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

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revision 87, Sat May 1 12:21:27 2010 UTC revision 303, Tue Jul 19 15:35:23 2011 UTC
# Line 1  Line 1 
1    ### combine lists or character strings
2    combine <- function(x,y)UseMethod("combine")
3    
4    ### combine character strings by pasting them together
5    combine.character <- function(x,y)
6        paste(x,y,sep="\n")
7    
8    ### combine lists by adding elements or adding to existing elements
9    combine.list <- function(x,y){
10      toadd <- if(".overwrite"%in%names(y)){
11        y <- y[names(y)!=".overwrite"]
12        rep(TRUE,length(y))
13      }else{
14        !names(y)%in%names(x)
15      }
16      toup <- names(y)[!toadd]
17      x[names(y)[toadd]] <- y[toadd]
18      for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
19      x
20    ### A list, same type as x, but with added elements from y.
21    }
22    
23    
24    getSource <- function
25    ### Extract a function's source code.
26    (fun.obj
27    ### A function.
28     ) {
29          srcref <- attr(fun.obj, "srcref")
30          if (!is.null(srcref)) unlist(strsplit(as.character(srcref), "\n"))
31          else attr(fun.obj, "source")
32    ### Source code lines as a character vector.
33    }
34    
35    ### Prefix for code comments used with grep and gsub.
36    prefix <- "^[ \t]*###[ \t]*"
37    
38    decomment <- function
39    ### Remove comment prefix and join lines of code to form a
40    ### documentation string.
41    (comments
42    ### Character vector of prefixed comment lines.
43     ){
44      gsub(prefix,"",comments)
45    ### String without prefixes or newlines.
46    }
47    
48    forall <- function
49  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
50  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
51  ### documentation list.  ### documentation list.
 forall <- function  
52  (FUN,  (FUN,
53  ### Function to apply to each element in the package.  ### Function to apply to each element in the package.
54   subfun=function(x)TRUE   subfun=function(x)TRUE
# Line 9  Line 56 
56  ### 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
57  ### the result will be returned.  ### the result will be returned.
58   ){   ){
59    function(objs,docs,...){    FUN <- FUN
60      f <- function(objs,docs,...){
61        if(length(objs)==0)return(list())
62      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
63      L <- list()      L <- list()
64      for(N in names(objs)){      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
65        for(N in union(names(docs),names(objs))){
66        o <- objs[[N]]        o <- objs[[N]]
67        L[[N]] <- FUN(src=attr(o,"source"),name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)        L[[N]] <- FUN(src=getSource(o),
68                        name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
69      }      }
70        on.exit()## remove warning message
71      L      L
72    }    }
73      class(f) <- c("allfun","function")
74      f
75  ### A Parser Function.  ### A Parser Function.
76  }  }
77    
78    ### Print method for functions constructed using forall.
79    print.allfun <- function(x,...){
80      e <- environment(x)
81      cat("Function to apply to every element.\nselector:")
82      print(e$subfun)
83      cat("processor:")
84      print(e$FUN)
85    }
86    
87  ### For each function in the package, do something.  ### For each function in the package, do something.
88  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
89    
90  ### Get last line (test)  kill.prefix.whitespace <- function
91  parsefuns <- forfun(function(src,name,...){  ### Figure out what the whitespace preceding the example code is, and
92    extract.docs.fun(src,name)  ### then delete that from every line.
93  })  (ex
94    ### character vector of example code lines.
 ### Fill in author from DESCRIPTION and titles.  
 author.from.description <- forall(function(desc,...){  
   list(author=desc[,"Maintainer"])  
 })  
   
 ### The format section sometimes causes problems, so erase it.  
 erase.format <- forall(function(...){  
   list(format="")  
 })  
   
 ### Convert the function name to a title.  
 title.from.name <- forall(function(name,...){  
   list(title=gsub("[._]"," ",name))  
 })  
   
 ### Get examples for FUN from the file test/FUN.R  
 examples.from.testfile <- 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 <- forfun(function(src,...){  
   rline <- grep("return([^)]*)",src)  
   if(length(rline)==0)return(list())  
   rline <- rline[length(rline)]  
   comment.line.nums <- grep(prefix,src)  
   if(!(comment.end <- rline+1)%in%comment.line.nums)return(list())  
   while(comment.end%in%comment.line.nums)comment.end <- comment.end+1  
   excode <- src[comment.end:(length(src)-1)]  
   list(examples=paste(gsub("^\\W*","",excode),collapse="\n"))  
 })  
   
 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))  
95                ){                ){
96        ## phew - this should only pick up R.oo S3 generic definitions like:    tlines <- gsub("\\s*","",ex)
97        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"    ##tlines <- gsub("#.*","",tlines)
98        NULL    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
99      } else res    FIND <- prefixes[which.min(nchar(prefixes))]
100    }    ## Eliminate leading tabulations or 2/4 spaces
101    doc.names <- names(objs)    sub(FIND, "", ex)
102    res <- sapply(doc.names,extract.docs,simplify=FALSE)  ### Character vector of code lines with preceding whitespace removed.
103    ## Special processing for S4 classes as they do not appear in normal ls()  }
104    for ( nn in names(parsed) ){  
105      if ( parsed[[nn]]@created == "setClass" ){  prefixed.lines <- structure(function(src,...){
106        S4class.docs <- extract.docs.setClass(parsed[[nn]])  ### The primary mechanism of inline documentation is via consecutive
107        docname <- paste(nn,"class",sep="-")  ### groups of lines matching the specified prefix regular expression
108        if ( is.null(res[[docname]]) ){  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
109          res[[docname]] <- S4class.docs  ### collected as follows into documentation sections:\describe{
110          doc.names <- c(doc.names,docname)  ### \item{description}{group starting at line 2 in the code}
111        } else {  ### \item{arguments}{group following each function argument}
112          stop(nn," appears as both S4 class and some other definition")  ### \item{value}{group ending at the penultimate line of the code}}
113        }  ### These may be added to by use of the \code{##<<} constructs
114      }  ### described below.
115    }    clines <- grep(prefix,src)
116    inherit.docs <- function(on){    if(length(clines)==0)return(list())
     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.  
 }  
   
 ### Default parsers to use with package.skeleton.dx  
 default.parsers <- list("parsefuns","extract.docs.file",  
                         "examples.after.return","examples.from.testfile",  
                         "author.from.description","erase.format","title.from.name")  
   
 extract.docs.fun <- function # Extract documentation from a function  
 ### Given source code of a function, return a list describing inline  
 ### documentation in that source code.  
 (code,  
 ### The function to examine.  
  name.fun  
 ### The name of the function/chunk to use in warning messages.  
  )  
 {  
   res <- list()  
   clines <- grep(prefix,code)  
   if(length(grep("#",code[1]))){  
     res$title <- gsub("[^#]*#\\s*(.*)","\\1",code[1],perl=TRUE)  
   }  
   if(length(clines) > 0){  
     ##details<<  
     ## The primary mechanism is that consecutive groups of lines matching  
     ## the specified prefix regular expression "\code{^### }" (i.e. lines  
     ## beginning with "\code{### }") are collected  
     ## as follows into documentation sections:\describe{  
     ## \item{description}{group starting at line 2 in the code}  
     ## \item{arguments}{group following each function argument}  
     ## \item{value}{group ending at the penultimate line of the code}}  
     ## These may be added to by use of the \code{##<<} constructs described  
     ## below.  
117      bounds <- which(diff(clines)!=1)      bounds <- which(diff(clines)!=1)
118      starts <- c(1,bounds+1)      starts <- c(1,bounds+1)
119      ends <- c(bounds,length(clines))      ends <- c(bounds,length(clines))
120      ## detect body of function using paren matching
121      code <- gsub("#.*","",src)
122      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
123      parens <- f("(")-f(")")
124      body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
125      if(length(body.begin)==0)body.begin <- 1 ## rare cases
126      is.arg <- function(){
127        gres <- grep("^\\s*#",src[start-1],perl=TRUE)
128        0 == length(gres) && start<=body.begin
129      }
130      res <- list()
131      for(i in seq_along(starts)){      for(i in seq_along(starts)){
132        start <- clines[starts[i]]        start <- clines[starts[i]]
133        end <- clines[ends[i]]        end <- clines[ends[i]]
134        lab <- if(end+1==length(code))"value"      lab <- if(all(gsub("[ }]","",src[(end+1):length(src)])==""))"value"
135        else if(start==2)"description"        else if(start==2)"description"
136        else if ( 0 == length(grep("^\\s*#",code[start-1],perl=TRUE)) ){      else if(is.arg()){
137           #arg <- gsub("^[ (]*","",code[start-1])        ##twutz: strip leading white spaces and brackets and ,
138           #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 ,  
139                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
140                   arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)   #twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
141          arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
142                   arg <- gsub("...", "\\dots", arg, fix = TRUE)                   arg <- gsub("...", "\\dots", arg, fix = TRUE)
143           paste("item{",arg,"}",sep="")           paste("item{",arg,"}",sep="")
144         } else {         } else {
145           next;           next;
146         }         }
147        res[[lab]] <- decomment(code[start:end])      res[[lab]] <- decomment(src[start:end])
     }  
148    }    }
149      res
150    },ex=function(){
151    test <- function
152    ### the description
153    (x,
154    ### the first argument
155     y ##<< another argument
156     ){
157      5
158    ### the return value
159    ##seealso<< foobar
160    }
161    src <- getSource(test)
162    prefixed.lines(src)
163    extract.xxx.chunks(src)
164    })
165    
166    extract.xxx.chunks <- function # Extract documentation from a function
167    ### Given source code of a function, return a list describing inline
168    ### documentation in that source code.
169    (src,
170    ### The source lines of the function to examine, as a character
171    ### vector.
172     name.fun="(unnamed function)",
173    ### The name of the function/chunk to use in warning messages.
174     ...
175    ### ignored.
176     ){
177      res <- list()
178    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
179    ## documented by appending \code{##<<} comments on the same line as the    ## documented by appending \code{##<<} comments on the same line as the
180    ## argument name. Mixing this mechanism with \code{###} comment lines for    ## argument name. Mixing this mechanism with \code{###} comment lines for
# Line 300  Line 247 
247          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
248        }        }
249        chunk.res <- NULL        chunk.res <- NULL
250        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
251          chunk.res <-          chunk.res <-
252            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
253            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
254        invisible(chunk.res)        invisible(chunk.res)
255      }      }
256    while ( k <= length(code) ){    while ( k <= length(src) ){
257      line <- code[k]      line <- src[k]
258      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
259        ## 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
260        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
261        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
# Line 383  Line 330 
330            first.describe <- TRUE;            first.describe <- TRUE;
331          }          }
332        }        }
333      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
334        ## append this line to current chunk        ## append this line to current chunk
335        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
336          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
337          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
338          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 398  Line 345 
345            payload <- stripped            payload <- stripped
346          }          }
347        }        }
348      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
349        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
350        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
351          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 407  Line 354 
354        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
355        in.chunk <- TRUE        in.chunk <- TRUE
356        if ( not.describe ){        if ( not.describe ){
357            ## TDH 2010-06-18 For item{}s in the documentation list names,
358            ## we don't need to have a backslash before, so delete it.
359            arg <- gsub("^[\\]+","",arg)
360          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
361          payload <- comment          payload <- comment
362        } else {        } else {
# Line 457  Line 407 
407  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
408  }  }
409    
410    leadingS3generic <- function # check whether function name is an S3 generic
411    ### Determines whether a function name looks like an S3 generic function
412    (name,                     ##<< name of function
413     env,                      ##<< environment to search for additional generics
414     ...)                      ##<< ignored here
415    {
416      ##details<< This function is one of the default parsers, but exposed as
417      ## possibly of more general interest. Given a function name of the form
418      ## x.y.z it looks for the generic function x applying to objects of class
419      ## y.z and also for generic function x.y applying to objects of class z.
420      ##
421      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
422      l <- length(parts)
423      if (l > 1) {
424        for (i in 1:(l - 1)) {
425          ## Look for a generic function (known by the system or defined
426          ## in the package) that matches that part of the function name
427          generic <- paste(parts[1:i], collapse = ".")
428          if (any(generic %in% utils:::getKnownS3generics()) ||
429              utils:::findGeneric(generic, env) != "") {
430            object <- paste(parts[(i + 1):l], collapse = ".")
431            ##details<< Assumes that the first name which matches any known
432            ## generics is the target generic function, so if both x and x.y
433            ## are generic functions, will assume generic x applying to objects
434            ## of class y.z
435            ##value<< If a matching generic found returns a list with a single component:
436            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
437          }
438        }
439      }
440      ##value<< If no matching generic functions are found, returns an empty list.
441      list()
442    }
443    
444    ### Parsers for each function that are constructed automatically. This
445    ### is a named list, and each element is a parser function for an
446    ### individual object.
447    forfun.parsers <-
448      list(prefixed.lines=prefixed.lines,
449           extract.xxx.chunks=extract.xxx.chunks,
450           ## title from first line of function def
451           title.from.firstline=function(src,...){
452             first <- src[1]
453             if(!is.character(first))return(list())
454             if(!grepl("#",first))return(list())
455             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
456           },
457           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
458           ## please, let me choose which dir to use for examples!
459           ## Get examples for FUN from the file tests/FUN.R
460           examples.from.testfile=function(name,...){
461             tsubdir <- getOption("inlinedocs.exdir")
462             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
463             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
464             if(file.exists(tfile))
465               list(examples=readLines(tfile))
466             else list()
467           },
468           definition.from.source=function(doc,src,...){
469             def <- doc$definition
470             is.empty <- function(x)is.null(x)||x==""
471             if(is.empty(def) && !is.empty(src))
472               list(definition=src)
473             else list()
474           })
475    
476    ### List of Parser Functions that can be applied to any object.
477    forall.parsers <-
478      list(## Fill in author from DESCRIPTION and titles.
479           author.from.description=function(desc,...){
480             list(author=desc[,"Maintainer"])
481           },
482           ## The format section sometimes causes problems, so erase it.
483           erase.format=function(...){
484             list(format="")
485           },
486           ## Convert the function name to a title.
487           title.from.name=function(name,doc,...){
488             if("title"%in%names(doc))list() else
489             list(title=gsub("[._]"," ",name))
490           },
491           ## PhG: here is what I propose for examples code in the 'ex' attribute
492           examples.in.attr =  function (name, o, ...) {
493             ex <- attr(o, "ex")
494             if (!is.null(ex)) {
495               ## Special case for code contained in a function
496               if (inherits(ex, "function")) {
497                 ## If source is available, start from there
498                 src <- getSource(ex)
499                 if (!is.null(src)) {
500                   ex <- src
501                 } else { ## Use the body of the function
502                   ex <- deparse(body(ex))
503                 }
504                 ## Eliminate leading and trailing code
505                 ex <- ex[-c(1, length(ex))]
506                 if(ex[1]=="{")ex <- ex[-1]
507                 ## all the prefixes
508                 ex <- kill.prefix.whitespace(ex)
509                 ## Add an empty line before and after example
510                 ex <- c("", ex, "")
511               }
512               list(examples = ex)
513             } else list()
514           },collapse=function(doc,...){
515             L <- lapply(doc,paste,collapse="\n")
516             L$.overwrite <- TRUE
517             L
518           },tag.s3methods=leadingS3generic
519           )
520    
521    ### List of parser functions that operate on single objects. This list
522    ### is useful for testing these functions.
523    lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
524      f <- function # title
525    ### description
526      (x, ##<< arg x
527       y
528    ### arg y
529       ){
530        ##value<< a list with elements
531        list(x=x, ##<< original x value
532             y=y, ##<< original y value
533             sum=x+y) ##<< their sum
534        ##end<<
535      }
536      src <- getSource(f)
537      lonely$extract.xxx.chunks(src)
538      lonely$prefixed.lines(src)
539    })
540    
541    extra.code.docs <- function # Extract documentation from code chunks
542    ### Parse R code to extract inline documentation from comments around
543    ### each function. These are not able to be retreived simply by
544    ### looking at the "source" attribute. This is a Parser Function that
545    ### can be used in the parser list of package.skeleton.dx(). TODO:
546    ### Modularize this into separate Parsers Functions for S4 classes,
547    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
548    (code,
549    ### Code lines in a character vector containing multiple R objects to
550    ### parse for documentation.
551     objs,
552    ### The objects defined in the code.
553     ...
554    ### ignored
555     ){
556      parsed <- extract.file.parse(code)
557      extract.docs.try <- function(o,on)
558        {
559          ## Note: we could use parsed information here too, but that
560          ## would produce different results for setMethodS3 etc.
561          doc <- list()
562          if ( !is.null(parsed[[on]]) ){
563            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
564              doc$definition <- paste(parsed[[on]]@code)
565            }
566            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
567              doc$description <- parsed[[on]]@description
568            }
569            ## if ( "setMethodS3" == parsed[[on]]@created ){
570            ##   gen <- leadingS3generic(on,topenv())
571            ##   if ( 0 < length(gen) ){
572            ##     doc$.s3method <- gen$.s3method
573            ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
574            ##   }
575            ## }
576          }
577          if("title" %in% names(doc) && !"description" %in% names(doc) ){
578            ## For short functions having both would duplicate, but a
579            ## description is required. Therefore automatically copy title
580            ## across to avoid errors at package build time.
581            doc$description <- doc$title
582          }
583          doc
584        }
585      extract.docs <- function(on){
586        res <- try({o <- objs[[on]]
587                    extract.docs.try(o, on)},FALSE)
588        if(class(res)=="try-error"){
589          cat("Failed to extract docs for: ",on,"\n\n")
590          list()
591        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
592          NULL
593        } else if(0 == length(res) && "function" %in% class(o)
594                  && 1 == length(osource <- getSource(o))
595                  && grepl(paste("UseMethod(",on,")",sep="\""),osource)
596                  ){
597          ## phew - this should only pick up R.oo S3 generic definitions like:
598          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
599          NULL
600        } else res
601      }
602      doc.names <- names(objs)
603      res <- sapply(doc.names,extract.docs,simplify=FALSE)
604      ## Special processing for S4 classes as they do not appear in normal ls()
605      for ( nn in names(parsed) ){
606        if ( parsed[[nn]]@created == "setClass" ){
607          S4class.docs <- extract.docs.setClass(parsed[[nn]])
608          docname <- paste(nn,"class",sep="-")
609          if ( is.null(res[[docname]]) ){
610            res[[docname]] <- S4class.docs
611            doc.names <- c(doc.names,docname)
612          } else {
613            stop(nn," appears as both S4 class and some other definition")
614          }
615        }
616      }
617      inherit.docs <- function(on){
618        in.res <- res[[on]]
619        if ( !is.null(parsed[[on]]) ){
620          for ( parent in parsed[[on]]@parent ){
621            if ( !is.na(parent) ){
622              if ( is.null(in.res) ){
623                in.res <- res[[parent]]
624              } else if ( parent %in% names(res) ){
625                parent.docs <- res[[parent]]
626                for ( nn in names(parent.docs) ){
627                  if ( !nn %in% names(in.res) ){
628                    in.res[[nn]] <- parent.docs[[nn]]
629                  }
630                }
631              }
632            }
633          }
634        }
635        invisible(in.res)
636      }
637      all.done <- FALSE
638      while ( !all.done ){
639        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
640        all.done <- identical(res1,res)
641        res <- res1
642      }
643      ## now strip out any generics (which have value NULL in res):
644      res.not.null <- sapply(res,function(x){!is.null(x)})
645      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
646        res <- res[res.not.null]
647      }
648      res
649    ### named list of lists, one for each object to document.
650    }
651    
652    ### List of parsers to use by default with package.skeleton.dx.
653    default.parsers <-
654      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
655        sapply(forfun.parsers,forfun),
656        edit.package.file=function(desc,...){
657          in.details <- setdiff(colnames(desc),"Description")
658          details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
659          L <-
660            list(list(title=desc[,"Title"],
661                      description=desc[,"Description"],
662                      `tabular{ll}`=details))
663          names(L) <- paste(desc[,"Package"],"-package",sep="")
664          L
665        },
666        sapply(forall.parsers,forall)
667        )
668    
669  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
670  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
671  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
672  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
673    ### the parent class.
674           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
675                          created="character", ##<< how created                          created="character", ##<< how created
676                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 495  Line 705 
705      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
706      default.description <- NULL      default.description <- NULL
707      while ( start > last.end+1      while ( start > last.end+1
708             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
709        start <- start-1        start <- start-1
710      }      }
711      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 522  Line 732 
732        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
733        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
734        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
735        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
736          parent <- chars[3]          parent <- chars[3]
737        }        }
738        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 554  Line 764 
764        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
765        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
766        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
767        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
768          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
769        }        }
770        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 574  Line 784 
784  ### Using the same conventions as for functions, definitions of S4 classes  ### Using the same conventions as for functions, definitions of S4 classes
785  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
786  ### scanned for inline comments.  ### scanned for inline comments.
787  (doc.link)  (doc.link
788  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{\link{extract.file.parse}}.
789  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
790  ### class definitions.  ### class definitions.
791  {   ){
792    chunk.source <- doc.link@code    chunk.source <- doc.link@code
793    ##details<<    ##details<<
794    ## Extraction of S4 class documentation is currently limited to expressions    ## Extraction of S4 class documentation is currently limited to expressions
# Line 595  Line 805 
805    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
806    ## following line.    ## following line.
807    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
808    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
809      ## also apply source parsing functions that I separated out into
810      ## separate functions
811      docs <- combine(docs,lonely$prefixed.lines(chunk.source))
812      docs$title <- lonely$title.from.firstline(chunk.source)
813    ##details<<    ##details<<
814    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
815    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
# Line 619  Line 833 
833    }    }
834    invisible(docs)    invisible(docs)
835  }  }
836    
837    apply.parsers <- function
838    ### Parse code to r objs, then run all the parsers and return the
839    ### documentation list.
840    (code,
841    ### Character vector of code lines.
842     parsers=default.parsers,
843    ### List of Parser Functions.
844     verbose=FALSE,
845    ### Echo names of Parser Functions?
846     ...
847    ### Additional arguments to pass to Parser Functions.
848     ){
849      e <- new.env()
850      ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
851      ## Error in assignClassDef(Class, classDef, where) :
852      ##   Class "DocLink" has a locked definition in package "inlinedocs"
853      ## Traced to "where" argument in setClassDef which defaults to topenv()
854      ## which in turn is inlinedocs when processing inlinedocs package, hence
855      ## the clash. The following works (under R 2.12.2), so that the topenv()
856      ## now finds e before finding the inlinedocs environment.
857      old <- options(keep.source=TRUE,topLevelEnvironment=e)
858      on.exit(options(old))
859      exprs <- parse(text=code)
860      ## TDH 2011-04-07 set this so that no warnings about creating a fake
861      ## package when we try to process S4 classes defined in code
862      e$.packageName <- "inlinedocs.processor"
863      for (i in exprs){
864        ## TDH 2011-04-07 Disable this tryCatch since it makes it harder
865        ##to debug errors/warnings in the evaluated code
866    
867        ##tryCatch({
868          eval(i, e)
869        ##},error=function(e){
870          ##print(e)
871        ##})
872      }
873      objs <- sapply(ls(e),get,e,simplify=FALSE)
874    
875      docs <- list()
876    
877      ## apply parsers in sequence to code and objs
878      for(i in seq_along(parsers)){
879        N <- names(parsers[i])
880        if(verbose){
881          if(is.character(N) && N!=""){
882            cat(N," ",sep="")
883          }else cat('. ')
884        }
885        p <- parsers[[i]]
886        ## This is the argument list that each parser receives:
887        L <- p(code=code,objs=objs,docs=docs,env=e,...)
888        docs <- combine(docs,L)
889      }
890      ## post-process to collapse all character vectors
891      for(i in seq_along(docs)){
892        for(j in seq_along(docs[[i]])){
893          if(names(docs[[i]])[j]!=".s3method")
894          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
895        }
896      }
897      if(verbose)cat("\n")
898      docs
899    ### A list of extracted documentation from code.
900    }
901    
902    ### Names of Parser Functions that operate on the desc arg.
903    descfile.names <- c("author.from.description","edit.package.file")
904    
905    ### Names of Parser Functions that do NOT use the desc arg.
906    non.descfile.names <-
907      names(default.parsers)[!names(default.parsers)%in%descfile.names]
908    
909    ### Parsers that operate only on R code, independently of the
910    ### description file.
911    nondesc.parsers <- default.parsers[non.descfile.names]
912    
913    extract.docs.file <- structure(function
914    ### Apply all parsers relevant to extract info from just 1 code file.
915    (f,
916    ### File name of R code to read and parse.
917     parsers=NULL,
918    ### Parser Functions to use to parse the code and extract
919    ### documentation.
920     ...
921    ### Other arguments to pass to Parser Functions.
922     ){
923      if(is.null(parsers))parsers <- nondesc.parsers
924      apply.parsers(readLines(f),parsers,verbose=FALSE,...)
925    },ex=function(){
926      f <- system.file("silly","R","silly.R",package="inlinedocs")
927      extract.docs.file(f)
928    })
929    

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