Author: Andreas Tille <tille@debian.org>
Date: Thu, 16 Oct 2014 13:46:33 +0200
Description: r-cran-locfit has a non-free license and thus can not be packaged
 for Debian.  So we have to skip those parts of the test suite that are using
 locfit.  Feel free to pick up the packaging from
   svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-locfit/trunk/
 to create a local package and remove this patch from series.

--- a/tests/edgeR-Tests.R
+++ b/tests/edgeR-Tests.R
@@ -75,13 +75,6 @@ summary(dglm$trended.dispersion)
 dglm <- estimateGLMTagwiseDisp(dglm,design,prior.df=20)
 summary(dglm$tagwise.dispersion)
 
-dglm2 <- estimateDisp(dglm, design)
-summary(dglm2$tagwise.dispersion)
-dglm2 <- estimateDisp(dglm, design, prior.df=20)
-summary(dglm2$tagwise.dispersion)
-dglm2 <- estimateDisp(dglm, design, robust=TRUE)
-summary(dglm2$tagwise.dispersion)
-
 # Continuous trend
 nlibs <- 3
 ntags <- 1000
@@ -104,13 +97,6 @@ topTags(results)
 d1 <- estimateGLMCommonDisp(d, design, verbose=TRUE)
 glmFit(d,design,dispersion=dispersion.true, prior.count=0.5/3)
 
-d2 <- estimateDisp(d, design)
-summary(d2$tagwise.dispersion)
-d2 <- estimateDisp(d, design, prior.df=20)
-summary(d2$tagwise.dispersion)
-d2 <- estimateDisp(d, design, robust=TRUE)
-summary(d2$tagwise.dispersion)
-
 # Exact tests
 y <- matrix(rnbinom(20,mu=10,size=3/2),5,4)
 group <- factor(c(1,1,2,2))
--- a/tests/edgeR-Tests.Rout.save
+++ b/tests/edgeR-Tests.Rout.save
@@ -295,19 +295,6 @@ Tag.8  -0.7918166 12.86353 0.7356185 0.3
    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  0.1385  0.1792  0.1964  0.1935  0.2026  0.2709 
 > 
-> dglm2 <- estimateDisp(dglm, design)
-> summary(dglm2$tagwise.dispersion)
-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
- 0.1766  0.1789  0.1814  0.1846  0.1870  0.2119 
-> dglm2 <- estimateDisp(dglm, design, prior.df=20)
-> summary(dglm2$tagwise.dispersion)
-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
- 0.1527  0.1669  0.1814  0.1858  0.1951  0.2497 
-> dglm2 <- estimateDisp(dglm, design, robust=TRUE)
-> summary(dglm2$tagwise.dispersion)
-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
- 0.1766  0.1789  0.1814  0.1846  0.1870  0.2119 
-> 
 > # Continuous trend
 > nlibs <- 3
 > ntags <- 1000