@@ -1,7 +1,7 @@

 Package: Streamer

 Type: Package

 Title: Enabling stream processing of large files

-Version: 1.3.7

+Version: 1.3.8

 Author: Martin Morgan, Nishant Gopalakrishnan

 Maintainer: Martin Morgan <mtmorgan@fhcrc.org>

 Description: Large data files can be difficult to work with in R,

@@ -1,39 +1,35 @@

 .Seq <- setRefClass("Seq",

     fields = list(

-      from="numeric", to="numeric", by="numeric", length.out="integer"),

+      .start="ANY",

+      from="ANY", to="ANY", by="ANY", yieldSize="integer"),

     contains="Producer",

     methods = list(

-      initialize = function(..., length.out) {

-          ## increment length.out to avoid repeated addition

-          callSuper(..., length.out=as.integer(length.out) + 1L)

+      initialize = function(..., yieldSize) {

+          ## increment yieldSize to avoid repeated addition

+          callSuper(..., yieldSize=as.integer(yieldSize) + 1L)

+      },

+      reset = function() {

+          from <<- .start

+          invisible(.self)

       },

       yield = function() {

           if ((from - to) * by > 0)

               return(numeric())

-          s <- seq(from, by=by, length.out=length.out)

-          from <<- as.numeric(s[length(s)])

+          s <- seq(from, by=by, length.out=yieldSize)

+          from <<- s[length(s)]

           s <- s[-length(s)]

           s[s <= to]

       },

       show = function() {

           cat("from:", from, "\nto:", to, "\nby:", by,

-              "\nlength.out:", length.out - 1L, "\n")

+              "\nyieldSize:", yieldSize - 1L, "\n")

       }))

 Seq <-

-    function(from=1L, to, by=1L, length.out=1L, ...)

+    function(from=1L, to=.Machine$integer.max, by=1L, yieldSize=1L,

+             ...)

 {

-    if (missing(to)) {

-        to <-

-            if (is.integer(from)) {

-                .Machine$integer.max

-            } else Inf

-        if (by < 0)

-            to <- -to

-    }

-

-    if (from > to)

-        stop("'from' must be less than or equal to 'to'")

-    length.out <- as.integer(length.out)

-    .Seq$new(from=from, to=to, by=by, length.out=length.out, ...)

+    yieldSize <- as.integer(yieldSize)

+    .Seq$new(.start=from, from=from, to=to, by=by,

+             yieldSize=yieldSize, ...)

 }

@@ -4,20 +4,20 @@ test_lapply_Producer <- function()

     exp <- unname(lapply(vals, mean))

     ## function

-    obs <- lapply(Seq(to=47, length.out=7), mean)

+    obs <- lapply(Seq(to=47, yieldSize=7), mean)

     checkIdentical(exp, obs)

     ## anonymous function

-    obs <- lapply(Seq(to=47, length.out=7), function(x) mean(x))

+    obs <- lapply(Seq(to=47, yieldSize=7), function(x) mean(x))

     checkIdentical(exp, obs)

     ## ... args

-    obs <- lapply(Seq(to=47, length.out=7), function(x, z) mean(z), z=1:10)

+    obs <- lapply(Seq(to=47, yieldSize=7), function(x, z) mean(z), z=1:10)

     checkIdentical(mean(1:10), unique(unlist(obs)))

     ## env

     ZZZ <- 1:10

-    res <- lapply(Seq(to=47, length.out=7), function(x) mean(ZZZ))

+    res <- lapply(Seq(to=47, yieldSize=7), function(x) mean(ZZZ))

     checkIdentical(mean(ZZZ), unique(unlist(res)))

     ## error

@@ -25,10 +25,10 @@ test_lapply_Producer <- function()

     checkException(lapply(Seq(to=5), fun), silent=TRUE)

     ## error partial results

-    res <- tryCatch(sapply(Seq(to=5), fun), error = function(err) {

+    res <- tryCatch(sapply(Seq(to=5L), fun), error = function(err) {

         err$partialResult

     })

-    checkIdentical(c(1, 2), res)

+    checkIdentical(1:2, res)

     ## trigger re-allocation

     ## res <- lapply(Seq(to=4096*4),

@@ -96,7 +96,7 @@

 showClass("Producer")

 showMethods(class="Producer", where="package:Streamer")

-sapply(Seq(to=47, length.out=7), function(elt) {

+sapply(Seq(to=47, yieldSize=7), function(elt) {

     c(n = length(elt), xbar = mean(elt))

 })

@@ -13,21 +13,23 @@

 }

-\usage{Seq(from = 1L, to, by = 1L, length.out=1L, ...)}

+\usage{

+Seq(from = 1L, to=.Machine$integer.max, by = 1L, yieldSize=1L,

+    ...)

+}

 \arguments{

-  \item{from}{A \code{numeric(1)} starting value.}

-

-  \item{to}{A \code{numeric(1)} ending value. If missing, it is set to

-    the maximum (or minimum, depending on \code{by}) value representable

-    for the class of \code{from}, creating an (effectively) infinite

-    stream.}

+  \item{from}{A starting value of any type (e.g., \code{integer},

+    \code{numeric} supported by \code{base::seq}.}

-  \item{by}{A \code{numeric(1)} indicating the increment between

-    successive numbers in the sequence.}

+  \item{to}{An ending value, typically of the same type as \code{from}.}

+  

+  \item{by}{A value, typically of the same class as \code{from},

+    indicating the increment between successive numbers in the

+    sequence. \code{by = 0} can create an infinite stream.}

-  \item{length.out}{A \code{integer(1)} indicating the length of the

+  \item{yieldSize}{A \code{integer(1)} indicating the length of the

     output sequence each time \code{yield()} is invoked.}

   \item{...}{Additional arguments passed to \code{\linkS4class{Producer}}.}

@@ -38,24 +40,15 @@

   Use \code{Seq} to construct instances of this class.

 }

-\section{Fields}{

-  Fields of this class are

-  \describe{

-    \item{\code{from}:}{\code{numeric(1)} (current) sequence starting value.}

-    \item{\code{to}:}{\code{numeric(1)} sequence ending value.}

-    \item{\code{by}:}{\code{numeric(1)} sequence increment value.}

-    \item{\code{length.out}:}{\code{integer(1)} sequence length on yield.}

-  }

-}

+\section{Internal Class Fields and Methods}{

-\section{Methods}{

-  Methods of this class are

-  \describe{

+  Internal fields of this class are are described with

+  \code{getRefClass("Seq")$fields}.

-    \item{\code{yield()}:}{A sequence as specified by current

-      \code{from}, \code{to}, \code{by}, and \code{length.out} values.}

+  Internal methods of this class are described with

+  \code{getRefClass("Seq")$methods()} and

+  \code{getRefClass("Seq")$help()}.

-  }

 }

 \author{Martin Morgan \url{mtmorgan@fhcrc.org}}

@@ -63,7 +56,7 @@

 \seealso{\code{\link{stream}}}

 \examples{

-s <- Seq(1, 10, length.out=5)

+s <- Seq(1, 10, yieldSize=5)

 while(length(y <- yield(s)))

     print(y)

 }

@@ -110,7 +110,7 @@

 \examples{

 if (.Platform$OS.type != "windows") {

     team <- Team(function(x) { Sys.sleep(1); mean(x) }, size=5)

-    s <- stream(Seq(to=50, length.out=5), team)

+    s <- stream(Seq(to=50, yieldSize=5), team)

     system.time({while(length(y <- yield(s)))

         print(y)

     })