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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 332, Mon Mar 12 12:12:10 2012 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 143  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 364  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 686  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 758  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 792  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 884  Line 966 
966    if(verbose)cat("Applying parsers:\n")    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,"\n",sep="")          cat(" this is parser:",N,"\n",sep="")
972        }else cat('.\n')        }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,env=e,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
977        # print("mm point1")
978        #save(docs,L,file="/home/mm/SoilR/scripts/docs_L.RData")
979      #print(paste(L,"\n"))      #print(paste(L,"\n"))
980      docs <- combine(docs,L)      #if(N=="exclude")browser()
981        docs <- combine(docs,L) #mm
982    }    }
983    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
984    for(i in seq_along(docs)){    for(i in seq_along(docs)){

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