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

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revision 104, Tue May 18 16:35:08 2010 UTC revision 158, Mon Nov 8 12:26:12 2010 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 <- !names(y)%in%names(x)
11      toup <- names(y)[names(y)%in%names(x)]
12      x[names(y)[toadd]] <- y[toadd]
13      for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
14      return(x)
15    ### A list, same type as x, but with added elements from y.
16    }
17    
18    ### Prefix for code comments used with grep and gsub.
19    prefix <- "^[ \t]*###[ \t]"
20    
21    decomment <- function
22    ### Remove comment prefix and join lines of code to form a
23    ### documentation string.
24    (comments
25    ### Character vector of prefixed comment lines.
26     ){
27      paste(gsub(prefix,"",comments),collapse="\n")
28    ### String without prefixes or newlines.
29    }
30    
31  ### For each object in the package that satisfies the criterion  ### For each object in the package that satisfies the criterion
32  ### checked by subfun, parse source using FUN and return the resulting  ### checked by subfun, parse source using FUN and return the resulting
33  ### documentation list.  ### documentation list.
# Line 9  Line 39 
39  ### 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
40  ### the result will be returned.  ### the result will be returned.
41   ){   ){
42    function(objs,docs,...){    FUN <- FUN
43      f <- function(objs,docs,...){
44      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
45      L <- list()      L <- list()
46      for(N in names(docs)){      for(N in names(docs)){
# Line 19  Line 50 
50      }      }
51      L      L
52    }    }
53      class(f) <- c("allfun","function")
54      f
55  ### A Parser Function.  ### A Parser Function.
56  }  }
57    
58    ### Print method for functions constructed using forall.
59    print.allfun <- function(x,...){
60      e <- environment(x)
61      cat("Function to apply to every element.\nselector:")
62      print(e$subfun)
63      cat("processor:")
64      print(e$FUN)
65    }
66    
67  ### For each function in the package, do something.  ### For each function in the package, do something.
68  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
69    
70  ### Parsers for each object/function that are constructed  examples.after.return <- function
71  ### automatically. This is a named list, each element is a list of 2  ### Get examples from inline definitions after return()
72  ### elements: forfun/forall, then a parser function for an individual  ### PhG: this does not work well! Think of these situations:
73  ### object.  ### 1) You have multiple return() in the code of your function,
74  forall.parsers <-  ### 2) You have return() appearing is some example code, ...
75    list(## Extract lots of info from normal functions.  ### I can hardly propose a hack here. The whole code of the function
76         parsefun=list(forfun,function(src,name,...){  ### must be parsed, and one must determine which one is the last line
77           extract.docs.fun(src,name)  ### of code that is actually executed.
78         }),  ###
79         ## Fill in author from DESCRIPTION and titles.  ### I make two propositions here
80         author.from.description=list(forall,function(desc,...){  ### 1) to keep the same mechanism that has the advantage of simplicity
81           list(author=desc[,"Maintainer"])  ###    but to use a special tag
82         }),  ###    ##examples<< or #{{{examples to separate
83         ## The format section sometimes causes problems, so erase it.  ###    function code from examples explicitly, and
84         erase.format=list(forall,function(...){  ### 2) to place the example in an "ex" attribute
85           list(format="")  ###    attached to the function
86         }),  ###    (see next parser). That solution will be also interesting for
87         ## Convert the function name to a title.  ###    documenting datasets, something not done yet by inlinedocs!
88         title.from.name=list(forall,function(name,doc,...){  (src,name="",...) {
89           if("title"%in%names(doc))list() else    ## Look for the examples mark
90           list(title=gsub("[._]"," ",name))    m <- grep("^\\s*(##examples<<|#\\{\\{\\{examples)", src)
91         }),    if (!length(m)) return(list())
92         ## Get examples for FUN from the file test/FUN.R    if (length(m) > 1)
93         examples.from.testfile=list(forfun,function(name,...){      warning("More than one examples tag for ", name,
94           tfile <- file.path("..","tests",paste(name,".R",sep=""))              ". Taking the last one")
95           if(file.exists(tfile))    m <- m[length(m)]
96             list(examples=paste(readLines(tfile),collapse="\n"))    ## Look for the lines containing return value comments just before
97           else list()    r <- grep("\\s*### ", src[1:(m-1)])
98         }),      if (!length(r)) {
99         ## Get examples from inline definitions after return()        value <- NULL
100         examples.after.return=list(forfun,function(name,src,...){      } else {
101           coll <- paste(src,collapse="\n")        ## Only take consecutive lines before the mark
102           thispre <- gsub("^[\\^]","",prefix)        keep <- rev((m - rev(r)) == 1:length(r))
103           FIND <- paste("(return|UseMethod)[(][^\\n]*\\n",thispre,sep="")        if (!any(keep)) {
104           m <- regexpr(FIND,coll)          value <- NULL
105           if(m[1]==-1)return(list())        } else {
106           after <- substr(coll,m[1],nchar(coll))          value <- decomment(src[r[keep]])
107           FIND <-        }
108             paste("[^\\n]*",# rest of the return line      }
109                   "((?:\\n###[^\\n]*)+)",#comment value lines \\1    ## Collect now the example code beneath the mark
110                   "([\\w\\W]*)[}]",#examples \\2    ex <- src[(m + 1):(length(src) - 1)]
111                   sep="")    ## Possibly eliminate a #}}} tag
112           SEP <- "-/-/-/-/-=====-----"    ex <- ex[!grepl("#}}}", ex)]
113           REP <- paste("\\1",SEP,"\\2",sep="")    ## Eliminate leading tabulations or four spaces
114           r <- strsplit(gsub(FIND,REP,after,perl=TRUE),split=SEP)[[1]]    prefixes <- gsub("(\\s*).*","\\1",ex,perl=TRUE)[grep("\\w",ex)]
          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)]  
115           FIND <- prefixes[which.min(nchar(prefixes))]           FIND <- prefixes[which.min(nchar(prefixes))]
116           list(examples=paste(sub(FIND,"",excode),collapse="\n"),    ex <- sub(FIND,"",ex)
117                value=decomment(l[[1]][-1]))    ## Add an empty line before and after example
118         }))    ex <- c("", ex, "")
119      ## Return examples and value
120  ### List of parser functions that operate on single objects. This list    list(examples = paste(ex, collapse = "\n"), value = value)
121  ### is useful for testing these functions, ie  }
122  ### lonely$parsefun(attr(extract.docs.file,"source"),"extract.docs.file")  
123  lonely <- sapply(forall.parsers,function(L)L[[2]])  prefixed.lines <- function(src,...){
124    ### The primary mechanism of inline documentation is via consecutive
125  extract.docs.file <- function # Extract documentation from a file  ### groups of lines matching the specified prefix regular expression
126  ### Parse R code to extract inline documentation from comments around  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
127  ### each function. These are not able to be retreived simply by  ### collected as follows into documentation sections:\describe{
128  ### looking at the "source" attribute. This is a Parser Function that  ### \item{description}{group starting at line 2 in the code}
129  ### can be used in the parser list of package.skeleton.dx().  ### \item{arguments}{group following each function argument}
130  (code,  ### \item{value}{group ending at the penultimate line of the code}}
131  ### Code lines in a character vector containing multiple R objects to  ### These may be added to by use of the \code{##<<} constructs
132  ### parse for documentation.  ### described below.
133   objs,    clines <- grep(prefix,src)
134  ### The objects defined in the code.    if(length(clines)==0)return(list())
  ...  
 ### ignored  
  ){  
   parsed <- extract.file.parse(code)  
   extract.docs.try <- function(o,on)  
     {  
       ## Note: we could use parsed information here too, but that  
       ## would produce different results for setMethodS3 etc.  
       doc <- list()  
       if ( !is.null(parsed[[on]]) ){  
         if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics  
           doc$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.  
 }  
   
 ### List of parsers to use by default with package.skeleton.dx.  
 default.parsers <- c(extract.docs.file=extract.docs.file,  
                      sapply(forall.parsers,function(L)L[[1]](L[[2]])))  
   
 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.  
135      bounds <- which(diff(clines)!=1)      bounds <- which(diff(clines)!=1)
136      starts <- c(1,bounds+1)      starts <- c(1,bounds+1)
137      ends <- c(bounds,length(clines))      ends <- c(bounds,length(clines))
138      ## detect body of function using paren matching
139      f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",src)))
140      parens <- f("(")-f(")")
141      body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
142      is.arg <- function(){
143        0 == length(grep("^\\s*#",src[start-1],perl=TRUE)) &&
144          start<=body.begin
145        }
146      res <- list()
147      for(i in seq_along(starts)){      for(i in seq_along(starts)){
148        start <- clines[starts[i]]        start <- clines[starts[i]]
149        end <- clines[ends[i]]        end <- clines[ends[i]]
150        lab <- if(end+1==length(code))"value"      lab <- if(end+1==length(src))"value"
151        else if(start==2)"description"        else if(start==2)"description"
152        else if ( 0 == length(grep("^\\s*#",code[start-1],perl=TRUE)) ){      else if(is.arg()){
153           #arg <- gsub("^[ (]*","",code[start-1])        ##twutz: strip leading white spaces and brackets and ,
154           #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 ,  
155                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)                   arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
156                   arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)   #twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
157          arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
158                   arg <- gsub("...", "\\dots", arg, fix = TRUE)                   arg <- gsub("...", "\\dots", arg, fix = TRUE)
159           paste("item{",arg,"}",sep="")           paste("item{",arg,"}",sep="")
160         } else {         } else {
161           next;           next;
162         }         }
163        res[[lab]] <- decomment(code[start:end])      res[[lab]] <- decomment(src[start:end])
164      }      }
165      res
166    }    }
167    
168    extract.xxx.chunks <- function # Extract documentation from a function
169    ### Given source code of a function, return a list describing inline
170    ### documentation in that source code.
171    (src,
172    ### The source lines of the function to examine, as a character
173    ### vector.
174     name.fun="(unnamed function)",
175    ### The name of the function/chunk to use in warning messages.
176     ...
177    ### ignored.
178     ){
179      res <- list()
180    ##details<< For simple functions/arguments, the argument may also be    ##details<< For simple functions/arguments, the argument may also be
181    ## documented by appending \code{##<<} comments on the same line as the    ## documented by appending \code{##<<} comments on the same line as the
182    ## argument name. Mixing this mechanism with \code{###} comment lines for    ## argument name. Mixing this mechanism with \code{###} comment lines for
# Line 324  Line 255 
255            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
256        invisible(chunk.res)        invisible(chunk.res)
257      }      }
258    while ( k <= length(code) ){    while ( k <= length(src) ){
259      line <- code[k]      line <- src[k]
260      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){
261        ## 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
262        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
# Line 425  Line 356 
356        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)        arg <- gsub(arg.pat,"\\\\item\\{\\1\\}",line,perl=TRUE)
357        in.chunk <- TRUE        in.chunk <- TRUE
358        if ( not.describe ){        if ( not.describe ){
359            ## TDH 2010-06-18 For item{}s in the documentation list names,
360            ## we don't need to have a backslash before, so delete it.
361            arg <- gsub("^[\\]+","",arg)
362          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots
363          payload <- comment          payload <- comment
364        } else {        } else {
# Line 475  Line 409 
409  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
410  }  }
411    
412    ### Parsers for each function that are constructed automatically. This
413    ### is a named list, and each element is a parser function for an
414    ### individual object.
415    forfun.parsers <-
416      list(prefixed.lines=prefixed.lines,
417           examples.after.return=examples.after.return,
418           extract.xxx.chunks=extract.xxx.chunks,
419           ## title from first line of function def
420           title.from.firstline=function(src,name,code,...){
421             if(length(grep("#",src[1]))){
422               list(title=gsub("[^#]*#\\s*(.*)","\\1",src[1],perl=TRUE))
423             } else list()
424           },
425           ## PhG: it is tests/FUN.R!!! I would like more flexibility here
426           ## please, let me choose which dir to use for examples!
427           ## Get examples for FUN from the file tests/FUN.R
428           examples.from.testfile=function(name,...){
429             tsubdir <- getOption("inlinedocs.exdir")
430             if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
431             tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
432             if(file.exists(tfile))
433               list(examples=paste(readLines(tfile),collapse="\n"))
434             else list()
435           },
436           definition.from.source=function(doc,src,...){
437             def <- doc$definition
438             is.empty <- function(x)is.null(x)||x==""
439             if(is.empty(def) && !is.empty(src))
440               list(definition=paste(src,collapse="\n"))
441             else list()
442           })
443    
444    ### List of Parser Functions that can be applied to any object.
445    forall.parsers <-
446      list(## Fill in author from DESCRIPTION and titles.
447           author.from.description=function(desc,...){
448             list(author=desc[,"Maintainer"])
449           },
450           ## The format section sometimes causes problems, so erase it.
451           erase.format=function(...){
452             list(format="")
453           },
454           ## Convert the function name to a title.
455           title.from.name=function(name,doc,...){
456             if("title"%in%names(doc))list() else
457             list(title=gsub("[._]"," ",name))
458           },
459           ## PhG: here is what I propose for examples code in the 'ex' attribute
460           examples.in.attr =  function (name, o, ...) {
461             ex <- attr(o, "ex")
462             if (!is.null(ex)) {
463               ## Special case for code contained in a function
464               if (inherits(ex, "function")) {
465                 ## If source is available, start from there
466                 src <- attr(ex, "source")
467                 if (!is.null(src)) {
468                   ex <- src
469                 } else { ## Use the body of the function
470                   ex <- deparse(body(ex))
471                 }
472                 ## Eliminate leading and trailing code
473                 ex <- ex[-c(1, length(ex))]
474                 ## Eliminate leading tabulations or 2/4 spaces
475                 ex <- sub("^\t|    |  ", "", ex)
476                 ## Add an empty line before and after example
477                 ex <- c("", ex, "")
478               }
479               list(examples = paste(ex, collapse = "\n"))
480             } else list()
481           })
482    
483    ### List of parser functions that operate on single objects. This list
484    ### is useful for testing these functions.
485    lonely <- c(forall.parsers,forfun.parsers)
486    attr(lonely,"ex") <- function(){
487      f <- function # title
488    ### description
489      (x, ##<< arg x
490       y
491    ### arg y
492       ){
493        ##value<< a list with elements
494        list(x=x, ##<< original x value
495             y=y, ##<< original y value
496             sum=x+y) ##<< their sum
497        ##end<<
498      }
499      src <- attr(f,"source")
500      lonely$extract.xxx.chunks(src)
501      lonely$prefixed.lines(src)
502    }
503    
504    extra.code.docs <- function # Extract documentation from code chunks
505    ### Parse R code to extract inline documentation from comments around
506    ### each function. These are not able to be retreived simply by
507    ### looking at the "source" attribute. This is a Parser Function that
508    ### can be used in the parser list of package.skeleton.dx(). TODO:
509    ### Modularize this into separate Parsers Functions for S4 classes,
510    ### prefixes, ##<<blocks, etc. Right now it is not very clean!
511    (code,
512    ### Code lines in a character vector containing multiple R objects to
513    ### parse for documentation.
514     objs,
515    ### The objects defined in the code.
516     ...
517    ### ignored
518     ){
519      parsed <- extract.file.parse(code)
520      extract.docs.try <- function(o,on)
521        {
522          ## Note: we could use parsed information here too, but that
523          ## would produce different results for setMethodS3 etc.
524          doc <- list()
525          if ( !is.null(parsed[[on]]) ){
526            if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
527              doc$definition <- paste(parsed[[on]]@code,collapse="\n")
528            }
529            if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
530              doc$description <- parsed[[on]]@description
531            }
532            if ( "setMethodS3" == parsed[[on]]@created ){
533              # PhG: this may be wrong! It does not catch correctly how the method
534              # must be splitted in case of methods containing dots. for instance,
535              # as.data.frame.matrix must be split into: m1 = as.data.frame and
536              # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!
537                      pattern <- "^([^\\.]+)\\.(.*)$"
538              doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),
539                  m2 <- gsub(pattern,"\\2",on,perl=TRUE))
540              if ( 0 < length(grep("\\W",m1,perl=TRUE)) ){
541                              m1 <- paste("`",m1,"`",sep="")
542              }
543              cat("S3method(",m1,",",m2,")\n",sep="")
544            }
545          }
546          if("title" %in% names(doc) && !"description" %in% names(doc) ){
547            ## For short functions having both would duplicate, but a
548            ## description is required. Therefore automatically copy title
549            ## across to avoid errors at package build time.
550            doc$description <- doc$title
551          }
552          doc
553        }
554      extract.docs <- function(on){
555        res <- try({o <- objs[[on]]
556                    extract.docs.try(o, on)},FALSE)
557        if(class(res)=="try-error"){
558          cat("Failed to extract docs for: ",on,"\n\n")
559          list()
560        } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
561          NULL
562        } else if(0 == length(res) && "function" %in% class(o)
563                  && 1 == length(osource <- attr(o,"source"))
564                  && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))
565                  ){
566          ## phew - this should only pick up R.oo S3 generic definitions like:
567          ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
568          NULL
569        } else res
570      }
571      doc.names <- names(objs)
572      res <- sapply(doc.names,extract.docs,simplify=FALSE)
573      ## Special processing for S4 classes as they do not appear in normal ls()
574      for ( nn in names(parsed) ){
575        if ( parsed[[nn]]@created == "setClass" ){
576          S4class.docs <- extract.docs.setClass(parsed[[nn]])
577          docname <- paste(nn,"class",sep="-")
578          if ( is.null(res[[docname]]) ){
579            res[[docname]] <- S4class.docs
580            doc.names <- c(doc.names,docname)
581          } else {
582            stop(nn," appears as both S4 class and some other definition")
583          }
584        }
585      }
586      inherit.docs <- function(on){
587        in.res <- res[[on]]
588        if ( !is.null(parsed[[on]]) ){
589          for ( parent in parsed[[on]]@parent ){
590            if ( !is.na(parent) ){
591              if ( is.null(in.res) ){
592                in.res <- res[[parent]]
593              } else if ( parent %in% names(res) ){
594                parent.docs <- res[[parent]]
595                for ( nn in names(parent.docs) ){
596                  if ( !nn %in% names(in.res) ){
597                    in.res[[nn]] <- parent.docs[[nn]]
598                  }
599                }
600              }
601            }
602          }
603        }
604        invisible(in.res)
605      }
606      all.done <- FALSE
607      while ( !all.done ){
608        res1 <- sapply(doc.names,inherit.docs,simplify=FALSE)
609        all.done <- identical(res1,res)
610        res <- res1
611      }
612      ## now strip out any generics (which have value NULL in res):
613      res.not.null <- sapply(res,function(x){!is.null(x)})
614      if ( 0 < length(res.not.null) && length(res.not.null) < length(res) ){
615        res <- res[res.not.null]
616      }
617      res
618    ### named list of lists, one for each object to document.
619    }
620    
621    ### List of parsers to use by default with package.skeleton.dx.
622    default.parsers <-
623      c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
624        sapply(forfun.parsers,forfun),
625        sapply(forall.parsers,forall),
626        edit.package.file=function(desc,...){
627          in.details <- setdiff(colnames(desc),"Description")
628          details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",
629                                 sep=""),collapse="\n")
630          L <-
631            list(list(title=desc[,"Title"],
632                      description=desc[,"Description"],
633                      `tabular{ll}`=details,
634                      author=desc[,"Maintainer"]))
635          names(L) <- paste(desc[,"Package"],"-package",sep="")
636          L
637        })
638    
639  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
640  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
641  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
# Line 613  Line 774 
774    ## the same line or \code{### } comments at the beginning of the    ## the same line or \code{### } comments at the beginning of the
775    ## following line.    ## following line.
776    f.n <- paste(class.name,"class",sep="-")    f.n <- paste(class.name,"class",sep="-")
777    docs <- extract.docs.fun(chunk.source,f.n)    docs <- extract.xxx.chunks(chunk.source,f.n)
778      ## also apply source parsing functions that I separated out into
779      ## separate functions
780      docs <- combine(docs,lonely$prefixed.lines(chunk.source))
781      docs$title <- lonely$title.from.firstline(chunk.source)
782    ##details<<    ##details<<
783    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
784    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
# Line 637  Line 802 
802    }    }
803    invisible(docs)    invisible(docs)
804  }  }
805    
806    apply.parsers <- function
807    ### Parse code to r objs, then run all the parsers and return the
808    ### documentation list.
809    (code,
810    ### Character vector of code lines.
811     parsers=default.parsers,
812    ### List of Parser Functions.
813     verbose=FALSE,
814    ### Echo names of Parser Functions?
815     ...
816    ### Additional arguments to pass to Parser Functions.
817     ){
818      e <- new.env()
819      old <- options(keep.source=TRUE)
820      on.exit(options(old))
821      exprs <- parse(text=code)
822      for (i in exprs){
823        tryCatch(eval(i, e),error=function(e){
824          ##print(e)
825        })
826      }
827      objs <- sapply(ls(e),get,e,simplify=FALSE)
828    
829      docs <- list()
830    
831      # PhG: Automatically determine who is S3 methods
832      for (name in names(objs)) {
833        parts <- strsplit(name, ".", fixed = TRUE)[[1]]
834            l <- length(parts)
835            if (l > 1) {
836            for (i in 1:(l - 1)) {
837                # Look for a generic function (known by the system or defined
838                # in the package) that matches that part of the function name
839                generic <- paste(parts[1:i], collapse = ".")
840                if (any(generic %in% utils:::getKnownS3generics()) ||
841                    utils:::findGeneric(generic, e) != "") {
842                    object <- paste(parts[(i + 1):l], collapse = ".")
843                    docs[[name]]$s3method <- c(generic, object)
844                    break
845                }
846            }
847        }
848      }
849      ## apply parsers in sequence to code and objs
850      for(i in seq_along(parsers)){
851        N <- names(parsers[i])
852        if(verbose){
853          if(is.character(N) && N!=""){
854            cat(N," ",sep="")
855          }else cat('. ')
856        }
857        p <- parsers[[i]]
858        ## This is the argument list that each parser receives:
859        L <- p(code=code,objs=objs,docs=docs,...)
860        docs <- combine(docs,L)
861      }
862      if(verbose)cat("\n")
863      docs
864    ### A list of extracted documentation from code.
865    }
866    
867    ### Names of Parser Functions that operate on the desc arg.
868    descfile.names <- c("author.from.description","edit.package.file")
869    
870    ### Names of Parser Functions that do NOT use the desc arg.
871    non.descfile.names <-
872      names(default.parsers)[!names(default.parsers)%in%descfile.names]
873    
874    ### Parsers that operate only on R code, independently of the
875    ### description file.
876    nondesc.parsers <- default.parsers[non.descfile.names]
877    
878    extract.docs.file <- function
879    ### Apply all parsers relevant to extract info from just 1 code file.
880    (f,
881    ### File name of R code to read and parse.
882     parsers=nondesc.parsers,
883    ### Parser Functions to use to parse the code and extract
884    ### documentation.
885     ...
886    ### Other arguments to pass to Parser Functions.
887     ){
888      apply.parsers(readLines(f),parsers,verbose=FALSE,...)
889    }

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