@@ -151,7 +151,7 @@ checkpointInFile=NULL, transposeData=FALSE, BPPARAM=NULL, ...)

 #' @importFrom methods new

 #' @examples

 #' data(SimpSim)

-#' scCoGAPS(SimpSim.data)

+#' scCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())

 scCoGAPS <- function(data, params=new("CogapsParams"), nThreads=1,

 messages=TRUE, outputFrequency=500, uncertainty=NULL,

 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,

@@ -173,7 +173,7 @@ checkpointInFile=NULL, transposeData=FALSE, BPPARAM=NULL, ...)

 #' @importFrom methods new

 #' @examples

 #' data(SimpSim)

-#' GWCoGAPS(SimpSim.data)

+#' GWCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())

 GWCoGAPS <- function(data, params=new("CogapsParams"), nThreads=1,

 messages=TRUE, outputFrequency=500, uncertainty=NULL,

 checkpointOutFile="gaps_checkpoint.out", checkpointInterval=1000,

@@ -51,8 +51,8 @@ NULL

 #' GIST gene expression uncertainty matrix from Ochs et al. (2009)

 #' @docType data

-#' @name GIST.matrix

-#' @usage GIST.matrix

+#' @name GIST.uncertainty

+#' @usage GIST.uncertainty

 NULL

 #' CoGAPS result from running on GIST dataset

@@ -451,7 +451,7 @@ configure:6353: gcc -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.c  >&

 configure:6353: $? = 0

 configure:6353: ./conftest

 configure:6353: $? = 0

-configure:6363: result: 806ea:5100800:7ffafbff:bfebfbff

+configure:6363: result: 806ea:6100800:7ffafbff:bfebfbff

 configure:6390: checking for x86 cpuid 0x00000007 output

 configure:6420: gcc -o conftest -UNDEBUG -Wall -pedantic -g -O0   conftest.c  >&5

 configure:6420: $? = 0

@@ -757,7 +757,7 @@ ax_cv_cxx_openmp=-fopenmp

 ax_cv_gcc_x86_avx_xgetbv_0x00000000=1f:0

 ax_cv_gcc_x86_avx_xgetbv_=unknown

 ax_cv_gcc_x86_cpuid_0x00000000=16:756e6547:6c65746e:49656e69

-ax_cv_gcc_x86_cpuid_0x00000001=806ea:5100800:7ffafbff:bfebfbff

+ax_cv_gcc_x86_cpuid_0x00000001=806ea:6100800:7ffafbff:bfebfbff

 ax_cv_gcc_x86_cpuid_0x00000007=0:29c6fbf:0:0

 ax_cv_gcc_x86_cpuid_0x80000000=80000008:0:0:0

 ax_cv_gcc_x86_cpuid_0x80000001=0:0:121:2c100800

@@ -5,12 +5,8 @@

 \alias{GIST.matrix}

 \title{GIST gene expression data from Ochs et al. (2009)}

 \usage{

-GIST.matrix

-

 GIST.matrix

 }

 \description{

 GIST gene expression data from Ochs et al. (2009)

-

-GIST gene expression uncertainty matrix from Ochs et al. (2009)

 }

new file mode 100644

@@ -0,0 +1,12 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/Package.R

+\docType{data}

+\name{GIST.uncertainty}

+\alias{GIST.uncertainty}

+\title{GIST gene expression uncertainty matrix from Ochs et al. (2009)}

+\usage{

+GIST.uncertainty

+}

+\description{

+GIST gene expression uncertainty matrix from Ochs et al. (2009)

+}

@@ -49,5 +49,5 @@ wrapper around genome-wide distributed algorithm for CoGAPS

 }

 \examples{

 data(SimpSim)

-GWCoGAPS(SimpSim.data)

+GWCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())

 }

@@ -49,5 +49,5 @@ wrapper around single-cell distributed algorithm for CoGAPS

 }

 \examples{

 data(SimpSim)

-scCoGAPS(SimpSim.data)

+scCoGAPS(SimpSim.data, BPPARAM=BiocParallel::SerialParam())

 }