SCM

SCM Repository

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

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

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 304, Tue Jul 19 17:03:18 2011 UTC revision 376, Mon Jan 28 01:08:01 2013 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 NULL objects.
61    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    
75  ### combine lists or character strings  ### combine lists or character strings
76  combine <- function(x,y)UseMethod("combine")  combine <- function(x,y){
77        UseMethod("combine")
78    }
79    
80  ### combine character strings by pasting them together  ### combine character strings by pasting them together
81  combine.character <- function(x,y)  combine.character <- function(x,y)
# Line 27  Line 103 
103  ### A function.  ### A function.
104   ) {   ) {
105        srcref <- attr(fun.obj, "srcref")        srcref <- attr(fun.obj, "srcref")
106        if (!is.null(srcref)) unlist(strsplit(as.character(srcref), "\n"))        if (!is.null(srcref)) {
107            ##unlist(strsplit(as.character(srcref), "\n"))
108            as.character(srcref)
109          }
110        else attr(fun.obj, "source")        else attr(fun.obj, "source")
111  ### Source code lines as a character vector.  ### Source code lines as a character vector.
112  }  }
# Line 140  Line 219 
219        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)        arg <- gsub("^([^=,]*)[=,].*", "\\1", arg)
220        ##twutz: remove trailing whitespaces        ##twutz: remove trailing whitespaces
221        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)        arg <- gsub("^([^ \t]*)([ \t]+)$","\\1",arg)
222        arg <- gsub("...", "\\dots", arg, fix = TRUE)        arg <- gsub("...", "\\dots", arg, fixed = TRUE)
223        paste("item{",arg,"}",sep="")        paste("item{",arg,"}",sep="")
224      } else {      } else {
225        next;        next;
# Line 256  Line 335 
335      }      }
336    while ( k <= length(src) ){    while ( k <= length(src) ){
337      line <- src[k]      line <- src[k]
338        ##print(line)
339        ##if(grepl("^$",line))browser()
340      if ( grepl(extra.regexp,line,perl=TRUE) ){      if ( grepl(extra.regexp,line,perl=TRUE) ){
341        ## 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
342        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)        new.field <- gsub(extra.regexp,"\\1",line,perl=TRUE)
343        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)        new.contents <- gsub(extra.regexp,"\\2",line,perl=TRUE)
344          ##cat(new.field,"\n-----\n",new.contents,"\n\n")
345        ##details<< As a special case, the construct \code{##describe<<} causes        ##details<< As a special case, the construct \code{##describe<<} causes
346        ## similar processing to the main function arguments to be        ## similar processing to the main function arguments to be
347        ## applied in order to construct a describe block within the        ## applied in order to construct a describe block within the
# Line 269  Line 350 
350        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.        ## block until terminated by a subsequent \code{##}\emph{xxx}\code{<<} line.
351        if ( "describe" == new.field ){        if ( "describe" == new.field ){
352          ##details<< Such regions may be nested, but not in such a way          ##details<< Such regions may be nested, but not in such a way
353          ## that the first element in a \code{describe} is another \code{describe}.          ## that the first element in a \code{describe} is another
354          ## Thus there must be at least one \code{##<<} comment between each          ## \code{describe}.  Thus there must be at least one
355          ## pair of \code{##describe<<} comments.          ## \code{##<<} comment between each pair of
356            ## \code{##describe<<} comments.
357          if ( first.describe ){          if ( first.describe ){
358            stop("consecutive ##describe<< at line",k,"in",name.fun)            stop("consecutive ##describe<< at line",k,"in",name.fun)
359          } else {          } else {
# Line 358  Line 440 
440          ## TDH 2010-06-18 For item{}s in the documentation list names,          ## TDH 2010-06-18 For item{}s in the documentation list names,
441          ## we don't need to have a backslash before, so delete it.          ## we don't need to have a backslash before, so delete it.
442          arg <- gsub("^[\\]+","",arg)          arg <- gsub("^[\\]+","",arg)
443          cur.field <- gsub("...","\\dots",arg,fix=TRUE) ##special case for dots          cur.field <- gsub("...","\\dots",arg,fixed=TRUE) ##special case for dots
444          payload <- comment          payload <- comment
445        } else {        } else {
446          ## 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 478  Line 560 
560  forall.parsers <-  forall.parsers <-
561    list(## Fill in author from DESCRIPTION and titles.    list(## Fill in author from DESCRIPTION and titles.
562         author.from.description=function(desc,...){         author.from.description=function(desc,...){
563           list(author=desc[,"Maintainer"])           list(author=desc[,"Author"])
564         },         },
565         ## The format section sometimes causes problems, so erase it.         ## The format section sometimes causes problems, so erase it.
566         erase.format=function(...){         erase.format=function(...){
# Line 680  Line 762 
762           )           )
763    
764  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
765  ### Using the base \code{\link{parse}} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
766  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
767  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
768  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3
# Line 752  Line 834 
834        generic.name <- chars[2]        generic.name <- chars[2]
835        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
836        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
837          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
838            ## since it causes problems on R CMD check.
839            ##* checking Rd cross-references ... WARNING
840            ##Error in find.package(package, lib.loc) :
841            ##  there is no package called ‘MASS’
842            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
843    
844            generic.desc <-
845              paste("Generic method behind \\code{",object.name,"}",sep="")
846          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
847                                     name=generic.name,                                     name=generic.name,
848                                     created=expr.type,                                     created=expr.type,
# Line 786  Line 876 
876  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
877  ### scanned for inline comments.  ### scanned for inline comments.
878  (doc.link  (doc.link
879  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
880  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
881  ### class definitions.  ### class definitions.
882   ){   ){
# Line 812  Line 902 
902    docs <- combine(docs,lonely$prefixed.lines(chunk.source))    docs <- combine(docs,lonely$prefixed.lines(chunk.source))
903    docs$title <- lonely$title.from.firstline(chunk.source)    docs$title <- lonely$title.from.firstline(chunk.source)
904    ##details<<    ##details<<
905      ## If there is no explicit title on the first line of setClass, then
906      ## one is made up from the class name.
907      if ( 0 == length(docs$title) ){
908        docs$title <- list(title=paste(class.name,"S4 class"))
909      }
910      ##details<<
911    ## The class definition skeleton includes an \code{Objects from the Class}    ## The class definition skeleton includes an \code{Objects from the Class}
912    ## section, to which any \code{##details<<} documentation chunks are    ## section, to which any \code{##details<<} documentation chunks are
913    ## written. It is given a vanilla content if there are no specific    ## written. It is given a vanilla content if there are no specific
# Line 862  Line 958 
958    ## package when we try to process S4 classes defined in code    ## package when we try to process S4 classes defined in code
959    e$.packageName <- "inlinedocs.processor"    e$.packageName <- "inlinedocs.processor"
960    for (i in exprs){    for (i in exprs){
     ## TDH 2011-04-07 Disable this tryCatch since it makes it harder  
     ##to debug errors/warnings in the evaluated code  
   
     ##tryCatch({  
961        eval(i, e)        eval(i, e)
     ##},error=function(e){  
       ##print(e)  
     ##})  
962    }    }
963    objs <- sapply(ls(e),get,e,simplify=FALSE)    objs <- sapply(ls(e),get,e,simplify=FALSE)
964    
965    docs <- list()    docs <- list()
966    
967    ## apply parsers in sequence to code and objs    ## apply parsers in sequence to code and objs
968      if(verbose)cat("Applying parsers:\n")
969    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
970      N <- names(parsers[i])      N <- names(parsers[i])
971      if(verbose){      #mm if(verbose){
972        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
973          cat(N," ",sep="")          cat(" this is parser:",N,"\n",sep="")
974        }else cat('. ')        }else cat('.\n')
975      }      #mm }
976      p <- parsers[[i]]      p <- parsers[[i]]
977      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
978      L <- p(code=code,objs=objs,docs=docs,env=e,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
979      docs <- combine(docs,L)      # print("mm point1")
980        #save(docs,L,file="/home/mm/SoilR/scripts/docs_L.RData")
981        #print(paste(L,"\n"))
982        #if(N=="exclude")browser()
983        docs <- combine(docs,L) #mm
984    }    }
985    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
986    for(i in seq_along(docs)){    for(i in seq_along(docs)){
# Line 896  Line 990 
990      }      }
991    }    }
992    if(verbose)cat("\n")    if(verbose)cat("\n")
993    docs    return(docs)
994  ### A list of extracted documentation from code.  ### A list of extracted documentation from code.
995  }  }
996    

Legend:
Removed from v.304  
changed lines
  Added in v.376

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge