fixed CRAN checking issue, i hope...

edwindj · May 11, 2015 · 7de1da7 · 7de1da7
1 parent 821a72b
commit 7de1da7
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Showing 18 changed files with 82 additions and 47 deletions.
diff --git a/examples/cumsum.R b/examples/cumsum.R
@@ -1,14 +1,14 @@
 x <- 1:10000
-tmp <- cumsum.ff(ff(x), BATCHBYTES=10000)
+tmp <- cumsum(ff(x))
 class(tmp)
 table(tmp[] == cumsum(x))
 
 x <- rnorm(1000)
-tmp <- cummax.ff(ff(x), BATCHBYTES=10000)
+tmp <- cummax(ff(x))
 table(tmp[] == cummax(x))
-tmp <- cummin.ff(ff(x), BATCHBYTES=10000)
+tmp <- cummin(ff(x))
 table(tmp[] == cummin(x))
-tmp <- cumprod.ff(ff(x), BATCHBYTES=10000)
+tmp <- cumprod(ff(x))
 table(tmp[] == cumprod(x))
 
 ## S3 type of calling

diff --git a/examples/extract.R b/examples/extract.R
@@ -1,12 +1,9 @@
-x <- ff(1:10)
-y <- ff(11:20)
-
 ## extractors
 x <- ff(1:10)
 y <- ff(11:20)
 idx <- ff(c(FALSE, TRUE, NA, TRUE))
 x[idx]
-idx <- ff(c(FALSE, FALSE, FALSE))
+idx <- ff(c(FALSE, FALSE, TRUE))
 x[idx]
 idx <- ff(1:3)
 x[idx]
@@ -15,8 +12,8 @@ x[idx]
 idx <- ff(c(FALSE, TRUE, NA, TRUE))
 x[idx] <- y[idx]
 x
-idx <- ff(c(FALSE, FALSE, FALSE))
-try(x[idx] <- y[idx]) ## not allowed
+idx <- ff(c(FALSE, FALSE, TRUE))
+try(x[idx] <- y[idx], silent = T) ## not allowed
 x
 idx <- ff(1:3)
 x[idx] <- y[idx]

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
@@ -11,7 +11,7 @@ Version: 0.12.0.2000
 URL: http://github.com/edwindj/ffbase
 Date: 2015-05-05
 Depends:
-    R (>= 2.12.0), ff (>= 2.2-11)
+    R (>= 2.12.0),ff(>= 2.2-11)
 Imports:
     fastmatch, bit
 Suggests:

diff --git a/pkg/NAMESPACE b/pkg/NAMESPACE
@@ -42,6 +42,10 @@ S3method(ceiling,ff_vector)
 S3method(compact,ff)
 S3method(cos,ff_vector)
 S3method(cosh,ff_vector)
+S3method(cummax,ff)
+S3method(cummin,ff)
+S3method(cumprod,ff)
+S3method(cumsum,ff)
 S3method(cut,ff)
 S3method(diff,ff)
 S3method(digamma,ff_vector)
@@ -74,15 +78,23 @@ S3method(signif,ff_vector)
 S3method(sin,ff_vector)
 S3method(sinh,ff_vector)
 S3method(sqrt,ff_vector)
+S3method(subset,ff)
+S3method(subset,ffdf)
+S3method(sum,ff)
 S3method(table,default)
 S3method(table,ff)
 S3method(tan,ff_vector)
 S3method(tanh,ff_vector)
+S3method(transform,ffdf)
 S3method(trigamma,ff_vector)
 S3method(trunc,ff_vector)
+S3method(unique,ff)
+S3method(unique,ffdf)
 S3method(with,ffdf)
 S3method(within,ffdf)
 export("%in%")
+export("[.ff")
+export("[<-.ff")
 export(addfforder)
 export(bigglm.ffdf)
 export(binned_sum)
@@ -93,10 +105,6 @@ export(bySum)
 export(chunkify)
 export(condMean)
 export(condSum)
-export(cummax.ff)
-export(cummin.ff)
-export(cumprod.ff)
-export(cumsum.ff)
 export(expand.ffgrid)
 export(ffappend)
 export(ffdfappend)
@@ -115,29 +123,54 @@ export(ffseq_len)
 export(ffsorted)
 export(ffwhich)
 export(ikey)
+export(is.na.ff)
 export(laf_to_ffdf)
 export(load.ffdf)
 export(log10.ff_vector)
 export(log2.ff_vector)
 export(move.ffdf)
 export(pack.ffdf)
-export(rbind.ffdf)
 export(rle_ff)
 export(save.ffdf)
 export(set_ffbase_logging)
-export(subset.ff)
-export(subset.ffdf)
-export(sum.ff)
 export(table)
 export(tabulate.ff)
-export(transform.ffdf)
-export(unique.ff)
-export(unique.ffdf)
 export(unpack.ffdf)
 import(bit)
 importFrom(fastmatch,fmatch)
+importFrom(ff,"finalizer<-")
+importFrom(ff,"nrow<-")
+importFrom(ff,'filename<-')
+importFrom(ff,.rambytes)
+importFrom(ff,.vNA)
+importFrom(ff,.vimplemented)
+importFrom(ff,.vmax)
+importFrom(ff,.vmin)
+importFrom(ff,.vmode)
+importFrom(ff,appendLevels)
+importFrom(ff,arrayIndex2vectorIndex)
+importFrom(ff,as.ff)
 importFrom(ff,as.ffdf)
 importFrom(ff,as.ram)
+importFrom(ff,ff)
+importFrom(ff,ffdf)
+importFrom(ff,ffdforder)
+importFrom(ff,ffindexget)
+importFrom(ff,ffindexorder)
+importFrom(ff,ffindexordersize)
+importFrom(ff,fforder)
+importFrom(ff,ffsort)
+importFrom(ff,ffvecapply)
+importFrom(ff,filename)
+importFrom(ff,hi)
+importFrom(ff,is.factor.ff)
+importFrom(ff,is.ff)
+importFrom(ff,is.ffdf)
+importFrom(ff,is.open)
+importFrom(ff,maxffmode)
+importFrom(ff,recodeLevels)
+importFrom(ff,set.ff)
+importFrom(ff,vmode)
 importFrom(stats,quantile)
 importFrom(stats,weighted.mean)
 importFrom(tools,file_ext)

diff --git a/pkg/R/Summary_ff.R b/pkg/R/Summary_ff.R
@@ -41,7 +41,7 @@ any.ff <- function(x, ..., na.rm=FALSE, range=NULL){
 #'
 #' @title Sum of \code{ff} vector Elements
 #' @method sum ff
-#' @export sum.ff
+#' @export
 #' @param x a \code{ff} object
 #' @param ... optional other (\code{ff}) objects
 #' @param na.rm should \code{NA} be removed?

diff --git a/pkg/R/as.R b/pkg/R/as.R
@@ -21,7 +21,6 @@ as.character.ff <- function(x, ...){
 	res		
 }
 
-
 as.ff_matrix <- function(x, ...){
   UseMethod("as.ff_matrix")
 }
@@ -75,13 +74,14 @@ as.ff_matrix.ffdf <- function(x, ...){
 #   return(y)
 # }
 
+
 #' Trivial implementation, but very handy
 #'
 #' Coerce a ffdf object to an ffdf object.
 #' @param x ffdf object
 #' @param ... not used.
-#' @importFrom ff as.ffdf
 #' @export
+#' @importFrom ff as.ffdf
 as.ffdf.ffdf <- function(x, ...){
   x
 }

diff --git a/pkg/R/bigglm.R b/pkg/R/bigglm.R
@@ -7,15 +7,15 @@
 #' @param formula a model formula
 #' @param data an object of class ffdf
 #' @param family A glm family object
-#' @param ... other parameters passed on to bigglm. See the bigglm package: \code{\link[biglm]{bigglm}}
+#' @param ... other parameters passed on to bigglm. See the biglm package: \code{\link[biglm]{biglm}}
 #' @param chunksize Size of chunks for processing the ffdf
 #' @return An object of class bigglm. See the bigglm package for a description: \code{\link[biglm]{bigglm}}
 #' @export 
 #' @seealso \code{\link[biglm]{bigglm}}
 #' @example ../examples/bigglm.R
 bigglm.ffdf<-function(formula, data, family = gaussian(), ..., chunksize=5000){
 
-  if (!requireNamespace("biglm")){
+  if (!requireNamespace("biglm", quietly = TRUE)){
     stop("This function needs the package 'biglm', which can be installed from CRAN")
   }
 
@@ -45,7 +45,7 @@ bigglm.ffdf<-function(formula, data, family = gaussian(), ..., chunksize=5000){
     Log$chunk(got)
     data[chunks[[got]], tablevars, drop=FALSE]
   }
-  rval<-bigglm(formula, data=ffchunk, family=family, ...)
+  rval <- biglm::bigglm(formula, data=ffchunk, family=family, ...)
   rval$call<-sys.call()
   #rval$call[[1]]<-as.name(.Generic)
   rval$call[[1]]<-as.name("bigglm")

diff --git a/pkg/R/cumsum.R b/pkg/R/cumsum.R
@@ -7,7 +7,7 @@
 #' @return An \code{ff} vector of the same length and type as x (after coercion), except that cumprod returns a numeric vector for integer input.\cr
 #' An NA value in x causes the corresponding and following elements of the return value to be NA, as does integer overflow in cumsum (with a warning). 
 #' @rdname cumsum.ff
-#' @export cumsum.ff
+#' @export
 #' @seealso \code{\link{cumsum}}, \code{\link{cumprod}}, \code{\link{cummax}}, \code{\link{cummin}}
 cumsum.ff <- function(x, ...){
   result <- clone(x, vmode = "double")
@@ -24,7 +24,7 @@ cumsum.ff <- function(x, ...){
 
 #' @rdname cumsum.ff
 #' @method cumprod ff
-#' @export cumprod.ff
+#' @export
 cumprod.ff <- function(x, ...){
   result <- clone(x, vmode = "double")
 
@@ -40,7 +40,7 @@ cumprod.ff <- function(x, ...){
 
 #' @rdname cumsum.ff
 #' @method cummax ff
-#' @export cummax.ff
+#' @export
 cummax.ff <- function(x, ...){
   result <- clone(x, vmode = "double")
 
@@ -55,7 +55,7 @@ cummax.ff <- function(x, ...){
 
 #' @rdname cumsum.ff
 #' @method cummin ff
-#' @export cummin.ff
+#' @export
 cummin.ff <- function(x, ...){
   result <- clone(x, vmode = "double")
 

diff --git a/pkg/R/extract.R b/pkg/R/extract.R
@@ -9,6 +9,7 @@
 #' to handle logical \code{ff} vectors as indexes.  
 #'
 #' @export
+#' @export [.ff
 #' @rdname ffextract
 #' @example ../examples/extract.R
 #' @param x an \code{ff} object 
@@ -38,6 +39,7 @@
 #' @rdname ffextract
 #' @usage \method{[}{ff} (x, i, add = FALSE, pack = FALSE) <- value
 #' @export
+#' @export [<-.ff
 `[<-.ff` <- function(x, i, add = FALSE, pack = FALSE, value){
   if(!missing(i) && is.ff(i) && length(i) > 0 && is.logical(i[1])){
     idx <- ffwhich(i, i==TRUE)    

diff --git a/pkg/R/isNA.R b/pkg/R/isNA.R
@@ -13,6 +13,7 @@
 #' @param value a suitable ff index vector for use with x
 #' @return A logical \code{ff} vector of the same length of x indicating if the ff vector contains missing values. 
 #' @export
+#' @export is.na.ff
 #' @seealso \code{\link[base]{is.na}, \link[ff]{ffvecapply}}
 is.na.ff <- function(x, ...){
 	res <- ff(vmode="logical", length=length(x))

diff --git a/pkg/R/pkg.R b/pkg/R/pkg.R
@@ -67,5 +67,9 @@
 #' @name ffbase-package 
 #' @aliases ffbase ffbase-package
 #' @import bit
+#' @importFrom ff ffdf ff is.ff is.ffdf fforder filename as.ff is.factor.ff vmode recodeLevels 
+#' @importFrom ff is.open ffdforder appendLevels ffvecapply 'filename<-' maxffmode
+#' @importFrom ff arrayIndex2vectorIndex nrow<- .rambytes set.ff hi ffindexordersize ffindexget
+#' @importFrom ff ffsort .vNA .vmax .vmin .vmode finalizer<- ffindexorder .vimplemented 
 #' @docType package 
 {}
diff --git a/pkg/R/rbind_ffdf.R b/pkg/R/rbind_ffdf.R
@@ -1,4 +1,3 @@
-#' @export
 rbind.ffdf <- function(..., deparse.level=1){
   a <- list(...)
   x <- clone(a[[1]])

diff --git a/pkg/R/subset.R b/pkg/R/subset.R
@@ -1,6 +1,6 @@
 #' Subsetting a ff vector or ffdfdata frame
 #'
-#' @export subset.ff subset.ffdf
+#' @export
 #' @aliases subset.ff subset.ffdf
 #' @method subset ff
 #' @param x \code{ff} vector or \code{ffdf} data.frame to be subset
@@ -18,6 +18,7 @@ subset.ff <- function(x, subset, ...){
 	x[idx]
 }
 
+#' @export
 subset.ffdf <- function(x, subset, select, drop = FALSE, ...){
   # remove rownames otherwise we have errors...
   rownames(x) <- NULL

diff --git a/pkg/R/transform.R b/pkg/R/transform.R
@@ -6,7 +6,7 @@
 #' @usage 
 #' \method{transform}{ffdf}(`_data`, \dots)
 #'
-#' @export transform.ffdf
+#' @export
 #'
 #' @example ../examples/transform.R
 #' @param _data \code{\link{ffdf}} data object to be transformed.

diff --git a/pkg/R/unique.R b/pkg/R/unique.R
@@ -1,7 +1,7 @@
 #' Unique values for ff and ffdf objects
 #'
 #' @rdname unique.ff
-#' @export unique.ff unique.ffdf
+#' @export
 #' @method unique ff
 #' @example ../examples/unique.R
 #' @param x \code{ff} object or \code{ffdf} object
@@ -57,6 +57,7 @@ unique.ff <- function(x, incomparables = FALSE, fromLast = FALSE, trace=FALSE, .
 
 #' @rdname unique.ff
 #' @method unique ffdf
+#' @export
 unique.ffdf <- function(x, incomparables = FALSE, fromLast=FALSE, trace=FALSE, ...){
   if (!identical(incomparables, FALSE)){
     .NotYetUsed("incomparables != FALSE")

diff --git a/pkg/man/bigglm.ffdf.Rd b/pkg/man/bigglm.ffdf.Rd
@@ -13,7 +13,7 @@ bigglm.ffdf(formula, data, family = gaussian(), ..., chunksize = 5000)
 
 \item{family}{A glm family object}
 
-\item{...}{other parameters passed on to bigglm. See the bigglm package: \code{\link[biglm]{bigglm}}}
+\item{...}{other parameters passed on to bigglm. See the biglm package: \code{\link[biglm]{biglm}}}
 
 \item{chunksize}{Size of chunks for processing the ffdf}
 }

diff --git a/pkg/man/cumsum.ff.Rd b/pkg/man/cumsum.ff.Rd
@@ -29,16 +29,16 @@ Cumulative Sums, Products, and Extremes
 }
 \examples{
 x <- 1:10000
-tmp <- cumsum.ff(ff(x), BATCHBYTES=10000)
+tmp <- cumsum(ff(x))
 class(tmp)
 table(tmp[] == cumsum(x))
 
 x <- rnorm(1000)
-tmp <- cummax.ff(ff(x), BATCHBYTES=10000)
+tmp <- cummax(ff(x))
 table(tmp[] == cummax(x))
-tmp <- cummin.ff(ff(x), BATCHBYTES=10000)
+tmp <- cummin(ff(x))
 table(tmp[] == cummin(x))
-tmp <- cumprod.ff(ff(x), BATCHBYTES=10000)
+tmp <- cumprod(ff(x))
 table(tmp[] == cumprod(x))
 
 ## S3 type of calling

diff --git a/pkg/man/ffextract.Rd b/pkg/man/ffextract.Rd
@@ -35,15 +35,12 @@ Mark that all other functionality from the extractor functions \code{[.ff} and \
 to handle logical \code{ff} vectors as indexes.
 }
 \examples{
-x <- ff(1:10)
-y <- ff(11:20)
-
 ## extractors
 x <- ff(1:10)
 y <- ff(11:20)
 idx <- ff(c(FALSE, TRUE, NA, TRUE))
 x[idx]
-idx <- ff(c(FALSE, FALSE, FALSE))
+idx <- ff(c(FALSE, FALSE, TRUE))
 x[idx]
 idx <- ff(1:3)
 x[idx]
@@ -52,8 +49,8 @@ x[idx]
 idx <- ff(c(FALSE, TRUE, NA, TRUE))
 x[idx] <- y[idx]
 x
-idx <- ff(c(FALSE, FALSE, FALSE))
-try(x[idx] <- y[idx]) ## not allowed
+idx <- ff(c(FALSE, FALSE, TRUE))
+try(x[idx] <- y[idx], silent = T) ## not allowed
 x
 idx <- ff(1:3)
 x[idx] <- y[idx]