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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 370, Fri Nov 9 19:48:27 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.NULL<-function(x,y){
62        if (class(x) == "NULL"){
63            # print(paste("mm x=",x))
64            # print(paste("mm class(x)=",class(x)))
65            x=list("")
66        }
67        if (class(y) == "NULL"){
68            # print(paste("mm y=",y))
69            # print(paste("mm class(y)=",class(y)))
70            y=list("")
71        }
72        return(combine(x,y))
73    }
74    combine <- function(x,y){
75        UseMethod("combine")
76    }
77    
78  ### combine character strings by pasting them together  ### combine character strings by pasting them together
79  combine.character <- function(x,y)  combine.character <- function(x,y)
# Line 7  Line 81 
81    
82  ### combine lists by adding elements or adding to existing elements  ### combine lists by adding elements or adding to existing elements
83  combine.list <- function(x,y){  combine.list <- function(x,y){
84    toadd <- !names(y)%in%names(x)    toadd <- if(".overwrite"%in%names(y)){
85    toup <- names(y)[names(y)%in%names(x)]      y <- y[names(y)!=".overwrite"]
86        rep(TRUE,length(y))
87      }else{
88        !names(y)%in%names(x)
89      }
90      toup <- names(y)[!toadd]
91    x[names(y)[toadd]] <- y[toadd]    x[names(y)[toadd]] <- y[toadd]
92    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
93    return(x)    x
94  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
95  }  }
96    
97    
98    getSource <- function
99    ### Extract a function's source code.
100    (fun.obj
101    ### A function.
102     ) {
103          srcref <- attr(fun.obj, "srcref")
104          if (!is.null(srcref)) {
105            ##unlist(strsplit(as.character(srcref), "\n"))
106            as.character(srcref)
107          }
108          else attr(fun.obj, "source")
109    ### Source code lines as a character vector.
110    }
111    
112  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
113  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
114    
115  decomment <- function  decomment <- function
116  ### 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 118 
118  (comments  (comments
119  ### Character vector of prefixed comment lines.  ### Character vector of prefixed comment lines.
120   ){   ){
121    paste(gsub(prefix,"",comments),collapse="\n")    gsub(prefix,"",comments)
122  ### String without prefixes or newlines.  ### String without prefixes or newlines.
123  }  }
124    
# Line 41  Line 135 
135   ){   ){
136    FUN <- FUN    FUN <- FUN
137    f <- function(objs,docs,...){    f <- function(objs,docs,...){
138        if(length(objs)==0)return(list())
139      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
140      L <- list()      L <- list()
141      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
142      for(N in names(docs)){      for(N in union(names(docs),names(objs))){
143        o <- objs[[N]]        o <- objs[[N]]
144        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
145                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
146      }      }
147      on.exit()## remove warning message      on.exit()## remove warning message
# Line 84  Line 179 
179  ### Character vector of code lines with preceding whitespace removed.  ### Character vector of code lines with preceding whitespace removed.
180  }  }
181    
182  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,...){  
183  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
184  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
185  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are  ### "\code{^### }" (i.e. lines beginning with "\code{### }") are
# Line 155  Line 199 
199    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))    f <- function(ch)cumsum(nchar(gsub(sprintf("[^%s]",ch),"",code)))
200    parens <- f("(")-f(")")    parens <- f("(")-f(")")
201    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2    body.begin <- which(diff(parens)<0 & parens[-1]==0)+2
202      if(length(body.begin)==0)body.begin <- 1 ## rare cases
203    is.arg <- function(){    is.arg <- function(){
204      gres <- grep("^\\s*#",src[start-1],perl=TRUE)      gres <- grep("^\\s*#",src[start-1],perl=TRUE)
205      0 == length(gres) && start<=body.begin      0 == length(gres) && start<=body.begin
# Line 163  Line 208 
208    for(i in seq_along(starts)){    for(i in seq_along(starts)){
209      start <- clines[starts[i]]      start <- clines[starts[i]]
210      end <- clines[ends[i]]      end <- clines[ends[i]]
211      lab <- if(end+1==length(src))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
212        lab <- if(all(processed==""))"value"
213      else if(start==2)"description"      else if(start==2)"description"
214      else if(is.arg()){      else if(is.arg()){
215        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 171  Line 217 
217        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
218        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
219        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
220        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
221        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
222      } else {      } else {
223        next;        next;
# Line 179  Line 225 
225      res[[lab]] <- decomment(src[start:end])      res[[lab]] <- decomment(src[start:end])
226    }    }
227    res    res
228  }  },ex=function(){
229    test <- function
230    ### the description
231    (x,
232    ### the first argument
233     y ##<< another argument
234     ){
235      5
236    ### the return value
237    ##seealso<< foobar
238    }
239    src <- getSource(test)
240    prefixed.lines(src)
241    extract.xxx.chunks(src)
242    })
243    
244  extract.xxx.chunks <- function # Extract documentation from a function  extract.xxx.chunks <- function # Extract documentation from a function
245  ### 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 325 
325          chunk.sep <- "\n\n"          chunk.sep <- "\n\n"
326        }        }
327        chunk.res <- NULL        chunk.res <- NULL
328        if ( 0 == length(grep("^\\s*$",payload,perl=TRUE)) )        if ( !grepl("^\\s*$",payload,perl=TRUE) )
329          chunk.res <-          chunk.res <-
330            if ( is.null(res[[field]]) ) payload            if ( is.null(res[[field]]) ) payload
331            else paste(res[[field]], payload, sep=chunk.sep)            else paste(res[[field]], payload, sep=chunk.sep)
# Line 273  Line 333 
333      }      }
334    while ( k <= length(src) ){    while ( k <= length(src) ){
335      line <- src[k]      line <- src[k]
336      if ( 0 < length(grep(extra.regexp,line,perl=TRUE) ) ){      ##print(line)
337        ##if(grepl("^$",line))browser()
338        if ( grepl(extra.regexp,line,perl=TRUE) ){
339        ## 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
340        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
341        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
342          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
343        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
344        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
345        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 286  Line 348 
348        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
349        if ( "describe" == new.field ){        if ( "describe" == new.field ){
350          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
351          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
352          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
353          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
354            ## \code{##describe<<} comments.
355          if ( first.describe ){          if ( first.describe ){
356            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
357          } else {          } else {
# Line 348  Line 411 
411            first.describe <- TRUE;            first.describe <- TRUE;
412          }          }
413        }        }
414      } else if ( in.chunk && 0<length(grep(cont.re,line,perl=TRUE)) ){      } else if ( in.chunk && grepl(cont.re,line,perl=TRUE) ){
415        ## append this line to current chunk        ## append this line to current chunk
416        if ( 0 == length(grep(prefix,line,perl=TRUE)) ){        if ( !grepl(prefix,line,perl=TRUE) ){
417          ##describe<< Any lines with "\code{### }" at the left hand          ##describe<< Any lines with "\code{### }" at the left hand
418          ## margin within the included chunks are handled separately,          ## margin within the included chunks are handled separately,
419          ## so if they appear in the documentation they will appear          ## so if they appear in the documentation they will appear
# Line 363  Line 426 
426            payload <- stripped            payload <- stripped
427          }          }
428        }        }
429      } else if ( 0 < length(grep(arg.pat,line,perl=TRUE)) ){      } else if ( grepl(arg.pat,line,perl=TRUE) ){
430        not.describe <- (0==in.describe && !first.describe)        not.describe <- (0==in.describe && !first.describe)
431        if ( in.chunk && not.describe){        if ( in.chunk && not.describe){
432          res[[cur.field]] <- end.chunk(cur.field,payload)          res[[cur.field]] <- end.chunk(cur.field,payload)
# Line 375  Line 438 
438          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
439          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
440          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
441          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
442          payload <- comment          payload <- comment
443        } else {        } else {
444          ## 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 425  Line 488 
488  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
489  }  }
490    
491    leadingS3generic <- function # check whether function name is an S3 generic
492    ### Determines whether a function name looks like an S3 generic function
493    (name,                     ##<< name of function
494     env,                      ##<< environment to search for additional generics
495     ...)                      ##<< ignored here
496    {
497      ##details<< This function is one of the default parsers, but exposed as
498      ## possibly of more general interest. Given a function name of the form
499      ## x.y.z it looks for the generic function x applying to objects of class
500      ## y.z and also for generic function x.y applying to objects of class z.
501      ##
502      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
503      l <- length(parts)
504      if (l > 1) {
505        for (i in 1:(l - 1)) {
506          ## Look for a generic function (known by the system or defined
507          ## in the package) that matches that part of the function name
508          generic <- paste(parts[1:i], collapse = ".")
509          if (any(generic %in% utils:::getKnownS3generics()) ||
510              utils:::findGeneric(generic, env) != "") {
511            object <- paste(parts[(i + 1):l], collapse = ".")
512            ##details<< Assumes that the first name which matches any known
513            ## generics is the target generic function, so if both x and x.y
514            ## are generic functions, will assume generic x applying to objects
515            ## of class y.z
516            ##value<< If a matching generic found returns a list with a single component:
517            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
518          }
519        }
520      }
521      ##value<< If no matching generic functions are found, returns an empty list.
522      list()
523    }
524    
525  ### Parsers for each function that are constructed automatically. This  ### Parsers for each function that are constructed automatically. This
526  ### 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
527  ### individual object.  ### individual object.
528  forfun.parsers <-  forfun.parsers <-
529    list(prefixed.lines=prefixed.lines,    list(prefixed.lines=prefixed.lines,
        examples.after.return=examples.after.return,  
530         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
531         ## title from first line of function def         ## title from first line of function def
532         title.from.firstline=function(src,name,code,...){         title.from.firstline=function(src,...){
533           if(length(grep("#",src[1]))){           first <- src[1]
534             list(title=gsub("[^#]*#\\s*(.*)","\\1",src[1],perl=TRUE))           if(!is.character(first))return(list())
535           } else list()           if(!grepl("#",first))return(list())
536             list(title=gsub("[^#]*#\\s*(.*)","\\1",first,perl=TRUE))
537         },         },
538         ## PhG: it is tests/FUN.R!!! I would like more flexibility here         ## PhG: it is tests/FUN.R!!! I would like more flexibility here
539         ## please, let me choose which dir to use for examples!         ## please, let me choose which dir to use for examples!
# Line 446  Line 543 
543           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value           if (is.null(tsubdir)) tsubdir <- "tests"       # Default value
544           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))           tfile <- file.path("..",tsubdir,paste(name,".R",sep=""))
545           if(file.exists(tfile))           if(file.exists(tfile))
546             list(examples=paste(readLines(tfile),collapse="\n"))             list(examples=readLines(tfile))
547           else list()           else list()
548         },         },
549         definition.from.source=function(doc,src,...){         definition.from.source=function(doc,src,...){
550           def <- doc$definition           def <- doc$definition
551           is.empty <- function(x)is.null(x)||x==""           is.empty <- function(x)is.null(x)||x==""
552           if(is.empty(def) && !is.empty(src))           if(is.empty(def) && !is.empty(src))
553             list(definition=paste(src,collapse="\n"))             list(definition=src)
554           else list()           else list()
555         })         })
556    
# Line 461  Line 558 
558  forall.parsers <-  forall.parsers <-
559    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
560         author.from.description=function(desc,...){         author.from.description=function(desc,...){
561           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
562         },         },
563         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
564         erase.format=function(...){         erase.format=function(...){
# Line 479  Line 576 
576             ## Special case for code contained in a function             ## Special case for code contained in a function
577             if (inherits(ex, "function")) {             if (inherits(ex, "function")) {
578               ## If source is available, start from there               ## If source is available, start from there
579               src <- attr(ex, "source")               src <- getSource(ex)
580               if (!is.null(src)) {               if (!is.null(src)) {
581                 ex <- src                 ex <- src
582               } else { ## Use the body of the function               } else { ## Use the body of the function
# Line 487  Line 584 
584               }               }
585               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
586               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
587                 if(ex[1]=="{")ex <- ex[-1]
588               ## all the prefixes               ## all the prefixes
589               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
590               ## Add an empty line before and after example               ## Add an empty line before and after example
591               ex <- c("", ex, "")               ex <- c("", ex, "")
592             }             }
593             list(examples = paste(ex, collapse = "\n"))             list(examples = ex)
594           } else list()           } else list()
595         })         },collapse=function(doc,...){
596             L <- lapply(doc,paste,collapse="\n")
597             L$.overwrite <- TRUE
598             L
599           },tag.s3methods=leadingS3generic
600           )
601    
602  ### List of parser functions that operate on single objects. This list  ### List of parser functions that operate on single objects. This list
603  ### is useful for testing these functions.  ### is useful for testing these functions.
604  lonely <- c(forall.parsers,forfun.parsers)  lonely <- structure(c(forall.parsers,forfun.parsers),ex=function(){
 attr(lonely,"ex") <- function(){  
605    f <- function # title    f <- function # title
606  ### description  ### description
607    (x, ##<< arg x    (x, ##<< arg x
# Line 512  Line 614 
614           sum=x+y) ##<< their sum           sum=x+y) ##<< their sum
615      ##end<<      ##end<<
616    }    }
617    src <- attr(f,"source")    src <- getSource(f)
618    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
619    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
620  }  })
621    
622  extra.code.docs <- function # Extract documentation from code chunks  extra.code.docs <- function # Extract documentation from code chunks
623  ### Parse R code to extract inline documentation from comments around  ### Parse R code to extract inline documentation from comments around
# Line 540  Line 642 
642        doc <- list()        doc <- list()
643        if ( !is.null(parsed[[on]]) ){        if ( !is.null(parsed[[on]]) ){
644          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
645            doc$definition <- paste(parsed[[on]]@code,collapse="\n")            doc$definition <- paste(parsed[[on]]@code)
646          }          }
647          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
648            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
649          }          }
650          if ( "setMethodS3" == parsed[[on]]@created ){          ## if ( "setMethodS3" == parsed[[on]]@created ){
651            # PhG: this may be wrong! It does not catch correctly how the method          ##   gen <- leadingS3generic(on,topenv())
652            # must be splitted in case of methods containing dots. for instance,          ##   if ( 0 < length(gen) ){
653            # as.data.frame.matrix must be split into: m1 = as.data.frame and          ##     doc$.s3method <- gen$.s3method
654            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!          ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
655                    pattern <- "^([^\\.]+)\\.(.*)$"          ##   }
656            doc$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="")  
         }  
657        }        }
658        if("title" %in% names(doc) && !"description" %in% names(doc) ){        if("title" %in% names(doc) && !"description" %in% names(doc) ){
659          ## For short functions having both would duplicate, but a          ## For short functions having both would duplicate, but a
# Line 576  Line 672 
672      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
673        NULL        NULL
674      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
675                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- getSource(o))
676                && 1 == length(grep(paste("UseMethod(",on,")",sep="\""),osource))                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
677                ){                ){
678        ## phew - this should only pick up R.oo S3 generic definitions like:        ## phew - this should only pick up R.oo S3 generic definitions like:
679        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"        ## attr(*, "source")= chr "function(...) UseMethod(\"select\")"
# Line 638  Line 734 
734  default.parsers <-  default.parsers <-
735    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
736      sapply(forfun.parsers,forfun),      sapply(forfun.parsers,forfun),
     sapply(forall.parsers,forall),  
737      edit.package.file=function(desc,...){      edit.package.file=function(desc,...){
738        in.details <- setdiff(colnames(desc),"Description")        in.details <- setdiff(colnames(desc),"Description")
739        details <- paste(paste(in.details,": \\tab ",desc[,in.details],"\\cr",        details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
                              sep=""),collapse="\n")  
740        L <-        L <-
741          list(list(title=desc[,"Title"],          list(list(title=desc[,"Title"],
742                    description=desc[,"Description"],                    description=desc[,"Description"],
743                    `tabular{ll}`=details,                    `tabular{ll}`=details))
                   author=desc[,"Maintainer"]))  
744        names(L) <- paste(desc[,"Package"],"-package",sep="")        names(L) <- paste(desc[,"Package"],"-package",sep="")
745        L        L
746      })      },
747        sapply(forall.parsers,forall)
748        )
749    
750  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
751  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
752  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
753  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
754    ### the parent class.
755           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
756                          created="character", ##<< how created                          created="character", ##<< how created
757                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 664  Line 760 
760           )           )
761    
762  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
763  ### Using the base \code{\link{parse}} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
764  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
765  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
766  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
# Line 690  Line 786 
786      ## "prefix" lines will be used instead.      ## "prefix" lines will be used instead.
787      default.description <- NULL      default.description <- NULL
788      while ( start > last.end+1      while ( start > last.end+1
789             && 1 == length(grep(prefix,code[start-1],perl=TRUE)) ){             && grepl(prefix,code[start-1],perl=TRUE) ){
790        start <- start-1        start <- start-1
791      }      }
792      if ( start < chunks[[k]][1] ){      if ( start < chunks[[k]][1] ){
# Line 717  Line 813 
813        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
814        ## the parent is that function. Test whether the the third value        ## the parent is that function. Test whether the the third value
815        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
816        if ( 1 == length(grep("^[\\._\\w]+$",chars[3],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[3],perl=TRUE) ){
817          parent <- chars[3]          parent <- chars[3]
818        }        }
819        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 736  Line 832 
832        generic.name <- chars[2]        generic.name <- chars[2]
833        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
834        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
835          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
836            ## since it causes problems on R CMD check.
837            ##* checking Rd cross-references ... WARNING
838            ##Error in find.package(package, lib.loc) :
839            ##  there is no package called ‘MASS’
840            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
841    
842            generic.desc <-
843              paste("Generic method behind \\code{",object.name,"}",sep="")
844          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
845                                     name=generic.name,                                     name=generic.name,
846                                     created=expr.type,                                     created=expr.type,
# Line 749  Line 853 
853        ## If the function definition is not embedded within the call, then        ## If the function definition is not embedded within the call, then
854        ## the parent is that function. Test whether the the fourth value        ## the parent is that function. Test whether the the fourth value
855        ## looks like a name and add it to parents if so.        ## looks like a name and add it to parents if so.
856        if ( 1 == length(grep("^[\\._\\w]+$",chars[4],perl=TRUE)) ){        if ( grepl("^[\\._\\w]+$",chars[4],perl=TRUE) ){
857          parent <- c(chars[4],parent)          parent <- c(chars[4],parent)
858        }        }
859        res[[object.name]] <- new("DocLink",name=object.name,        res[[object.name]] <- new("DocLink",name=object.name,
# Line 770  Line 874 
874  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
875  ### scanned for inline comments.  ### scanned for inline comments.
876  (doc.link  (doc.link
877  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
878  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
879  ### class definitions.  ### class definitions.
880   ){   ){
# Line 796  Line 900 
900    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
901    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
902    ##details<<    ##details<<
903      ## If there is no explicit title on the first line of setClass, then
904      ## one is made up from the class name.
905      if ( 0 == length(docs$title) ){
906        docs$title <- list(title=paste(class.name,"S4 class"))
907      }
908      ##details<<
909    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
910    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
911    ## 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 942 
942  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
943   ){   ){
944    e <- new.env()    e <- new.env()
945    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
946      ## Error in assignClassDef(Class, classDef, where) :
947      ##   Class "DocLink" has a locked definition in package "inlinedocs"
948      ## Traced to "where" argument in setClassDef which defaults to topenv()
949      ## which in turn is inlinedocs when processing inlinedocs package, hence
950      ## the clash. The following works (under R 2.12.2), so that the topenv()
951      ## now finds e before finding the inlinedocs environment.
952      old <- options(keep.source=TRUE,topLevelEnvironment=e)
953    on.exit(options(old))    on.exit(options(old))
954    exprs <- parse(text=code)    exprs <- parse(text=code)
955      ## TDH 2011-04-07 set this so that no warnings about creating a fake
956      ## package when we try to process S4 classes defined in code
957      e$.packageName <- "inlinedocs.processor"
958    for (i in exprs){    for (i in exprs){
959      tryCatch(eval(i, e),error=function(e){        eval(i, e)
       ##print(e)  
     })  
960    }    }
961    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
962    
963    docs <- list()    docs <- list()
964    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
965    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
966      if(verbose)cat("Applying parsers:\n")
967    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
968      N <- names(parsers[i])      N <- names(parsers[i])
969      if(verbose){      #mm if(verbose){
970        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
971          cat(N," ",sep="")          cat(" this is parser:",N,"\n",sep="")
972        }else cat('. ')        }else cat('.\n')
973      }      #mm }
974      p <- parsers[[i]]      p <- parsers[[i]]
975      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
976      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
977      docs <- combine(docs,L)      # print("mm point1")
978        #save(docs,L,file="/home/mm/SoilR/scripts/docs_L.RData")
979        #print(paste(L,"\n"))
980        #if(N=="exclude")browser()
981        docs <- combine(docs,L) #mm
982      }
983      ## post-process to collapse all character vectors
984      for(i in seq_along(docs)){
985        for(j in seq_along(docs[[i]])){
986          if(names(docs[[i]])[j]!=".s3method")
987          docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
988        }
989    }    }
990    if(verbose)cat("\n")    if(verbose)cat("\n")
991    docs    return(docs)
992  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
993  }  }
994    
# Line 891  Line 1003 
1003  ### description file.  ### description file.
1004  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
1005    
1006  extract.docs.file <- function  extract.docs.file <- structure(function
1007  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
1008  (f,  (f,
1009  ### File name of R code to read and parse.  ### File name of R code to read and parse.
1010   parsers=nondesc.parsers,   parsers=NULL,
1011  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
1012  ### documentation.  ### documentation.
1013   ...   ...
1014  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
1015   ){   ){
1016      if(is.null(parsers))parsers <- nondesc.parsers
1017    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
1018  }  },ex=function(){
1019      f <- system.file("silly","R","silly.R",package="inlinedocs")
1020      extract.docs.file(f)
1021    })
1022    

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