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 332, Mon Mar 12 12:12:10 2012 UTC revision 393, Tue Oct 1 07:15:26 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 143  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 364  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 432  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 510  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 564  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 573  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 686  Line 764 
764           )           )
765    
766  extract.file.parse <- function # File content analysis  extract.file.parse <- function # File content analysis
767  ### Using the base \code{\link{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 725  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 747  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 758  Line 836 
836        generic.name <- chars[2]        generic.name <- chars[2]
837        object.name <- paste(generic.name,chars[3],sep=".")        object.name <- paste(generic.name,chars[3],sep=".")
838        if ( is.null(res[[generic.name]]) ){        if ( is.null(res[[generic.name]]) ){
839          generic.desc <- paste("Generic method behind \\code{\\link{",object.name,"}}",sep="")          ## TDH 9 April 2012 Do NOT add \\link in generic.desc below,
840            ## since it causes problems on R CMD check.
841            ##* checking Rd cross-references ... WARNING
842            ##Error in find.package(package, lib.loc) :
843            ##  there is no package called ‘MASS’
844            ##Calls: <Anonymous> -> lapply -> FUN -> find.package
845    
846            generic.desc <-
847              paste("Generic method behind \\code{",object.name,"}",sep="")
848          res[[generic.name]] <- new("DocLink",          res[[generic.name]] <- new("DocLink",
849                                     name=generic.name,                                     name=generic.name,
850                                     created=expr.type,                                     created=expr.type,
# Line 792  Line 878 
878  ### in the form \code{setClass("classname",\dots)} are also located and  ### in the form \code{setClass("classname",\dots)} are also located and
879  ### scanned for inline comments.  ### scanned for inline comments.
880  (doc.link  (doc.link
881  ### DocLink object as created by \code{\link{extract.file.parse}}.  ### DocLink object as created by \code{extract.file.parse}.
882  ### Note that \code{source} statements are \emph{ignored} when scanning for  ### Note that \code{source} statements are \emph{ignored} when scanning for
883  ### class definitions.  ### class definitions.
884   ){   ){
# Line 884  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      docs <- combine(docs,L)      #if(N=="exclude")browser()
985        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)){

Legend:
Removed from v.332  
changed lines
  Added in v.393

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