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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 356, Mon Apr 9 15:39:09 2012 UTC revision 393, Tue Oct 1 07:15:26 2013 UTC
# Line 57  Line 57 
57    setwd(owd)    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 491  Line 508 
508        ## Look for a generic function (known by the system or defined        ## Look for a generic function (known by the system or defined
509        ## in the package) that matches that part of the function name        ## in the package) that matches that part of the function name
510        generic <- paste(parts[1:i], collapse = ".")        generic <- paste(parts[1:i], collapse = ".")
511        if (any(generic %in% utils:::getKnownS3generics()) ||        if (any(generic %in% getKnownS3generics()) ||
512            utils:::findGeneric(generic, env) != "") {            findGeneric(generic, env) != "") {
513          object <- paste(parts[(i + 1):l], collapse = ".")          object <- paste(parts[(i + 1):l], collapse = ".")
514          ##details<< Assumes that the first name which matches any known          ##details<< Assumes that the first name which matches any known
515          ## generics is the target generic function, so if both x and x.y          ## generics is the target generic function, so if both x and x.y
# Line 569  Line 586 
586               }               }
587               ## Eliminate leading and trailing code               ## Eliminate leading and trailing code
588               ex <- ex[-c(1, length(ex))]               ex <- ex[-c(1, length(ex))]
589                 if( length(ex) ){  # avoid error on yet empty example
590               if(ex[1]=="{")ex <- ex[-1]               if(ex[1]=="{")ex <- ex[-1]
591               ## all the prefixes               ## all the prefixes
592               ex <- kill.prefix.whitespace(ex)               ex <- kill.prefix.whitespace(ex)
593                 }
594               ## Add an empty line before and after example               ## Add an empty line before and after example
595               ex <- c("", ex, "")               ex <- c("", ex, "")
596             }             }
# Line 623  Line 642 
642    extract.docs.try <- function(o,on)    extract.docs.try <- function(o,on)
643      {      {
644        ## Note: we could use parsed information here too, but that        ## Note: we could use parsed information here too, but that
645        ## would produce different results for setMethodS3 etc.        ## would produce different results for R.methodsS3::setMethodS3 etc.
646        doc <- list()        doc <- list()
647        if ( !is.null(parsed[[on]]) ){        if ( !is.null(parsed[[on]]) ){
648          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics          if ( !is.na(parsed[[on]]@code[1]) ){ # no code given for generics
# Line 632  Line 651 
651          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){          if(!"description"%in%names(doc) && !is.na(parsed[[on]]@description) ){
652            doc$description <- parsed[[on]]@description            doc$description <- parsed[[on]]@description
653          }          }
654          ## if ( "setMethodS3" == parsed[[on]]@created ){          ## if ( "R.methodsS3::setMethodS3" == parsed[[on]]@created ){
655          ##   gen <- leadingS3generic(on,topenv())          ##   gen <- leadingS3generic(on,topenv())
656          ##   if ( 0 < length(gen) ){          ##   if ( 0 < length(gen) ){
657          ##     doc$.s3method <- gen$.s3method          ##     doc$.s3method <- gen$.s3method
# Line 748  Line 767 
767  ### Using the base \code{parse} function, analyse the file to link  ### Using the base \code{parse} function, analyse the file to link
768  ### preceding "prefix" comments to each active chunk. Those comments form  ### preceding "prefix" comments to each active chunk. Those comments form
769  ### the default description for that chunk. The analysis also looks for  ### the default description for that chunk. The analysis also looks for
770  ### S4 class "setClass" calls and R.oo setConstructorS3 and setMethodS3  ### S4 class "setClass" calls and R.oo setConstructorS3 and R.methodsS3::setMethodS3
771  ### calls in order to link the documentation of those properly.  ### calls in order to link the documentation of those properly.
772  (code  (code
773  ### Lines of R source code in a character vector - note that any  ### Lines of R source code in a character vector - note that any
# Line 784  Line 803 
803      ## \item{assignment (<-)}{Ordinary assignment of value/function;}      ## \item{assignment (<-)}{Ordinary assignment of value/function;}
804      ## \item{setClass}{Definition of S4 class;}      ## \item{setClass}{Definition of S4 class;}
805      ## \item{setConstructorS3}{Definition of S3 class using R.oo package;}      ## \item{setConstructorS3}{Definition of S3 class using R.oo package;}
806      ## \item{setMethodS3}{Definition of method for S3 class using R.oo package.}}      ## \item{R.methodsS3::setMethodS3}{Definition of method for S3 class using R.oo package.}}
807      ## Additionally, the value may be a name of a function defined elsewhere,      ## Additionally, the value may be a name of a function defined elsewhere,
808      ## in which case the documentation should be copied from that other definition.      ## in which case the documentation should be copied from that other definition.
809      ## This is handled using the concept of documentation links.      ## This is handled using the concept of documentation links.
# Line 806  Line 825 
825                                  parent=parent,                                  parent=parent,
826                                  code=paste(chunks[[k]],sep=""),                                  code=paste(chunks[[k]],sep=""),
827                                  description=default.description)                                  description=default.description)
828      } else if ( expr.type == "setMethodS3" ){      } else if ( expr.type == "R.methodsS3::setMethodS3" || expr.type ==  "R.methodsS3::R.methodsS3::setMethodS3"){
829        ##details<< The \code{setMethodS3} calls introduce additional        ##details<< The \code{R.methodsS3::setMethodS3} calls introduce additional
830        ## complexity: they will define an additional S3 generic (which        ## complexity: they will define an additional S3 generic (which
831        ## needs documentation to avoid warnings at package build time)        ## needs documentation to avoid warnings at package build time)
832        ## unless one already exists. This also is handled by "linking"        ## unless one already exists. This also is handled by "linking"
# Line 951  Line 970 
970    if(verbose)cat("Applying parsers:\n")    if(verbose)cat("Applying parsers:\n")
971    for(i in seq_along(parsers)){    for(i in seq_along(parsers)){
972      N <- names(parsers[i])      N <- names(parsers[i])
973      if(verbose){      #mm if(verbose){
974        if(is.character(N) && N!=""){        if(is.character(N) && N!=""){
975          cat(N,"\n",sep="")          cat(" this is parser:",N,"\n",sep="")
976        }else cat('.\n')        }else cat('.\n')
977      }      #mm }
978      p <- parsers[[i]]      p <- parsers[[i]]
979      ## This is the argument list that each parser receives:      ## This is the argument list that each parser receives:
980      L <- p(code=code,objs=objs,docs=docs,env=e,...)      L <- p(code=code,objs=objs,docs=docs,env=e,...)
981        # print("mm point1")
982        #save(docs,L,file="/home/mm/SoilR/scripts/docs_L.RData")
983      #print(paste(L,"\n"))      #print(paste(L,"\n"))
984      #if(N=="exclude")browser()      #if(N=="exclude")browser()
985      docs <- combine(docs,L)      docs <- combine(docs,L) #mm
986    }    }
987    ## post-process to collapse all character vectors    ## post-process to collapse all character vectors
988    for(i in seq_along(docs)){    for(i in seq_along(docs)){

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