Merge c366be8 into c6a6b19

HenrikBengtsson · Aug 19, 2015 · f332a7c · f332a7c
2 parents c6a6b19 + c366be8
commit f332a7c
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Showing 54 changed files with 2,197 additions and 369 deletions.
diff --git a/R/rowCounts.R b/R/rowCounts.R
@@ -84,7 +84,7 @@ rowCounts <- function(x, rows=NULL, cols=NULL, value=TRUE, na.rm=FALSE, dim.=dim
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    counts <- .Call("rowCounts", x, dim., rows, cols, value, 2L, na.rm, hasNAs, PACKAGE="matrixStats")
+    counts <- .Call("rowCounts", x, dim., rows, cols, value, 2L, na.rm, hasNAs, mc.cores, PACKAGE="matrixStats")
   } else {
     if (is.vector(x)) dim(x) <- dim.
 
@@ -130,7 +130,7 @@ colCounts <- function(x, rows=NULL, cols=NULL, value=TRUE, na.rm=FALSE, dim.=dim
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    counts <- .Call("colCounts", x, dim., rows, cols, value, 2L, na.rm, hasNAs, PACKAGE="matrixStats")
+    counts <- .Call("colCounts", x, dim., rows, cols, value, 2L, na.rm, hasNAs, mc.cores, PACKAGE="matrixStats")
   } else {
     if (is.vector(x)) dim(x) <- dim.
 
@@ -193,7 +193,7 @@ rowAlls <- function(x, rows=NULL, cols=NULL, value=TRUE, na.rm=FALSE, dim.=dim(x
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    counts <- .Call("rowCounts", x, dim., rows, cols, value, 0L, na.rm, hasNAs, PACKAGE="matrixStats")
+    counts <- .Call("rowCounts", x, dim., rows, cols, value, 0L, na.rm, hasNAs, mc.cores, PACKAGE="matrixStats")
     as.logical(counts)
   } else {
     if (is.vector(x)) dim(x) <- dim.
@@ -216,7 +216,7 @@ colAlls <- function(x, rows=NULL, cols=NULL, value=TRUE, na.rm=FALSE, dim.=dim(x
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    counts <- .Call("colCounts", x, dim., rows, cols, value, 0L, na.rm, hasNAs, PACKAGE="matrixStats")
+    counts <- .Call("colCounts", x, dim., rows, cols, value, 0L, na.rm, hasNAs, mc.cores, PACKAGE="matrixStats")
     as.logical(counts)
   } else {
     if (is.vector(x)) dim(x) <- dim.
@@ -260,7 +260,7 @@ rowAnys <- function(x, rows=NULL, cols=NULL, value=TRUE, na.rm=FALSE, dim.=dim(x
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    counts <- .Call("rowCounts", x, dim., rows, cols, value, 1L, na.rm, hasNAs, PACKAGE="matrixStats")
+    counts <- .Call("rowCounts", x, dim., rows, cols, value, 1L, na.rm, hasNAs, mc.cores, PACKAGE="matrixStats")
     as.logical(counts)
   } else {
     if (is.vector(x)) dim(x) <- dim.
@@ -283,7 +283,7 @@ colAnys <- function(x, rows=NULL, cols=NULL, value=TRUE, na.rm=FALSE, dim.=dim(x
   if (is.numeric(x) || is.logical(x)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    counts <- .Call("colCounts", x, dim., rows, cols, value, 1L, na.rm, hasNAs, PACKAGE="matrixStats")
+    counts <- .Call("colCounts", x, dim., rows, cols, value, 1L, na.rm, hasNAs, mc.cores, PACKAGE="matrixStats")
     as.logical(counts)
   } else {
     if (is.vector(x)) dim(x) <- dim.

diff --git a/R/rowCumsums.R b/R/rowCumsums.R
@@ -56,44 +56,44 @@
 #*/###########################################################################
 rowCumsums <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCumsums", x, dim, rows, cols, TRUE, PACKAGE="matrixStats")
+  .Call("rowCumsums", x, dim, rows, cols, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colCumsums <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCumsums", x, dim, rows, cols, FALSE, PACKAGE="matrixStats")
+  .Call("rowCumsums", x, dim, rows, cols, FALSE, mc.cores, PACKAGE="matrixStats")
 }
 
 
 rowCumprods <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCumprods", x, dim, rows, cols, TRUE, PACKAGE="matrixStats")
+  .Call("rowCumprods", x, dim, rows, cols, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colCumprods <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCumprods", x, dim, rows, cols, FALSE, PACKAGE="matrixStats")
+  .Call("rowCumprods", x, dim, rows, cols, FALSE, mc.cores, PACKAGE="matrixStats")
 }
 
 
 rowCummins <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCummins", x, dim, rows, cols, TRUE, PACKAGE="matrixStats")
+  .Call("rowCummins", x, dim, rows, cols, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colCummins <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCummins", x, dim, rows, cols, FALSE, PACKAGE="matrixStats")
+  .Call("rowCummins", x, dim, rows, cols, FALSE, mc.cores, PACKAGE="matrixStats")
 }
 
 rowCummaxs <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCummaxs", x, dim, rows, cols, TRUE, PACKAGE="matrixStats")
+  .Call("rowCummaxs", x, dim, rows, cols, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colCummaxs <- function(x, rows=NULL, cols=NULL, dim.=dim(x), mc.cores=1L, ...) {
   dim <- as.integer(dim.);
-  .Call("rowCummaxs", x, dim, rows, cols, FALSE, PACKAGE="matrixStats")
+  .Call("rowCummaxs", x, dim, rows, cols, FALSE, mc.cores, PACKAGE="matrixStats")
 }
 
 

diff --git a/R/rowDiffs.R b/R/rowDiffs.R
@@ -42,11 +42,11 @@
 # @keyword univar
 #*/###########################################################################
 rowDiffs <- function(x, rows=NULL, cols=NULL, lag=1L, differences=1L, mc.cores=1L, ...) {
-  .Call("rowDiffs", x, dim(x), rows, cols, as.integer(lag), as.integer(differences), TRUE, PACKAGE="matrixStats")
+  .Call("rowDiffs", x, dim(x), rows, cols, as.integer(lag), as.integer(differences), TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colDiffs <- function(x, rows=NULL, cols=NULL, lag=1L, differences=1L, mc.cores=1L, ...) {
-  .Call("rowDiffs", x, dim(x), rows, cols, as.integer(lag), as.integer(differences), FALSE, PACKAGE="matrixStats")
+  .Call("rowDiffs", x, dim(x), rows, cols, as.integer(lag), as.integer(differences), FALSE, mc.cores, PACKAGE="matrixStats")
 }
 
 

diff --git a/R/rowLogSumExps.R b/R/rowLogSumExps.R
@@ -53,7 +53,7 @@ rowLogSumExps <- function(lx, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(lx), m
   hasNA <- TRUE;
   res <- .Call("rowLogSumExps",
                lx, dim., rows, cols,
-               as.logical(na.rm), as.logical(hasNA), TRUE,
+               as.logical(na.rm), as.logical(hasNA), TRUE, mc.cores,
                PACKAGE="matrixStats");
 
   # Preserve names
@@ -71,7 +71,7 @@ colLogSumExps <- function(lx, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(lx), m
   hasNA <- TRUE;
   res <- .Call("rowLogSumExps",
                lx, dim., rows, cols,
-               as.logical(na.rm), as.logical(hasNA), FALSE,
+               as.logical(na.rm), as.logical(hasNA), FALSE, mc.cores,
                PACKAGE="matrixStats");
 
   # Preserve names

diff --git a/R/rowMads.R b/R/rowMads.R
@@ -12,7 +12,7 @@ rowMads <- function(x, rows=NULL, cols=NULL, center=NULL, constant=1.4826, na.rm
     na.rm <- as.logical(na.rm)
     constant = as.numeric(constant)
     hasNAs <- TRUE
-    x <- .Call("rowMads", x, dim., rows, cols, constant, na.rm, hasNAs, TRUE, PACKAGE="matrixStats")
+    x <- .Call("rowMads", x, dim., rows, cols, constant, na.rm, hasNAs, TRUE, mc.cores, PACKAGE="matrixStats")
   } else {
     # Apply subset on 'x'
     if (is.vector(x)) dim(x) <- dim.
@@ -27,7 +27,7 @@ rowMads <- function(x, rows=NULL, cols=NULL, center=NULL, constant=1.4826, na.rm
     x <- x - center
     if (is.null(dim(x))) dim(x) <- dim. # prevent from dim dropping
     x <- abs(x)
-    x <- rowMedians(x, na.rm=na.rm, ...)
+    x <- rowMedians(x, na.rm=na.rm, mc.cores=mc.cores, ...)
     x <- constant*x
   }
   x
@@ -48,7 +48,7 @@ colMads <- function(x, rows=NULL, cols=NULL, center=NULL, constant=1.4826, na.rm
     na.rm <- as.logical(na.rm)
     constant = as.numeric(constant)
     hasNAs <- TRUE
-    x <- .Call("rowMads", x, dim., rows, cols, constant, na.rm, hasNAs, FALSE, PACKAGE="matrixStats")
+    x <- .Call("rowMads", x, dim., rows, cols, constant, na.rm, hasNAs, FALSE, mc.cores, PACKAGE="matrixStats")
   } else {
     # Apply subset on 'x'
     if (is.vector(x)) dim(x) <- dim.
@@ -67,7 +67,7 @@ colMads <- function(x, rows=NULL, cols=NULL, center=NULL, constant=1.4826, na.rm
     ## FAST:
     x <- t_tx_OP_y(x, center, OP="-", na.rm=FALSE)
     x <- abs(x)
-    x <- colMedians(x, na.rm=na.rm, ...)
+    x <- colMedians(x, na.rm=na.rm, mc.cores=mc.cores, ...)
     x <- constant*x
   }
   x

diff --git a/R/rowMedians.S4.R b/R/rowMedians.S4.R
@@ -63,7 +63,7 @@ setMethod("rowMedians", signature(x="matrix"), function(x, rows=NULL, cols=NULL,
   na.rm <- as.logical(na.rm);
   hasNAs <- TRUE;  # Add as an argument? /2007-08-24
 
-  .Call("rowMedians", x, dim., rows, cols, na.rm, hasNAs, TRUE, PACKAGE="matrixStats");
+  .Call("rowMedians", x, dim., rows, cols, na.rm, hasNAs, TRUE, mc.cores, PACKAGE="matrixStats");
 })
 
 
@@ -76,7 +76,7 @@ setMethod("colMedians", signature(x="matrix"), function(x, rows=NULL, cols=NULL,
   na.rm <- as.logical(na.rm);
   hasNAs <- TRUE;  # Add as an argument? /2007-08-24
 
-  .Call("rowMedians", x, dim., rows, cols, na.rm, hasNAs, FALSE, PACKAGE="matrixStats");
+  .Call("rowMedians", x, dim., rows, cols, na.rm, hasNAs, FALSE, mc.cores, PACKAGE="matrixStats");
 })
 
 

diff --git a/R/rowOrderStats.R b/R/rowOrderStats.R
@@ -67,7 +67,7 @@ rowOrderStats <- function(x, rows=NULL, cols=NULL, which, dim.=dim(x), mc.cores=
   }
 
   which <- as.integer(which)
-  .Call("rowOrderStats", x, dim., rows, cols, which, PACKAGE="matrixStats");
+  .Call("rowOrderStats", x, dim., rows, cols, which, mc.cores, PACKAGE="matrixStats");
 }
 
 
@@ -80,7 +80,7 @@ colOrderStats <- function(x, rows=NULL, cols=NULL, which, dim.=dim(x), mc.cores=
   }
 
   which <- as.integer(which)
-  .Call("colOrderStats", x, dim., rows, cols, which, PACKAGE="matrixStats");
+  .Call("colOrderStats", x, dim., rows, cols, which, mc.cores, PACKAGE="matrixStats");
 }
 
 

diff --git a/R/rowRanges.R b/R/rowRanges.R
@@ -57,38 +57,38 @@
 rowRanges <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(x), mc.cores=1L, ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
-  .Call("rowRanges", x, dim., rows, cols, 2L, na.rm, TRUE, PACKAGE="matrixStats")
+  .Call("rowRanges", x, dim., rows, cols, 2L, na.rm, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 rowMins <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(x), mc.cores=1L, ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
-  .Call("rowRanges", x, dim., rows, cols, 0L, na.rm, TRUE, PACKAGE="matrixStats")
+  .Call("rowRanges", x, dim., rows, cols, 0L, na.rm, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 rowMaxs <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(x), mc.cores=1L, ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
-  .Call("rowRanges", x, dim., rows, cols, 1L, na.rm, TRUE, PACKAGE="matrixStats")
+  .Call("rowRanges", x, dim., rows, cols, 1L, na.rm, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 
 colRanges <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(x), mc.cores=1L, ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
-  .Call("colRanges", x, dim., rows, cols, 2L, na.rm, TRUE, PACKAGE="matrixStats")
+  .Call("colRanges", x, dim., rows, cols, 2L, na.rm, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colMins <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(x), mc.cores=1L, ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
-  .Call("colRanges", x, dim., rows, cols, 0L, na.rm, TRUE, PACKAGE="matrixStats")
+  .Call("colRanges", x, dim., rows, cols, 0L, na.rm, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 colMaxs <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, dim.=dim(x), mc.cores=1L, ...) {
   dim. <- as.integer(dim.)
   na.rm <- as.logical(na.rm)
-  .Call("colRanges", x, dim., rows, cols, 1L, na.rm, TRUE, PACKAGE="matrixStats")
+  .Call("colRanges", x, dim., rows, cols, 1L, na.rm, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 

diff --git a/R/rowRanks.R b/R/rowRanks.R
@@ -111,7 +111,7 @@ rowRanks <- function(x, rows=NULL, cols=NULL, ties.method=c("max", "average", "m
 
   dim. <- as.integer(dim.)
   # byrow=TRUE
-  .Call("rowRanksWithTies", x, dim., rows, cols, tiesMethod, TRUE, PACKAGE="matrixStats")
+  .Call("rowRanksWithTies", x, dim., rows, cols, tiesMethod, TRUE, mc.cores, PACKAGE="matrixStats")
 }
 
 
@@ -133,7 +133,7 @@ colRanks <- function(x, rows=NULL, cols=NULL, ties.method=c("max", "average", "m
 
   dim. <- as.integer(dim.)
   # byrow=FALSE
-  y <- .Call("rowRanksWithTies", x, dim., rows, cols, tiesMethod, FALSE, PACKAGE="matrixStats")
+  y <- .Call("rowRanksWithTies", x, dim., rows, cols, tiesMethod, FALSE, mc.cores, PACKAGE="matrixStats")
   if (!preserveShape) y <- t(y)
   y
 }

diff --git a/R/rowVars.R b/R/rowVars.R
@@ -53,7 +53,7 @@ rowVars <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, center=NULL, dim.=dim(
   if (is.null(center)) {
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    sigma2 <- .Call("rowVars", x, dim., rows, cols, na.rm, hasNAs, TRUE, PACKAGE="matrixStats");
+    sigma2 <- .Call("rowVars", x, dim., rows, cols, na.rm, hasNAs, TRUE, mc.cores, PACKAGE="matrixStats");
     return(sigma2)
   }
 
@@ -112,7 +112,7 @@ colVars <- function(x, rows=NULL, cols=NULL, na.rm=FALSE, center=NULL, dim.=dim(
     dim. <- as.integer(dim.)
     na.rm <- as.logical(na.rm)
     hasNAs <- TRUE
-    sigma2 <- .Call("rowVars", x, dim., rows, cols, na.rm, hasNAs, FALSE, PACKAGE="matrixStats");
+    sigma2 <- .Call("rowVars", x, dim., rows, cols, na.rm, hasNAs, FALSE, mc.cores, PACKAGE="matrixStats");
     return(sigma2)
   }
 

diff --git a/inst/benchmarking/colRowCummins_parallel.md.rsp b/inst/benchmarking/colRowCummins_parallel.md.rsp
@@ -23,7 +23,7 @@ This report benchmark the performance of <%=colname%>() and <%=rowname%>() on mu
 ```r
 <%=withCapture({
 <%@include file="R/random-matrices.R"%>
-data <- rmatrices(mode=mode)
+data <- rmatrices(mode=mode, scale=20)
 })%>
 ```
 

diff --git a/inst/benchmarking/colRowCumprods_parallel.md.rsp b/inst/benchmarking/colRowCumprods_parallel.md.rsp
@@ -23,7 +23,7 @@ This report benchmark the performance of <%=colname%>() and <%=rowname%>() on mu
 ```r
 <%=withCapture({
 <%@include file="R/random-matrices.R"%>
-data <- rmatrices(mode=mode, range=c(-1,1))
+data <- rmatrices(mode=mode, range=c(-1,1), scale=20)
 })%>
 ```
 

diff --git a/inst/benchmarking/colRowCumsums_parallel.md.rsp b/inst/benchmarking/colRowCumsums_parallel.md.rsp
@@ -23,7 +23,7 @@ This report benchmark the performance of <%=colname%>() and <%=rowname%>() on mu
 ```r
 <%=withCapture({
 <%@include file="R/random-matrices.R"%>
-data <- rmatrices(mode=mode)
+data <- rmatrices(mode=mode, scale=20)
 })%>
 ```
 

diff --git a/src/Makevars b/src/Makevars
@@ -0,0 +1,2 @@
+PKG_CFLAGS=-pthread
+PKG_LIBS=-pthread