@@ -1,9 +1,8 @@

 Package: preprocessCore

-Version: 1.27.4

+Version: 1.27.7

 Title: A collection of pre-processing functions

 Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>

 Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>

-Depends: methods

 Imports: stats

 Description: A library of core preprocessing routines 

 License: LGPL (>= 2)

@@ -32,8 +32,7 @@ rcModelPLMd(y,group.labels)

   Next the residuals for each row are compared to the group variable. In cases

   where there appears to be a significant relationship, the row-effect is "split" and separate row-effect parameters, one for each group, replace the single row effect.

 }

-\seealso{

-}

+\seealso{\code{\link{rcModelPLM}},\code{\link{rcModelPLMr}}}

 \examples{

 col.effects <- c(10,11,10.5,12,9.5)

 row.effects <- c(seq(-0.5,-0.1,by=0.1),seq(0.1,0.5,by=0.1))

@@ -63,4 +62,4 @@ matplot(rcModelPLMd(y,group.labels=c(1,1,1,2,2,2))$Residuals,col=c(rep("red",3),

 }

 \author{B. M. Bolstad \email{bmb@bmbolstad.com}}

-\keyword{models}

\ No newline at end of file

+\keyword{models}

@@ -50,8 +50,7 @@ rcModelWPLMrc(y, w)

 }

-\seealso{

-}

+\seealso{\code{\link{rcModelPLM}},\code{\link{rcModelPLMd}}}

 \examples{

 col.effects <- c(10,11,10.5,12,9.5)

 row.effects <- c(seq(-0.5,-0.1,by=0.1),seq(0.1,0.5,by=0.1))

@@ -116,4 +115,4 @@ matplot(y,type="l")

 }

 \author{B. M. Bolstad \email{bmb@bmbolstad.com}}

-\keyword{models}

\ No newline at end of file

+\keyword{models}

@@ -43,8 +43,7 @@ rcModelMedianPolish(y)

        The function \code{rcModelMedianPolish} uses the median polish algorithm.

 }

-\seealso{

-}

+\seealso{\code{\link{rcModelPLMr}},\code{\link{rcModelPLMd}}}

 \examples{

 col.effects <- c(10,11,10.5,12,9.5)

 row.effects <- c(seq(-0.5,-0.1,by=0.1),seq(0.1,0.5,by=0.1))

@@ -78,4 +77,4 @@ rcModelWPLM(y,w,row.effects=row.effects,input.scale=1.0)

 }

 \author{B. M. Bolstad \email{bmb@bmbolstad.com}}

-\keyword{models}

\ No newline at end of file

+\keyword{models}

@@ -47,8 +47,8 @@ subrcModelMedianPolish(y, group.labels)

        The function \code{rcModelMedianPolish} uses the median polish algorithm.

 }

-\seealso{

-}

+\seealso{\link{rcModelPLM}}

+

 \examples{

 y <- matrix(c(10+rnorm(50),20+rnorm(50)),20,5,byrow=TRUE)

@@ -77,7 +77,7 @@ SEXP R_rlm_rma_default_model(SEXP Y, SEXP PsiCode, SEXP PsiK, SEXP Scales){

   double *weights;

   double *se;

-  double scale=-1.0;

+  /* double scale=-1.0; */

   double *scaleptr;

   double residSE;

@@ -187,7 +187,7 @@ SEXP R_wrlm_rma_default_model(SEXP Y, SEXP PsiCode, SEXP PsiK, SEXP Weights, SEX

   double *weights;

   double *se;

-  double scale=-1.0;

+  /* double scale=-1.0;*/

   double *scaleptr;

   double residSE;

@@ -303,8 +303,8 @@ SEXP R_medianpolish_rma_default_model(SEXP Y){

   double *beta;

   double *residuals;

-  double *weights;

-  double *se;

+  /*double *weights;

+    double *se; */

   double intercept;

@@ -136,7 +136,7 @@ static double AvgSE(double *x, double mean, size_t length){

  */

 void colaverage_no_copy(double *data, size_t rows, size_t cols, double *results, double *resultsSE){

-  int i,j;

+  int j;

   for (j = 0; j < cols; j++){

     results[j] = Avg(&data[j*rows],rows);

@@ -140,7 +140,7 @@ void logmedian(double *data, size_t rows, size_t cols, double *results, double *

 void logmedian_no_copy(double *data, size_t rows, size_t cols, double *results, double *resultsSE){

-  size_t i,j;

+  size_t j;

   for (j=0; j < cols; j++){

     results[j] = log_median(&data[j*rows],rows); 

@@ -214,7 +214,7 @@ void colmedian(double *data, size_t rows, size_t cols, double *results, double *

 void colmedian_no_copy(double *data, size_t rows, size_t cols, double *results, double *resultsSE){

-  size_t i,j;

+  size_t j;

   for (j=0; j < cols; j++){

     results[j] = colmedian_wrapper(&data[j*rows],rows);