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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 162, Wed Nov 10 09:18:20 2010 UTC revision 356, Mon Apr 9 15:39:09 2012 UTC
# Line 1  Line 1 
1    do.not.generate <- structure(function
2    ### Make a Parser Function used to indicate that certain Rd files
3    ### should not be generated.
4    (...
5    ### Character strings indicating Rd files without the .Rd suffix.
6     ){
7      filenames <- c(...)
8      function(docs,...){
9        for(fn in filenames){
10          docs[[fn]] <- list()
11        }
12        docs$.overwrite <- TRUE
13        docs
14      }
15    ### A Parser Function that will delete items from the outer
16    ### Documentation List.
17    },ex=function(){
18      silly.pkg <- system.file("silly",package="inlinedocs")
19      owd <- setwd(tempdir())
20      file.copy(silly.pkg,".",recursive=TRUE)
21    
22      ## define a custom Parser Function that will not generate some Rd
23      ## files
24      custom <- do.not.generate("silly-package","Silly-class")
25      parsers <- c(default.parsers,list(exclude=custom))
26    
27      ## At first, no Rd files in the man subdirectory.
28      man.dir <- file.path("silly","man")
29      dir(man.dir)
30    
31      ## Running package.skeleton.dx will generate bare-bones files for
32      ## those specified in do.not.generate, if they do not exist.
33      package.skeleton.dx("silly",parsers)
34      Rd.files <- c("silly-package.Rd","Silly-class.Rd","silly.example.Rd")
35      Rd.paths <- file.path(man.dir,Rd.files)
36      stopifnot(all(file.exists(Rd.paths)))
37    
38      ## Save the modification times of the Rd files
39      old <- file.info(Rd.paths)$mtime
40    
41      ## make sure there is at least 2 seconds elapsed, which is the
42      ## resolution for recording times on windows file systems.
43      Sys.sleep(4)
44    
45      ## However, it will NOT generate Rd for files specified in
46      ## do.not.generate, if they DO exist already.
47      package.skeleton.dx("silly",parsers)
48      mtimes <- data.frame(old,new=file.info(Rd.paths)$mtime)
49      rownames(mtimes) <- Rd.files
50      mtimes$changed <- mtimes$old != mtimes$new
51      print(mtimes)
52      stopifnot(mtimes["silly-package.Rd","changed"]==FALSE)
53      stopifnot(mtimes["Silly-class.Rd","changed"]==FALSE)
54      stopifnot(mtimes["silly.example.Rd","changed"]==TRUE)
55    
56      unlink("silly",recursive=TRUE)
57      setwd(owd)
58    })
59    
60  ### combine lists or character strings  ### combine lists or character strings
61  combine <- function(x,y)UseMethod("combine")  combine <- function(x,y)UseMethod("combine")
62    
# Line 7  Line 66 
66    
67  ### combine lists by adding elements or adding to existing elements  ### combine lists by adding elements or adding to existing elements
68  combine.list <- function(x,y){  combine.list <- function(x,y){
69    toadd <- !names(y)%in%names(x)    toadd <- if(".overwrite"%in%names(y)){
70    toup <- names(y)[names(y)%in%names(x)]      y <- y[names(y)!=".overwrite"]
71        rep(TRUE,length(y))
72      }else{
73        !names(y)%in%names(x)
74      }
75      toup <- names(y)[!toadd]
76    x[names(y)[toadd]] <- y[toadd]    x[names(y)[toadd]] <- y[toadd]
77    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
78    return(x)    x
79  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
80  }  }
81    
82    
83    getSource <- function
84    ### Extract a function's source code.
85    (fun.obj
86    ### A function.
87     ) {
88          srcref <- attr(fun.obj, "srcref")
89          if (!is.null(srcref)) {
90            ##unlist(strsplit(as.character(srcref), "\n"))
91            as.character(srcref)
92          }
93          else attr(fun.obj, "source")
94    ### Source code lines as a character vector.
95    }
96    
97  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
98  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
99    
100  decomment <- function  decomment <- function
101  ### 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 103 
103  (comments  (comments
104  ### Character vector of prefixed comment lines.  ### Character vector of prefixed comment lines.
105   ){   ){
106    paste(gsub(prefix,"",comments),collapse="\n")    gsub(prefix,"",comments)
107  ### String without prefixes or newlines.  ### String without prefixes or newlines.
108  }  }
109    
# Line 41  Line 120 
120   ){   ){
121    FUN <- FUN    FUN <- FUN
122    f <- function(objs,docs,...){    f <- function(objs,docs,...){
123        if(length(objs)==0)return(list())
124      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
125      L <- list()      L <- list()
126      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
127      for(N in names(docs)){      for(N in union(names(docs),names(objs))){
128        o <- objs[[N]]        o <- objs[[N]]
129        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
130                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
131      }      }
132      on.exit()## remove warning message      on.exit()## remove warning message
# Line 69  Line 149 
149  ### For each function in the package, do something.  ### For each function in the package, do something.
150  forfun <- function(FUN)forall(FUN,is.function)  forfun <- function(FUN)forall(FUN,is.function)
151    
152  examples.after.return <- function  kill.prefix.whitespace <- function
153  ### Get examples from inline definitions after return()  ### Figure out what the whitespace preceding the example code is, and
154  ### PhG: this does not work well! Think of these situations:  ### then delete that from every line.
155  ### 1) You have multiple return() in the code of your function,  (ex
156  ### 2) You have return() appearing is some example code, ...  ### character vector of example code lines.
157  ### I can hardly propose a hack here. The whole code of the function   ){
158  ### must be parsed, and one must determine which one is the last line    tlines <- gsub("\\s*","",ex)
159  ### of code that is actually executed.    ##tlines <- gsub("#.*","",tlines)
160  ###    prefixes <- unique(gsub("\\S.*","",ex[tlines!=""]))
 ### 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  
   prefixes <- gsub("(\\s*).*","\\1",ex,perl=TRUE)[grep("\\w",ex)]  
161    FIND <- prefixes[which.min(nchar(prefixes))]    FIND <- prefixes[which.min(nchar(prefixes))]
162    ex <- sub(FIND,"",ex)    ## Eliminate leading tabulations or 2/4 spaces
163    ## Add an empty line before and after example    sub(FIND, "", ex)
164    ex <- c("", ex, "")  ### Character vector of code lines with preceding whitespace removed.
   ## Return examples and value  
   list(examples = paste(ex, collapse = "\n"), value = value)  
165  }  }
166    
167  prefixed.lines <- function(src,...){  prefixed.lines <- structure(function(src,...){
168  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
169  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
170  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
# Line 142  Line 184 
184    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
185    parens <- f("(")-f(")")    parens <- f("(")-f(")")
186    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
187      if(length(body.begin)==0)body.begin <- 1 ## rare cases
188    is.arg <- function(){    is.arg <- function(){
189      gres <- grep("^\\s*#",src[start-1],perl=TRUE)      gres <- grep("^\\s*#",src[start-1],perl=TRUE)
190      0 == length(gres) && start<=body.begin      0 == length(gres) && start<=body.begin
# Line 150  Line 193 
193    for(i in seq_along(starts)){    for(i in seq_along(starts)){
194      start <- clines[starts[i]]      start <- clines[starts[i]]
195      end <- clines[ends[i]]      end <- clines[ends[i]]
196      lab <- if(end+1==length(src))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
197        lab <- if(all(processed==""))"value"
198      else if(start==2)"description"      else if(start==2)"description"
199      else if(is.arg()){      else if(is.arg()){
200        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 158  Line 202 
202        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
203        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
204        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
205        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
206        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
207      } else {      } else {
208        next;        next;
# Line 166  Line 210 
210      res[[lab]] <- decomment(src[start:end])      res[[lab]] <- decomment(src[start:end])
211    }    }
212    res    res
213  }  },ex=function(){
214    test <- function
215    ### the description
216    (x,
217    ### the first argument
218     y ##<< another argument
219     ){
220      5
221    ### the return value
222    ##seealso<< foobar
223    }
224    src <- getSource(test)
225    prefixed.lines(src)
226    extract.xxx.chunks(src)
227    })
228    
229  extract.xxx.chunks <- function # Extract documentation from a function  extract.xxx.chunks <- function # Extract documentation from a function
230  ### Given source code of a function, return a list describing inline  ### Given source code of a function, return a list describing inline
# Line 252  Line 310 
310          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
311        }        }
312        chunk.res <- NULL        chunk.res <- NULL
313        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
314          chunk.res <-          chunk.res <-
315            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
316            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
# Line 260  Line 318 
318      }      }
319    while ( k <= length(src) ){    while ( k <= length(src) ){
320      line <- src[k]      line <- src[k]
321      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      ##print(line)
322        ##if(grepl("^$",line))browser()
323        if ( grepl(extra.regexp,line,perl=TRUE) ){
324        ## 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
325        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
326        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
327          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
328        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
329        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
330        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 273  Line 333 
333        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
334        if ( "describe" == new.field ){        if ( "describe" == new.field ){
335          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
336          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
337          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
338          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
339            ## \code{##describe<<} comments.
340          if ( first.describe ){          if ( first.describe ){
341            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
342          } else {          } else {
# Line 335  Line 396 
396            first.describe <- TRUE;            first.describe <- TRUE;
397          }          }
398        }        }
399      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
400        ## append this line to current chunk        ## append this line to current chunk
401        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
402          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
403          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
404          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 350  Line 411 
411            payload <- stripped            payload <- stripped
412          }          }
413        }        }
414      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
415        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
416        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
417          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 362  Line 423 
423          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
424          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
425          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
426          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
427          payload <- comment          payload <- comment
428        } else {        } else {
429          ## this is a describe block, so we need to paste with existing          ## this is a describe block, so we need to paste with existing
# Line 412  Line 473 
473  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
474  }  }
475    
476    leadingS3generic <- function # check whether function name is an S3 generic
477    ### Determines whether a function name looks like an S3 generic function
478    (name,                     ##<< name of function
479     env,                      ##<< environment to search for additional generics
480     ...)                      ##<< ignored here
481    {
482      ##details<< This function is one of the default parsers, but exposed as
483      ## possibly of more general interest. Given a function name of the form
484      ## x.y.z it looks for the generic function x applying to objects of class
485      ## y.z and also for generic function x.y applying to objects of class z.
486      ##
487      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
488      l <- length(parts)
489      if (l > 1) {
490        for (i in 1:(l - 1)) {
491          ## Look for a generic function (known by the system or defined
492          ## in the package) that matches that part of the function name
493          generic <- paste(parts[1:i], collapse = ".")
494          if (any(generic %in% utils:::getKnownS3generics()) ||
495              utils:::findGeneric(generic, env) != "") {
496            object <- paste(parts[(i + 1):l], collapse = ".")
497            ##details<< Assumes that the first name which matches any known
498            ## generics is the target generic function, so if both x and x.y
499            ## are generic functions, will assume generic x applying to objects
500            ## of class y.z
501            ##value<< If a matching generic found returns a list with a single component:
502            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
503          }
504        }
505      }
506      ##value<< If no matching generic functions are found, returns an empty list.
507      list()
508    }
509    
510  ### Parsers for each function that are constructed automatically. This  ### Parsers for each function that are constructed automatically. This
511  ### 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
512  ### individual object.  ### individual object.
513  forfun.parsers <-  forfun.parsers <-
514    list(prefixed.lines=prefixed.lines,    list(prefixed.lines=prefixed.lines,
        examples.after.return=examples.after.return,  
515         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
516         ## title from first line of function def         ## title from first line of function def
517         title.from.firstline=function(src,name,code,...){         title.from.firstline=function(src,...){
518           if(length(grep("#",src[1]))){           first <- src[1]
519             list(title=gsub("[^#]*#\\s*(.*)","\\1",src[1],perl=TRUE))           if(!is.character(first))return(list())
520           } else list()           if(!grepl("#",first))return(list())
521             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
522         },         },
523         ## PhG: it is tests/FUN.R!!! I would like more flexibility here         ## PhG: it is tests/FUN.R!!! I would like more flexibility here
524         ## please, let me choose which dir to use for examples!         ## please, let me choose which dir to use for examples!
# Line 433  Line 528 
528           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
529           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
530           if(file.exists(tfile))           if(file.exists(tfile))
531             list(examples=paste(readLines(tfile),collapse="\n"))             list(examples=readLines(tfile))
532           else list()           else list()
533         },         },
534         definition.from.source=function(doc,src,...){         definition.from.source=function(doc,src,...){
535           def <- doc$definition           def <- doc$definition
536           is.empty <- function(x)is.null(x)||x==""           is.empty <- function(x)is.null(x)||x==""
537           if(is.empty(def) && !is.empty(src))           if(is.empty(def) && !is.empty(src))
538             list(definition=paste(src,collapse="\n"))             list(definition=src)
539           else list()           else list()
540         })         })
541    
# Line 448  Line 543 
543  forall.parsers <-  forall.parsers <-
544    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
545         author.from.description=function(desc,...){         author.from.description=function(desc,...){
546           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
547         },         },
548         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
549         erase.format=function(...){         erase.format=function(...){
# Line 466  Line 561 
561             ## Special case for code contained in a function             ## Special case for code contained in a function
562             if (inherits(ex, "function")) {             if (inherits(ex, "function")) {
563               ## If source is available, start from there               ## If source is available, start from there
564               src <- attr(ex, "source")               src <- getSource(ex)
565               if (!is.null(src)) {               if (!is.null(src)) {
566                 ex <- src                 ex <- src
567               } else { ## Use the body of the function               } else { ## Use the body of the function
# Line 474  Line 569 
569               }               }
570               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
571               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
572               ## Eliminate leading tabulations or 2/4 spaces               if(ex[1]=="{")ex <- ex[-1]
573               ex <- sub("^\t|    |  ", "", ex)               ## all the prefixes
574                 ex <- kill.prefix.whitespace(ex)
575               ## Add an empty line before and after example               ## Add an empty line before and after example
576               ex <- c("", ex, "")               ex <- c("", ex, "")
577             }             }
578             list(examples = paste(ex, collapse = "\n"))             list(examples = ex)
579           } else list()           } else list()
580         })         },collapse=function(doc,...){
581             L <- lapply(doc,paste,collapse="\n")
582             L$.overwrite <- TRUE
583             L
584           },tag.s3methods=leadingS3generic
585           )
586    
587  ### List of parser functions that operate on single objects. This list  ### List of parser functions that operate on single objects. This list
588  ### is useful for testing these functions.  ### is useful for testing these functions.
589  lonely <- c(forall.parsers,forfun.parsers)  lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
 attr(lonely,"ex") <- function(){  
590    f <- function # title    f <- function # title
591  ### description  ### description
592    (x, ##<< arg x    (x, ##<< arg x
# Line 499  Line 599 
599           sum=x+y) ##<< their sum           sum=x+y) ##<< their sum
600      ##end<<      ##end<<
601    }    }
602    src <- attr(f,"source")    src <- getSource(f)
603    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
604    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
605  }  })
606    
607  extra.code.docs <- function # Extract documentation from code chunks  extra.code.docs <- function # Extract documentation from code chunks
608  ### Parse R code to extract inline documentation from comments around  ### Parse R code to extract inline documentation from comments around
# Line 527  Line 627 
627        doc <- list()        doc <- list()
628        if ( !is.null(parsed[[on]]) ){        if ( !is.null(parsed[[on]]) ){
629          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
630            doc$definition <- paste(parsed[[on]]@code,collapse="\n")            doc$definition <- paste(parsed[[on]]@code)
631          }          }
632          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
633            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
634          }          }
635          if ( "setMethodS3" == parsed[[on]]@created ){          ## if ( "setMethodS3" == parsed[[on]]@created ){
636            # PhG: this may be wrong! It does not catch correctly how the method          ##   gen <- leadingS3generic(on,topenv())
637            # must be splitted in case of methods containing dots. for instance,          ##   if ( 0 < length(gen) ){
638            # as.data.frame.matrix must be split into: m1 = as.data.frame and          ##     doc$.s3method <- gen$.s3method
639            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!          ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
640                    pattern <- "^([^\\.]+)\\.(.*)$"          ##   }
641            doc$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="")  
         }  
642        }        }
643        if("title" %in% names(doc) && !"description" %in% names(doc) ){        if("title" %in% names(doc) && !"description" %in% names(doc) ){
644          ## For short functions having both would duplicate, but a          ## For short functions having both would duplicate, but a
# Line 563  Line 657 
657      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
658        NULL        NULL
659      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
660                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- getSource(o))
661                && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
662                ){                ){
663        ## phew - this should only pick up R.oo S3 generic definitions like:        ## phew - this should only pick up R.oo S3 generic definitions like:
664        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
# Line 625  Line 719 
719  default.parsers <-  default.parsers <-
720    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
721      sapply(forfun.parsers,forfun),      sapply(forfun.parsers,forfun),
     sapply(forall.parsers,forall),  
722      edit.package.file=function(desc,...){      edit.package.file=function(desc,...){
723        in.details <- setdiff(colnames(desc),"Description")        in.details <- setdiff(colnames(desc),"Description")
724        details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",        details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
                              sep=""),collapse="\n")  
725        L <-        L <-
726          list(list(title=desc[,"Title"],          list(list(title=desc[,"Title"],
727                    description=desc[,"Description"],                    description=desc[,"Description"],
728                    `tabular{ll}`=details,                    `tabular{ll}`=details))
                   author=desc[,"Maintainer"]))  
729        names(L) <- paste(desc[,"Package"],"-package",sep="")        names(L) <- paste(desc[,"Package"],"-package",sep="")
730        L        L
731      })      },
732        sapply(forall.parsers,forall)
733        )
734    
735  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
736  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
737  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
738  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
739    ### the parent class.
740           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
741                          created="character", ##<< how created                          created="character", ##<< how created
742                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 651  Line 745 
745           )           )
746    
747  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
748  ### Using the base \code{\link{parse}} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
749  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
750  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
751  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
# Line 677  Line 771 
771      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
772      default.description <- NULL      default.description <- NULL
773      while ( start > last.end+1      while ( start > last.end+1
774             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
775        start <- start-1        start <- start-1
776      }      }
777      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 704  Line 798 
798        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
799        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
800        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
801        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
802          parent <- chars[3]          parent <- chars[3]
803        }        }
804        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 723  Line 817 
817        generic.name <- chars[2]        generic.name <- chars[2]
818        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
819        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
820          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
821            ## since it causes problems on R CMD check.
822            ##* checking Rd cross-references ... WARNING
823            ##Error in find.package(package, lib.loc) :
824            ##  there is no package called ‘MASS’
825            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
826    
827            generic.desc <-
828              paste("Generic method behind \\code{",object.name,"}",sep="")
829          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
830                                     name=generic.name,                                     name=generic.name,
831                                     created=expr.type,                                     created=expr.type,
# Line 736  Line 838 
838        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
839        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
840        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
841        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
842          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
843        }        }
844        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 757  Line 859 
859  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
860  ### scanned for inline comments.  ### scanned for inline comments.
861  (doc.link  (doc.link
862  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
863  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
864  ### class definitions.  ### class definitions.
865   ){   ){
# Line 783  Line 885 
885    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
886    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
887    ##details<<    ##details<<
888      ## If there is no explicit title on the first line of setClass, then
889      ## one is made up from the class name.
890      if ( 0 == length(docs$title) ){
891        docs$title <- list(title=paste(class.name,"S4 class"))
892      }
893      ##details<<
894    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
895    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
896    ## 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 819  Line 927 
927  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
928   ){   ){
929    e <- new.env()    e <- new.env()
930    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
931      ## Error in assignClassDef(Class, classDef, where) :
932      ##   Class "DocLink" has a locked definition in package "inlinedocs"
933      ## Traced to "where" argument in setClassDef which defaults to topenv()
934      ## which in turn is inlinedocs when processing inlinedocs package, hence
935      ## the clash. The following works (under R 2.12.2), so that the topenv()
936      ## now finds e before finding the inlinedocs environment.
937      old <- options(keep.source=TRUE,topLevelEnvironment=e)
938    on.exit(options(old))    on.exit(options(old))
939    exprs <- parse(text=code)    exprs <- parse(text=code)
940      ## TDH 2011-04-07 set this so that no warnings about creating a fake
941      ## package when we try to process S4 classes defined in code
942      e$.packageName <- "inlinedocs.processor"
943    for (i in exprs){    for (i in exprs){
944      tryCatch(eval(i, e),error=function(e){        eval(i, e)
       ##print(e)  
     })  
945    }    }
946    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
947    
948    docs <- list()    docs <- list()
949    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
950    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
951      if(verbose)cat("Applying parsers:\n")
952    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
953      N <- names(parsers[i])      N <- names(parsers[i])
954      if(verbose){      if(verbose){
955        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
956          cat(N," ",sep="")          cat(N,"\n",sep="")
957        }else cat('. ')        }else cat('.\n')
958      }      }
959      p <- parsers[[i]]      p <- parsers[[i]]
960      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
961      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
962        #print(paste(L,"\n"))
963        #if(N=="exclude")browser()
964      docs <- combine(docs,L)      docs <- combine(docs,L)
965    }    }
966      ## post-process to collapse all character vectors
967      for(i in seq_along(docs)){
968        for(j in seq_along(docs[[i]])){
969          if(names(docs[[i]])[j]!=".s3method")
970          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
971        }
972     }
973    if(verbose)cat("\n")    if(verbose)cat("\n")
974    docs    return(docs)
975  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
976  }  }
977    
# Line 878  Line 986 
986  ### description file.  ### description file.
987  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
988    
989  extract.docs.file <- function  extract.docs.file <- structure(function
990  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
991  (f,  (f,
992  ### File name of R code to read and parse.  ### File name of R code to read and parse.
993   parsers=nondesc.parsers,   parsers=NULL,
994  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
995  ### documentation.  ### documentation.
996   ...   ...
997  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
998   ){   ){
999      if(is.null(parsers))parsers <- nondesc.parsers
1000    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
1001  }  },ex=function(){
1002      f <- system.file("silly","R","silly.R",package="inlinedocs")
1003      extract.docs.file(f)
1004    })
1005    

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