinedocs environment.
926      old <- options(keep.source=TRUE,topLevelEnvironment=e)
927      on.exit(options(old))
928      exprs <- parse(text=code)
929      ## TDH 2011-04-07 set this so that no warnings about creating a fake
930      ## package when we try to process S4 classes defined in code
931      e$.packageName <- "inlinedocs.processor"
932      for (i in exprs){
933          eval(i, e)
934      }
935    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
936    
   ## apply parsers in sequence to code and objs  
937    docs <- list()    docs <- list()
938    
939      ## apply parsers in sequence to code and objs
940      if(verbose)cat("Applying parsers:\n")
941    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
942      N <- names(parsers[i])      N <- names(parsers[i])
943      if(verbose){      if(verbose){
944        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
945          cat(N," ",sep="")          cat(N,"\n",sep="")
946        }else cat('. ')        }else cat('.\n')
947      }      }
948      p <- parsers[[i]]      p <- parsers[[i]]
949      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
950      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
951        #print(paste(L,"\n"))
952        #if(N=="exclude")browser()
953      docs <- combine(docs,L)      docs <- combine(docs,L)
954    }    }
955      ## post-process to collapse all character vectors
956      for(i in seq_along(docs)){
957        for(j in seq_along(docs[[i]])){
958          if(names(docs[[i]])[j]!=".s3method")
959          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
960        }
961     }
962    if(verbose)cat("\n")    if(verbose)cat("\n")
963    docs    return(docs)
964  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
965  }  }
966    
967    ### Names of Parser Functions that operate on the desc arg.
968    descfile.names <- c("author.from.description","edit.package.file")
969    
970    ### Names of Parser Functions that do NOT use the desc arg.
971    non.descfile.names <-
972      names(default.parsers)[!names(default.parsers)%in%descfile.names]
973    
974    ### Parsers that operate only on R code, independently of the
975    ### description file.
976    nondesc.parsers <- default.parsers[non.descfile.names]
977    
978    extract.docs.file <- structure(function
979    ### Apply all parsers relevant to extract info from just 1 code file.
980    (f,
981    ### File name of R code to read and parse.
982     parsers=NULL,
983    ### Parser Functions to use to parse the code and extract
984    ### documentation.
985     ...
986    ### Other arguments to pass to Parser Functions.
987     ){
988      if(is.null(parsers))parsers <- nondesc.parsers
989      apply.parsers(readLines(f),parsers,verbose=FALSE,...)
990    },ex=function(){
991      f <- system.file("silly","R","silly.R",package="inlinedocs")
992      extract.docs.file(f)
993    })
994    

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