Fixed the dontrun bug.

kaneplusplus · Oct 16, 2015 · 74f74b8 · 74f74b8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: bigmemory
-Version: 4.5.3
-Date: 2015-10-14
+Version: 4.5.4
+Date: 2015-10-16
 Title: Manage Massive Matrices with Shared Memory and Memory-Mapped Files
 Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson <jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles Determan Jr. <cdetermanjr@gmail.com>
 Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>

diff --git a/man-roxygen/attach.big.matrix_template.R b/man-roxygen/attach.big.matrix_template.R
@@ -30,7 +30,7 @@
 #' \email{<bigmemoryauthors@@gmail.com>}
 #' @seealso \code{\link{bigmemory}}, \code{\link{big.matrix}}, or the class 
 #' documentation \code{\linkS4class{big.matrix}}.
-#' @examples \dontrun{
+#' @examples 
 #' # The example is quite silly, as you wouldn't likely do this in a
 #' # single R session.  But if zdescription were passed to another R session
 #' # via SNOW, foreach, or even by a simple file read/write,
@@ -53,5 +53,4 @@
 #' zz[1,1] <- -100
 #' y[,]
 #' z[,]
-#' }
 #' @keywords classes methods
diff --git a/man-roxygen/core_template.R b/man-roxygen/core_template.R
@@ -118,8 +118,7 @@
 #' \code{\linkS4class{big.matrix}}; \code{\link{attach.big.matrix}} and
 #' \code{\link{describe}}.  Sister packages \pkg{biganalytics}, \pkg{bigtabulate},
 #' \pkg{synchronicity}, and \pkg{bigalgebra} provide advanced functionality.
-#' @examples \dontrun{
-#' # Not Run
+#' @examples 
 #' library(bigmemory)
 #' x <- big.matrix(10, 2, type='integer', init=-5)
 #' options(bigmemory.allow.dimnames=TRUE)
@@ -140,7 +139,6 @@
 #' # second R process would give access to the same object in memory.
 #' # Please see the package vignette for real examples.
 #' 
-#' # Not run
 #' z <- big.matrix(3, 3, type='integer', init=3)
 #' z[,]
 #' dim(z)
@@ -173,5 +171,4 @@
 #' zz[1,1] <- 0
 #' zzz <- attach.big.matrix(describe(z))
 #' zzz[,]
-#' }
 #' @keywords classes methods
diff --git a/man-roxygen/deepcopy_template.R b/man-roxygen/deepcopy_template.R
@@ -36,11 +36,9 @@
 #' @seealso \code{\link{big.matrix}}
 #' @keywords methods
 #' @examples
-#' \dontrun{
 #' x <- as.big.matrix(matrix(1:30, 10, 3))
 #' y <- deepcopy(x, -1)    # Don't include the first column.
 #' x
 #' y
 #' head(x)
 #' head(y)
-#' }
diff --git a/man-roxygen/flush_template.R b/man-roxygen/flush_template.R
@@ -11,12 +11,11 @@
 #'    on flushing creates a bottleneck (likely near the threshold of available \acronym{RAM}).
 #' @return \code{TRUE} or \code{FALSE} (invisible), indicating whether or not the flush was successful.
 #' @author John W. Emerson and Michael J. Kane
-#' @examples \dontrun{
+#' @examples 
 #' x <- big.matrix(nrow=3, ncol=3, backingfile='flushtest.bin',
 #'                 descriptorfile='flushtest.desc', type='integer')
 #' x[1,1] <- 0
 #' flush(x)
-#' }
 #' @docType methods
 #' @rdname flush-methods
 #' @keywords methods
diff --git a/man-roxygen/morder_template.R b/man-roxygen/morder_template.R
@@ -43,12 +43,11 @@
 #' 
 #' @author Michael J. Kane \email{<bigmemoryauthors@@gmail.com>}
 #' @seealso \code{\link{order}}
-#' @examples \dontrun{
+#' @examples 
 #' m = matrix(as.double(as.matrix(iris)), nrow=nrow(iris))
 #' morder(m, 1)
 #' order(m[,1])
 #' 
 #' m[order(m[,1]), 2]
 #' mpermute(m, cols=1)
 #' m[,2]
-#' }
diff --git a/man-roxygen/mwhich_template.R b/man-roxygen/mwhich_template.R
@@ -38,7 +38,7 @@
 #' @return a vector of row indices satisfying the criteria.
 #' @author John W. Emerson \email{<bigmemoryauthors@@gmail.com>}
 #' @seealso \code{\link{big.matrix}}, \code{\link{which}}
-#' @examples \dontrun{
+#' @examples
 #' x <- as.big.matrix(matrix(1:30, 10, 3))
 #' options(bigmemory.allow.dimnames=TRUE)
 #' colnames(x) <- c("A", "B", "C")
@@ -77,5 +77,4 @@
 #' mwhich(x, 1, Inf, 'eq')
 #' mwhich(x, 1, 1, 'gt')
 #' mwhich(x, 1, 1, 'le')
-#' }
 #' @keywords methods
diff --git a/man-roxygen/sub.big.matrix_template.R b/man-roxygen/sub.big.matrix_template.R
@@ -24,12 +24,11 @@
 #' It is not a physical copy.  Only contiguous blocks may form a submatrix.
 #' @author John W. Emerson and Michael J. Kane
 #' @seealso \code{\link{big.matrix}}
-#' @examples \dontrun{
+#' @examples 
 #' x <- big.matrix(10, 5, init=0, type="double")
 #' x[,] <- 1:50
 #' y <- sub.big.matrix(x, 2, 9, 2, 3)
 #' y[,]
 #' y[1,1] <- -99
 #' x[,]
-#' }
 #' @keywords methods
diff --git a/man-roxygen/write.big.matrix_template.R b/man-roxygen/write.big.matrix_template.R
@@ -64,7 +64,7 @@
 #' @author John W. Emerson and Michael J. Kane 
 #' \email{<bigmemoryauthors@@gmail.com>}
 #' @seealso \code{\link{big.matrix}}
-#' @examples \dontrun{
+#' @examples
 #' # Without specifying the type, this big.matrix x will hold integers.
 #' 
 #' x <- as.big.matrix(matrix(1:10, 5, 2))
@@ -99,5 +99,4 @@
 #' 
 #' # The following would fail with a dimension mismatch:
 #' if (FALSE) y <- read.big.matrix("IrisData.txt", header=TRUE)
-#' }
 #' @keywords methods
diff --git a/man/big.matrix.Rd b/man/big.matrix.Rd
@@ -200,8 +200,6 @@ factors numeric before forming the \code{big.matrix}.  Level labels are
 not preserved and must be managed by the user if desired.
 }
 \examples{
-\dontrun{
-# Not Run
 library(bigmemory)
 x <- big.matrix(10, 2, type='integer', init=-5)
 options(bigmemory.allow.dimnames=TRUE)
@@ -222,7 +220,6 @@ x[,]
 # second R process would give access to the same object in memory.
 # Please see the package vignette for real examples.
 
-# Not run
 z <- big.matrix(3, 3, type='integer', init=3)
 z[,]
 dim(z)
@@ -256,7 +253,6 @@ zz[1,1] <- 0
 zzz <- attach.big.matrix(describe(z))
 zzz[,]
 }
-}
 \author{
 John W. Emerson and Michael J. Kane
 \email{<bigmemoryauthors@gmail.com>}

diff --git a/man/deepcopy.Rd b/man/deepcopy.Rd
@@ -58,15 +58,13 @@ traditional syntax would only copy the object (the pointer to the
 It can also make a copy of only a subset of columns.
 }
 \examples{
-\dontrun{
 x <- as.big.matrix(matrix(1:30, 10, 3))
 y <- deepcopy(x, -1)    # Don't include the first column.
 x
 y
 head(x)
 head(y)
 }
-}
 \seealso{
 \code{\link{big.matrix}}
 }

diff --git a/man/flush-methods.Rd b/man/flush-methods.Rd
@@ -27,13 +27,11 @@ This function flushes any modified data (in \acronym{RAM}) of a file-backed
    on flushing creates a bottleneck (likely near the threshold of available \acronym{RAM}).
 }
 \examples{
-\dontrun{
 x <- big.matrix(nrow=3, ncol=3, backingfile='flushtest.bin',
                 descriptorfile='flushtest.desc', type='integer')
 x[1,1] <- 0
 flush(x)
 }
-}
 \author{
 John W. Emerson and Michael J. Kane
 }

diff --git a/man/morder.Rd b/man/morder.Rd
@@ -70,7 +70,6 @@ this function has side-effects, that is \code{x} is changed when this
 function is called.
 }
 \examples{
-\dontrun{
 m = matrix(as.double(as.matrix(iris)), nrow=nrow(iris))
 morder(m, 1)
 order(m[,1])
@@ -79,7 +78,6 @@ m[order(m[,1]), 2]
 mpermute(m, cols=1)
 m[,2]
 }
-}
 \author{
 Michael J. Kane \email{<bigmemoryauthors@gmail.com>}
 }

diff --git a/man/mwhich.Rd b/man/mwhich.Rd
@@ -53,7 +53,6 @@ and \code{\link{intersect}}, for example) on the results of multiple
  pointer trick (accessor) in \acronym{C++}.
 }
 \examples{
-\dontrun{
 x <- as.big.matrix(matrix(1:30, 10, 3))
 options(bigmemory.allow.dimnames=TRUE)
 colnames(x) <- c("A", "B", "C")
@@ -93,7 +92,6 @@ mwhich(x, 1, Inf, 'eq')
 mwhich(x, 1, 1, 'gt')
 mwhich(x, 1, 1, 'le')
 }
-}
 \author{
 John W. Emerson \email{<bigmemoryauthors@gmail.com>}
 }

diff --git a/man/sub.big.matrix.Rd b/man/sub.big.matrix.Rd
@@ -50,15 +50,13 @@ object that references a contiguous set of columns and rows of another
  otherwise.
 }
 \examples{
-\dontrun{
 x <- big.matrix(10, 5, init=0, type="double")
 x[,] <- 1:50
 y <- sub.big.matrix(x, 2, 9, 2, 3)
 y[,]
 y[1,1] <- -99
 x[,]
 }
-}
 \author{
 John W. Emerson and Michael J. Kane
 }

diff --git a/man/write.big.matrix.Rd b/man/write.big.matrix.Rd
@@ -110,7 +110,6 @@ Or perhaps to specify columns targeted for factor or character conversion
 to numeric values.  Would you use such features?  Email us and let us know!
 }
 \examples{
-\dontrun{
 # Without specifying the type, this big.matrix x will hold integers.
 
 x <- as.big.matrix(matrix(1:10, 5, 2))
@@ -146,7 +145,6 @@ head(y)
 # The following would fail with a dimension mismatch:
 if (FALSE) y <- read.big.matrix("IrisData.txt", header=TRUE)
 }
-}
 \author{
 John W. Emerson and Michael J. Kane
 \email{<bigmemoryauthors@gmail.com>}