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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 196, Fri Feb 18 12:52:48 2011 UTC revision 352, Mon Apr 9 12:43:46 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      Sys.sleep(1/60) ## to make sure there is at least 1 second elapsed
41    
42      ## However, it will NOT generate Rd for files specified in
43      ## do.not.generate, if they DO exist already.
44      package.skeleton.dx("silly",parsers)
45      mtimes <- data.frame(old,new=file.info(Rd.paths)$mtime)
46      rownames(mtimes) <- Rd.files
47      mtimes$changed <- mtimes$old != mtimes$new
48      print(mtimes)
49      stopifnot(mtimes["silly-package.Rd","changed"]==FALSE)
50      stopifnot(mtimes["Silly-class.Rd","changed"]==FALSE)
51      stopifnot(mtimes["silly.example.Rd","changed"]==TRUE)
52    
53      unlink("silly",recursive=TRUE)
54      setwd(owd)
55    })
56    
57  ### combine lists or character strings  ### combine lists or character strings
58  combine <- function(x,y)UseMethod("combine")  combine <- function(x,y)UseMethod("combine")
59    
# Line 7  Line 63 
63    
64  ### combine lists by adding elements or adding to existing elements  ### combine lists by adding elements or adding to existing elements
65  combine.list <- function(x,y){  combine.list <- function(x,y){
66    toadd <- !names(y)%in%names(x)    toadd <- if(".overwrite"%in%names(y)){
67        y <- y[names(y)!=".overwrite"]
68        rep(TRUE,length(y))
69      }else{
70        !names(y)%in%names(x)
71      }
72    toup <- names(y)[!toadd]    toup <- names(y)[!toadd]
   ##if("doc"%in%names(x))return(x$doc)  
   ##if("doc"%in%names(y))return(y$doc)  
73    x[names(y)[toadd]] <- y[toadd]    x[names(y)[toadd]] <- y[toadd]
74    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])    for(up in toup)x[[up]] <- combine(x[[up]],y[[up]])
75    return(x)    x
76  ### A list, same type as x, but with added elements from y.  ### A list, same type as x, but with added elements from y.
77  }  }
78    
79    
80    getSource <- function
81    ### Extract a function's source code.
82    (fun.obj
83    ### A function.
84     ) {
85          srcref <- attr(fun.obj, "srcref")
86          if (!is.null(srcref)) {
87            ##unlist(strsplit(as.character(srcref), "\n"))
88            as.character(srcref)
89          }
90          else attr(fun.obj, "source")
91    ### Source code lines as a character vector.
92    }
93    
94  ### Prefix for code comments used with grep and gsub.  ### Prefix for code comments used with grep and gsub.
95  prefix <- "^[ \t]*###[ \t]"  prefix <- "^[ \t]*###[ \t]*"
96    
97  decomment <- function  decomment <- function
98  ### Remove comment prefix and join lines of code to form a  ### Remove comment prefix and join lines of code to form a
# Line 43  Line 117 
117   ){   ){
118    FUN <- FUN    FUN <- FUN
119    f <- function(objs,docs,...){    f <- function(objs,docs,...){
120        if(length(objs)==0)return(list())
121      objs <- objs[sapply(objs,subfun)]      objs <- objs[sapply(objs,subfun)]
122      L <- list()      L <- list()
123      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))      on.exit(cat(sprintf("Parser Function failed on %s\n",N)))
124      for(N in names(docs)){      for(N in union(names(docs),names(objs))){
125        o <- objs[[N]]        o <- objs[[N]]
126        L[[N]] <- FUN(src=attr(o,"source"),        L[[N]] <- FUN(src=getSource(o),
127                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)                      name=N,objs=objs,o=o,docs=docs,doc=docs[[N]],...)
128      }      }
129      on.exit()## remove warning message      on.exit()## remove warning message
# Line 86  Line 161 
161  ### Character vector of code lines with preceding whitespace removed.  ### Character vector of code lines with preceding whitespace removed.
162  }  }
163    
 examples.after.return <- function  
 ### 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 = ex, value = value)  
 }  
   
164  prefixed.lines <- structure(function(src,...){  prefixed.lines <- structure(function(src,...){
165  ### The primary mechanism of inline documentation is via consecutive  ### The primary mechanism of inline documentation is via consecutive
166  ### groups of lines matching the specified prefix regular expression  ### groups of lines matching the specified prefix regular expression
# Line 166  Line 190 
190    for(i in seq_along(starts)){    for(i in seq_along(starts)){
191      start <- clines[starts[i]]      start <- clines[starts[i]]
192      end <- clines[ends[i]]      end <- clines[ends[i]]
193      lab <- if(all(grepl("^\\s*#",src[end:(length(src)-1)])))"value"      processed <- gsub("#.*","",gsub("[ }]","",src[(end+1):length(src)]))
194        lab <- if(all(processed==""))"value"
195      else if(start==2)"description"      else if(start==2)"description"
196      else if(is.arg()){      else if(is.arg()){
197        ##twutz: strip leading white spaces and brackets and ,        ##twutz: strip leading white spaces and brackets and ,
# Line 174  Line 199 
199        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
200        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
201        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
202        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
203        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
204      } else {      } else {
205        next;        next;
# Line 193  Line 218 
218  ### the return value  ### the return value
219  ##seealso<< foobar  ##seealso<< foobar
220  }  }
221  src <- attr(test,"source")  src <- getSource(test)
222  prefixed.lines(src)  prefixed.lines(src)
223  extract.xxx.chunks(src)  extract.xxx.chunks(src)
224  })  })
# Line 290  Line 315 
315      }      }
316    while ( k <= length(src) ){    while ( k <= length(src) ){
317      line <- src[k]      line <- src[k]
318        ##print(line)
319        ##if(grepl("^$",line))browser()
320      if ( grepl(extra.regexp,line,perl=TRUE) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
321        ## 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
322        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
323        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
324          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
325        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
326        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
327        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 303  Line 330 
330        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
331        if ( "describe" == new.field ){        if ( "describe" == new.field ){
332          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
333          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
334          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
335          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
336            ## \code{##describe<<} comments.
337          if ( first.describe ){          if ( first.describe ){
338            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
339          } else {          } else {
# Line 392  Line 420 
420          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
421          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
422          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
423          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
424          payload <- comment          payload <- comment
425        } else {        } else {
426          ## 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 442  Line 470 
470  ### with the string in this list (implemented in modify.Rd.file).  ### with the string in this list (implemented in modify.Rd.file).
471  }  }
472    
473    leadingS3generic <- function # check whether function name is an S3 generic
474    ### Determines whether a function name looks like an S3 generic function
475    (name,                     ##<< name of function
476     env,                      ##<< environment to search for additional generics
477     ...)                      ##<< ignored here
478    {
479      ##details<< This function is one of the default parsers, but exposed as
480      ## possibly of more general interest. Given a function name of the form
481      ## x.y.z it looks for the generic function x applying to objects of class
482      ## y.z and also for generic function x.y applying to objects of class z.
483      ##
484      parts <- strsplit(name, ".", fixed = TRUE)[[1]]
485      l <- length(parts)
486      if (l > 1) {
487        for (i in 1:(l - 1)) {
488          ## Look for a generic function (known by the system or defined
489          ## in the package) that matches that part of the function name
490          generic <- paste(parts[1:i], collapse = ".")
491          if (any(generic %in% utils:::getKnownS3generics()) ||
492              utils:::findGeneric(generic, env) != "") {
493            object <- paste(parts[(i + 1):l], collapse = ".")
494            ##details<< Assumes that the first name which matches any known
495            ## generics is the target generic function, so if both x and x.y
496            ## are generic functions, will assume generic x applying to objects
497            ## of class y.z
498            ##value<< If a matching generic found returns a list with a single component:
499            return(list(.s3method=c(generic, object))) ##<< a character vector containing generic name and object name.
500          }
501        }
502      }
503      ##value<< If no matching generic functions are found, returns an empty list.
504      list()
505    }
506    
507  ### Parsers for each function that are constructed automatically. This  ### Parsers for each function that are constructed automatically. This
508  ### 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
509  ### individual object.  ### individual object.
510  forfun.parsers <-  forfun.parsers <-
511    list(prefixed.lines=prefixed.lines,    list(prefixed.lines=prefixed.lines,
        examples.after.return=examples.after.return,  
512         extract.xxx.chunks=extract.xxx.chunks,         extract.xxx.chunks=extract.xxx.chunks,
513         ## title from first line of function def         ## title from first line of function def
514         title.from.firstline=function(src,...){         title.from.firstline=function(src,...){
# Line 479  Line 540 
540  forall.parsers <-  forall.parsers <-
541    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
542         author.from.description=function(desc,...){         author.from.description=function(desc,...){
543           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
544         },         },
545         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
546         erase.format=function(...){         erase.format=function(...){
# Line 497  Line 558 
558             ## Special case for code contained in a function             ## Special case for code contained in a function
559             if (inherits(ex, "function")) {             if (inherits(ex, "function")) {
560               ## If source is available, start from there               ## If source is available, start from there
561               src <- attr(ex, "source")               src <- getSource(ex)
562               if (!is.null(src)) {               if (!is.null(src)) {
563                 ex <- src                 ex <- src
564               } else { ## Use the body of the function               } else { ## Use the body of the function
# Line 505  Line 566 
566               }               }
567               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
568               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
569                 if(ex[1]=="{")ex <- ex[-1]
570               ## all the prefixes               ## all the prefixes
571               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
572               ## Add an empty line before and after example               ## Add an empty line before and after example
# Line 512  Line 574 
574             }             }
575             list(examples = ex)             list(examples = ex)
576           } else list()           } else list()
577         }         },collapse=function(doc,...){
578             L <- lapply(doc,paste,collapse="\n")
579             L$.overwrite <- TRUE
580             L
581           },tag.s3methods=leadingS3generic
582         )         )
583    
584  ### List of parser functions that operate on single objects. This list  ### List of parser functions that operate on single objects. This list
# Line 530  Line 596 
596           sum=x+y) ##<< their sum           sum=x+y) ##<< their sum
597      ##end<<      ##end<<
598    }    }
599    src <- attr(f,"source")    src <- getSource(f)
600    lonely$extract.xxx.chunks(src)    lonely$extract.xxx.chunks(src)
601    lonely$prefixed.lines(src)    lonely$prefixed.lines(src)
602  })  })
# Line 563  Line 629 
629          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
630            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
631          }          }
632          if ( "setMethodS3" == parsed[[on]]@created ){          ## if ( "setMethodS3" == parsed[[on]]@created ){
633            # PhG: this may be wrong! It does not catch correctly how the method          ##   gen <- leadingS3generic(on,topenv())
634            # must be splitted in case of methods containing dots. for instance,          ##   if ( 0 < length(gen) ){
635            # as.data.frame.matrix must be split into: m1 = as.data.frame and          ##     doc$.s3method <- gen$.s3method
636            # m2 = matrix... here you got m1 = as, and m2 = data.frame.matrix!!!          ##     cat("S3method(",gen$.s3method[1],",",gen$.s3method[2],")\n",sep="")
637                    pattern <- "^([^\\.]+)\\.(.*)$"          ##   }
638            doc$s3method=c(m1 <- gsub(pattern,"\\1",on,perl=TRUE),          ## }
               m2 <- gsub(pattern,"\\2",on,perl=TRUE))  
           if ( grepl("\\W",m1,perl=TRUE) ){  
                           m1 <- paste("`",m1,"`",sep="")  
           }  
           cat("S3method(",m1,",",m2,")\n",sep="")  
         }  
639        }        }
640        if("title" %in% names(doc) && !"description" %in% names(doc) ){        if("title" %in% names(doc) && !"description" %in% names(doc) ){
641          ## For short functions having both would duplicate, but a          ## For short functions having both would duplicate, but a
# Line 594  Line 654 
654      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){      } else if(0 == length(res) && inherits(objs[[on]],"standardGeneric")){
655        NULL        NULL
656      } else if(0 == length(res) && "function" %in% class(o)      } else if(0 == length(res) && "function" %in% class(o)
657                && 1 == length(osource <- attr(o,"source"))                && 1 == length(osource <- getSource(o))
658                && grepl(paste("UseMethod(",on,")",sep="\""),osource)                && grepl(paste("UseMethod(",on,")",sep="\""),osource)
659                ){                ){
660        ## phew - this should only pick up R.oo S3 generic definitions like:        ## phew - this should only pick up R.oo S3 generic definitions like:
# Line 656  Line 716 
716  default.parsers <-  default.parsers <-
717    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!    c(extra.code.docs=extra.code.docs, ## TODO: cleanup!
718      sapply(forfun.parsers,forfun),      sapply(forfun.parsers,forfun),
     sapply(forall.parsers,forall),  
719      edit.package.file=function(desc,...){      edit.package.file=function(desc,...){
720        in.details <- setdiff(colnames(desc),"Description")        in.details <- setdiff(colnames(desc),"Description")
721        details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])        details <- sprintf("%s: \\tab %s\\cr",in.details,desc[,in.details])
# Line 666  Line 725 
725                    `tabular{ll}`=details))                    `tabular{ll}`=details))
726        names(L) <- paste(desc[,"Package"],"-package",sep="")        names(L) <- paste(desc[,"Package"],"-package",sep="")
727        L        L
728      }      },
729        sapply(forall.parsers,forall)
730      )      )
731    
732  setClass("DocLink", # Link documentation among related functions  setClass("DocLink", # Link documentation among related functions
733  ### The \code{.DocLink} class provides the basis for hooking together  ### The \code{.DocLink} class provides the basis for hooking together
734  ### documentation of related classes/functions/objects. The aim is that  ### documentation of related classes/functions/objects. The aim is that
735  ### documentation sections missing from the child are  ### documentation sections missing from the child are inherited from
736    ### the parent class.
737           representation(name="character", ##<< name of object           representation(name="character", ##<< name of object
738                          created="character", ##<< how created                          created="character", ##<< how created
739                          parent="character", ##<< parent class or NA                          parent="character", ##<< parent class or NA
# Line 813  Line 874 
874    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
875    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
876    ##details<<    ##details<<
877      ## If there is no explicit title on the first line of setClass, then
878      ## one is made up from the class name.
879      if ( 0 == length(docs$title) ){
880        docs$title <- list(title=paste(class.name,"S4 class"))
881      }
882      ##details<<
883    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
884    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
885    ## 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 849  Line 916 
916  ### Additional arguments to pass to Parser Functions.  ### Additional arguments to pass to Parser Functions.
917   ){   ){
918    e <- new.env()    e <- new.env()
919    old <- options(keep.source=TRUE)    ## KMP 2011-03-09 fix problem with DocLink when inlinedocs ran on itself
920      ## Error in assignClassDef(Class, classDef, where) :
921      ##   Class "DocLink" has a locked definition in package "inlinedocs"
922      ## Traced to "where" argument in setClassDef which defaults to topenv()
923      ## which in turn is inlinedocs when processing inlinedocs package, hence
924      ## the clash. The following works (under R 2.12.2), so that the topenv()
925      ## now finds e before finding the inlinedocs environment.
926      old <- options(keep.source=TRUE,topLevelEnvironment=e)
927    on.exit(options(old))    on.exit(options(old))
928    exprs <- parse(text=code)    exprs <- parse(text=code)
929      ## TDH 2011-04-07 set this so that no warnings about creating a fake
930      ## package when we try to process S4 classes defined in code
931      e$.packageName <- "inlinedocs.processor"
932    for (i in exprs){    for (i in exprs){
933      tryCatch(eval(i, e),error=function(e){        eval(i, e)
       ##print(e)  
     })  
934    }    }
935    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
936    
937    docs <- list()    docs <- list()
938    
   # PhG: Automatically determine who is S3 methods  
   for (name in names(objs)) {  
     parts <- strsplit(name, ".", fixed = TRUE)[[1]]  
         l <- length(parts)  
         if (l > 1) {  
         for (i in 1:(l - 1)) {  
             # Look for a generic function (known by the system or defined  
             # in the package) that matches that part of the function name  
             generic <- paste(parts[1:i], collapse = ".")  
             if (any(generic %in% utils:::getKnownS3generics()) ||  
                 utils:::findGeneric(generic, e) != "") {  
                 object <- paste(parts[(i + 1):l], collapse = ".")  
                 docs[[name]]$s3method <- c(generic, object)  
                 break  
             }  
         }  
     }  
   }  
939    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
940      if(verbose)cat("Applying parsers:\n")
941    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
942      N <- names(parsers[i])      N <- names(parsers[i])
943      if(verbose){      if(verbose){
944        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
945          cat(N," ",sep="")          cat(N,"\n",sep="")
946        }else cat('. ')        }else cat('.\n')
947      }      }
948      p <- parsers[[i]]      p <- parsers[[i]]
949      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
950      L <- p(code=code,objs=objs,docs=docs,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
951        #print(paste(L,"\n"))
952        #if(N=="exclude")browser()
953      docs <- combine(docs,L)      docs <- combine(docs,L)
954    }    }
955    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
956    for(i in seq_along(docs)){    for(i in seq_along(docs)){
957      for(j in seq_along(docs[[i]])){      for(j in seq_along(docs[[i]])){
958          if(names(docs[[i]])[j]!=".s3method")
959        docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")        docs[[i]][[j]] <- paste(docs[[i]][[j]],collapse="\n")
960      }      }
961    }    }
962    if(verbose)cat("\n")    if(verbose)cat("\n")
963    docs    return(docs)
964  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
965  }  }
966    
# Line 914  Line 975 
975  ### description file.  ### description file.
976  nondesc.parsers <- default.parsers[non.descfile.names]  nondesc.parsers <- default.parsers[non.descfile.names]
977    
978  extract.docs.file <- function  extract.docs.file <- structure(function
979  ### Apply all parsers relevant to extract info from just 1 code file.  ### Apply all parsers relevant to extract info from just 1 code file.
980  (f,  (f,
981  ### File name of R code to read and parse.  ### File name of R code to read and parse.
982   parsers=nondesc.parsers,   parsers=NULL,
983  ### Parser Functions to use to parse the code and extract  ### Parser Functions to use to parse the code and extract
984  ### documentation.  ### documentation.
985   ...   ...
986  ### Other arguments to pass to Parser Functions.  ### Other arguments to pass to Parser Functions.
987   ){   ){
988      if(is.null(parsers))parsers <- nondesc.parsers
989    apply.parsers(readLines(f),parsers,verbose=FALSE,...)    apply.parsers(readLines(f),parsers,verbose=FALSE,...)
990  }  },ex=function(){
991      f <- system.file("silly","R","silly.R",package="inlinedocs")
992      extract.docs.file(f)
993    })
994    

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