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

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revision 163, Tue Nov 16 12:06:29 2010 UTC revision 305, Tue Aug 16 11:48:38 2011 UTC
# Line 7  Line 7 
7    
8  ### combine lists by adding elements or adding to existing elements  ### combine lists by adding elements or adding to existing elements
9  combine.list <- function(x,y){  combine.list <- function(x,y){
10    toadd <- !names(y)%in%names(x)    toadd <- if(".overwrite"%in%names(y)){
11    toup <- names(y)[names(y)%in%names(x)]      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]    x[names(y)[toadd]] <- y[toadd]
18    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
19    return(x)    x
20  ### A list, same type as x, but with added elements from y.  ### 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.  ### Prefix for code comments used with grep and gsub.
36  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
37    
38  decomment <- function  decomment <- function
39  ### Remove comment prefix and join lines of code to form a  ### Remove comment prefix and join lines of code to form a
# Line 24  Line 41 
41  (comments  (comments
42  ### Character vector of prefixed comment lines.  ### Character vector of prefixed comment lines.
43   ){   ){
44    paste(gsub(prefix,"",comments),collapse="\n")    gsub(prefix,"",comments)
45  ### String without prefixes or newlines.  ### String without prefixes or newlines.
46  }  }
47    
# Line 41  Line 58 
58   ){   ){
59    FUN <- FUN    FUN <- FUN
60    f <- function(objs,docs,...){    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      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
65      for(N in names(docs)){      for(N in union(names(docs),names(objs))){
66        o <- objs[[N]]        o <- objs[[N]]
67        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
68                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
69      }      }
70      on.exit()## remove warning message      on.exit()## remove warning message
# Line 84  Line 102 
102  ### Character vector of code lines with preceding whitespace removed.  ### Character vector of code lines with preceding whitespace removed.
103  }  }
104    
105  examples.after.return <- function  prefixed.lines <- structure(function(src,...){
 ### Get examples from inline definitions after return()  
 ### PhG: this does not work well! Think of these situations:  
 ### 1) You have multiple return() in the code of your function,  
 ### 2) You have return() appearing is some example code, ...  
 ### I can hardly propose a hack here. The whole code of the function  
 ### must be parsed, and one must determine which one is the last line  
 ### of code that is actually executed.  
 ###  
 ### I make two propositions here  
 ### 1) to keep the same mechanism that has the advantage of simplicity  
 ###    but to use a special tag  
 ###    ##examples<< or #{{{examples to separate  
 ###    function code from examples explicitly, and  
 ### 2) to place the example in an "ex" attribute  
 ###    attached to the function  
 ###    (see next parser). That solution will be also interesting for  
 ###    documenting datasets, something not done yet by inlinedocs!  
 (src,name="",...) {  
   ## Look for the examples mark  
   m <- grep("^\\s*(##examples<<|#\\{\\{\\{examples)", src)  
   if (!length(m)) return(list())  
   if (length(m) > 1)  
     warning("More than one examples tag for ", name,  
             ". Taking the last one")  
   m <- m[length(m)]  
   ## Look for the lines containing return value comments just before  
   r <- grep("\\s*### ", src[1:(m-1)])  
     if (!length(r)) {  
       value <- NULL  
     } else {  
       ## Only take consecutive lines before the mark  
       keep <- rev((m - rev(r)) == 1:length(r))  
       if (!any(keep)) {  
         value <- NULL  
       } else {  
         value <- decomment(src[r[keep]])  
       }  
     }  
   ## Collect now the example code beneath the mark  
   ex <- src[(m + 1):(length(src) - 1)]  
   ## Possibly eliminate a #}}} tag  
   ex <- ex[!grepl("#}}}", ex)]  
   ## Eliminate leading tabulations or four spaces  
   ex <- kill.prefix.whitespace(ex)  
   ## Add an empty line before and after example  
   ex <- c("", ex, "")  
   ## Return examples and value  
   list(examples = paste(ex, collapse = "\n"), value = value)  
 }  
   
 prefixed.lines <- function(src,...){  
106  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
107  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
108  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
# Line 155  Line 122 
122    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
123    parens <- f("(")-f(")")    parens <- f("(")-f(")")
124    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2    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(){    is.arg <- function(){
127      gres <- grep("^\\s*#",src[start-1],perl=TRUE)      gres <- grep("^\\s*#",src[start-1],perl=TRUE)
128      0 == length(gres) && start<=body.begin      0 == length(gres) && start<=body.begin
# Line 163  Line 131 
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(src))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
135        lab <- if(all(processed==""))"value"
136      else if(start==2)"description"      else if(start==2)"description"
137      else if(is.arg()){      else if(is.arg()){
138        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 179  Line 148 
148      res[[lab]] <- decomment(src[start:end])      res[[lab]] <- decomment(src[start:end])
149    }    }
150    res    res
151  }  },ex=function(){
152    test <- function
153    ### the description
154    (x,
155    ### the first argument
156     y ##<< another argument
157     ){
158      5
159    ### the return value
160    ##seealso<< foobar
161    }
162    src <- getSource(test)
163    prefixed.lines(src)
164    extract.xxx.chunks(src)
165    })
166    
167  extract.xxx.chunks <- function # Extract documentation from a function  extract.xxx.chunks <- function # Extract documentation from a function
168  ### Given source code of a function, return a list describing inline  ### Given source code of a function, return a list describing inline
# Line 265  Line 248 
248          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
249        }        }
250        chunk.res <- NULL        chunk.res <- NULL
251        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
252          chunk.res <-          chunk.res <-
253            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
254            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
# Line 273  Line 256 
256      }      }
257    while ( k <= length(src) ){    while ( k <= length(src) ){
258      line <- src[k]      line <- src[k]
259      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
260        ## 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
261        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
262        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
# Line 348  Line 331 
331            first.describe <- TRUE;            first.describe <- TRUE;
332          }          }
333        }        }
334      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
335        ## append this line to current chunk        ## append this line to current chunk
336        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
337          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
338          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
339          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 363  Line 346 
346            payload <- stripped            payload <- stripped
347          }          }
348        }        }
349      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
350        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
351        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
352          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 425  Line 408 
408  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
409  }  }
410    
411    leadingS3generic <- function # check whether function name is an S3 generic
412    ### Determines whether a function name looks like an S3 generic function
413    (name,                     ##<< name of function
414     env,                      ##<< environment to search for additional generics
415     ...)                      ##<< ignored here
416    {
417      ##details<< This function is one of the default parsers, but exposed as
418      ## possibly of more general interest. Given a function name of the form
419      ## x.y.z it looks for the generic function x applying to objects of class
420      ## y.z and also for generic function x.y applying to objects of class z.
421      ##
422      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
423      l <- length(parts)
424      if (l > 1) {
425        for (i in 1:(l - 1)) {
426          ## Look for a generic function (known by the system or defined
427          ## in the package) that matches that part of the function name
428          generic <- paste(parts[1:i], collapse = ".")
429          if (any(generic %in% utils:::getKnownS3generics()) ||
430              utils:::findGeneric(generic, env) != "") {
431            object <- paste(parts[(i + 1):l], collapse = ".")
432            ##details<< Assumes that the first name which matches any known
433            ## generics is the target generic function, so if both x and x.y
434            ## are generic functions, will assume generic x applying to objects
435            ## of class y.z
436            ##value<< If a matching generic found returns a list with a single component:
437            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
438          }
439        }
440      }
441      ##value<< If no matching generic functions are found, returns an empty list.
442      list()
443    }
444    
445  ### Parsers for each function that are constructed automatically. This  ### Parsers for each function that are constructed automatically. This
446  ### is a named list, and each element is a parser function for an  ### is a named list, and each element is a parser function for an
447  ### individual object.  ### individual object.
448  forfun.parsers <-  forfun.parsers <-
449    list(prefixed.lines=prefixed.lines,    list(prefixed.lines=prefixed.lines,
        examples.after.return=examples.after.return,  
450         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
451         ## title from first line of function def         ## title from first line of function def
452         title.from.firstline=function(src,name,code,...){         title.from.firstline=function(src,...){
453           if(length(grep("#",src[1]))){           first <- src[1]
454             list(title=gsub("[^#]*#\\s*(.*)","\\1",src[1],perl=TRUE))           if(!is.character(first))return(list())
455           } else list()           if(!grepl("#",first))return(list())
456             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
457         },         },
458         ## PhG: it is tests/FUN.R!!! I would like more flexibility here         ## PhG: it is tests/FUN.R!!! I would like more flexibility here
459         ## please, let me choose which dir to use for examples!         ## please, let me choose which dir to use for examples!
# Line 446  Line 463 
463           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
464           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
465           if(file.exists(tfile))           if(file.exists(tfile))
466             list(examples=paste(readLines(tfile),collapse="\n"))             list(examples=readLines(tfile))
467           else list()           else list()
468         },         },
469         definition.from.source=function(doc,src,...){         definition.from.source=function(doc,src,...){
470           def <- doc$definition           def <- doc$definition
471           is.empty <- function(x)is.null(x)||x==""           is.empty <- function(x)is.null(x)||x==""
472           if(is.empty(def) && !is.empty(src))           if(is.empty(def) && !is.empty(src))
473             list(definition=paste(src,collapse="\n"))             list(definition=src)
474           else list()           else list()
475         })         })
476    
# Line 479  Line 496 
496             ## Special case for code contained in a function             ## Special case for code contained in a function
497             if (inherits(ex, "function")) {             if (inherits(ex, "function")) {
498               ## If source is available, start from there               ## If source is available, start from there
499               src <- attr(ex, "source")               src <- getSource(ex)
500               if (!is.null(src)) {               if (!is.null(src)) {
501                 ex <- src                 ex <- src
502               } else { ## Use the body of the function               } else { ## Use the body of the function
# Line 487  Line 504 
504               }               }
505               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
506               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
507                 if(ex[1]=="{")ex <- ex[-1]
508               ## all the prefixes               ## all the prefixes
509               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
510               ## Add an empty line before and after example               ## Add an empty line before and after example
511               ex <- c("", ex, "")               ex <- c("", ex, "")
512             }             }
513             list(examples = paste(ex, collapse = "\n"))             list(examples = ex)
514           } else list()           } else list()
515         })         },collapse=function(doc,...){
516             L <- lapply(doc,paste,collapse="\n")
517             L$.overwrite <- TRUE
518             L
519           },tag.s3methods=leadingS3generic
520           )
521    
522  ### List of parser functions that operate on single objects. This list  ### List of parser functions that operate on single objects. This list
523  ### is useful for testing these functions.  ### is useful for testing these functions.
524  lonely <- c(forall.parsers,forfun.parsers)  lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
 attr(lonely,"ex") <- function(){  
525    f <- function # title    f <- function # title
526  ### description  ### description
527    (x, ##<< arg x    (x, ##<< arg x
# Line 512  Line 534 
534           sum=x+y) ##<< their sum           sum=x+y) ##<< their sum
535      ##end<<      ##end<<
536    }    }
537    src <- attr(f,"source")    src <- getSource(f)
538    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
539    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
540  }  })
541    
542  extra.code.docs <- function # Extract documentation from code chunks  extra.code.docs <- function # Extract documentation from code chunks
543  ### Parse R code to extract inline documentation from comments around  ### Parse R code to extract inline documentation from comments around
# Line 540  Line 562 
562        doc <- list()        doc <- list()
563        if ( !is.null(parsed[[on]]) ){        if ( !is.null(parsed[[on]]) ){
564          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
565            doc$definition <- paste(parsed[[on]]@code,collapse="\n")            doc$definition <- paste(parsed[[on]]@code)
566          }          }
567          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
568            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
569          }          }
570          if ( "setMethodS3" == parsed[[on]]@created ){          ## if ( "setMethodS3" == parsed[[on]]@created ){
571            # PhG: this may be wrong! It does not catch correctly how the method          ##   gen <- leadingS3generic(on,topenv())
572            # must be splitted in case of methods containing dots. for instance,          ##   if ( 0 < length(gen) ){
573            # as.data.frame.matrix must be split into: m1 = as.data.frame and          ##     doc$.s3method <- gen$.s3method
574            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!          ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
575                    pattern <- "^([^\\.]+)\\.(.*)$"          ##   }
576            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="")  
         }  
577        }        }
578        if("title" %in% names(doc) && !"description" %in% names(doc) ){        if("title" %in% names(doc) && !"description" %in% names(doc) ){
579          ## For short functions having both would duplicate, but a          ## For short functions having both would duplicate, but a
# Line 576  Line 592 
592      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
593        NULL        NULL
594      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
595                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- getSource(o))
596                && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
597                ){                ){
598        ## phew - this should only pick up R.oo S3 generic definitions like:        ## phew - this should only pick up R.oo S3 generic definitions like:
599        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
# Line 638  Line 654 
654  default.parsers <-  default.parsers <-
655    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
656      sapply(forfun.parsers,forfun),      sapply(forfun.parsers,forfun),
     sapply(forall.parsers,forall),  
657      edit.package.file=function(desc,...){      edit.package.file=function(desc,...){
658        in.details <- setdiff(colnames(desc),"Description")        in.details <- setdiff(colnames(desc),"Description")
659        details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",        details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
                              sep=""),collapse="\n")  
660        L <-        L <-
661          list(list(title=desc[,"Title"],          list(list(title=desc[,"Title"],
662                    description=desc[,"Description"],                    description=desc[,"Description"],
663                    `tabular{ll}`=details,                    `tabular{ll}`=details))
                   author=desc[,"Maintainer"]))  
664        names(L) <- paste(desc[,"Package"],"-package",sep="")        names(L) <- paste(desc[,"Package"],"-package",sep="")
665        L        L
666      })      },
667        sapply(forall.parsers,forall)
668        )
669    
670  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
671  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
672  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
673  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
674    ### the parent class.
675           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
676                          created="character", ##<< how created                          created="character", ##<< how created
677                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 690  Line 706 
706      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
707      default.description <- NULL      default.description <- NULL
708      while ( start > last.end+1      while ( start > last.end+1
709             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
710        start <- start-1        start <- start-1
711      }      }
712      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 717  Line 733 
733        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
734        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
735        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
736        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
737          parent <- chars[3]          parent <- chars[3]
738        }        }
739        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 749  Line 765 
765        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
766        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
767        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
768        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
769          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
770        }        }
771        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 796  Line 812 
812    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
813    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
814    ##details<<    ##details<<
815      ## If there is no explicit title on the first line of setClass, then
816      ## one is made up from the class name.
817      if ( 0 == length(docs$title) ){
818        docs$title <- list(title=paste(class.name,"S4 class"))
819      }
820      ##details<<
821    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
822    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
823    ## written. It is given a vanilla content if there are no specific    ## written. It is given a vanilla content if there are no specific
# Line 832  Line 854 
854  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
855   ){   ){
856    e <- new.env()    e <- new.env()
857    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
858      ## Error in assignClassDef(Class, classDef, where) :
859      ##   Class "DocLink" has a locked definition in package "inlinedocs"
860      ## Traced to "where" argument in setClassDef which defaults to topenv()
861      ## which in turn is inlinedocs when processing inlinedocs package, hence
862      ## the clash. The following works (under R 2.12.2), so that the topenv()
863      ## now finds e before finding the inlinedocs environment.
864      old <- options(keep.source=TRUE,topLevelEnvironment=e)
865    on.exit(options(old))    on.exit(options(old))
866    exprs <- parse(text=code)    exprs <- parse(text=code)
867      ## TDH 2011-04-07 set this so that no warnings about creating a fake
868      ## package when we try to process S4 classes defined in code
869      e$.packageName <- "inlinedocs.processor"
870    for (i in exprs){    for (i in exprs){
871      tryCatch(eval(i, e),error=function(e){      ## TDH 2011-04-07 Disable this tryCatch since it makes it harder
872        ##to debug errors/warnings in the evaluated code
873    
874        ##tryCatch({
875          eval(i, e)
876        ##},error=function(e){
877        ##print(e)        ##print(e)
878      })      ##})
879    }    }
880    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
881    
882    docs <- list()    docs <- list()
883    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
884    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
885    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
886      N <- names(parsers[i])      N <- names(parsers[i])
# Line 872  Line 891 
891      }      }
892      p <- parsers[[i]]      p <- parsers[[i]]
893      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
894      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
895      docs <- combine(docs,L)      docs <- combine(docs,L)
896    }    }
897      ## post-process to collapse all character vectors
898      for(i in seq_along(docs)){
899        for(j in seq_along(docs[[i]])){
900          if(names(docs[[i]])[j]!=".s3method")
901          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
902        }
903      }
904    if(verbose)cat("\n")    if(verbose)cat("\n")
905    docs    docs
906  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
# Line 891  Line 917 
917  ### description file.  ### description file.
918  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
919    
920  extract.docs.file <- function  extract.docs.file <- structure(function
921  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
922  (f,  (f,
923  ### File name of R code to read and parse.  ### File name of R code to read and parse.
924   parsers=nondesc.parsers,   parsers=NULL,
925  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
926  ### documentation.  ### documentation.
927   ...   ...
928  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
929   ){   ){
930      if(is.null(parsers))parsers <- nondesc.parsers
931    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
932  }  },ex=function(){
933      f <- system.file("silly","R","silly.R",package="inlinedocs")
934      extract.docs.file(f)
935    })
936    

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