[med-svn] [r-bioc-edger] 06/07: Refresh patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-edger.

commit 71f59e7b9f024fa90258c15fc54cfa89d8beb3f2
Author: Andreas Tille <tille at debian.org>
Date:   Fri May 20 11:59:53 2016 +0200

    Refresh patches
---
 debian/patches/do_not_attempt_locfit_test.patch | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/debian/patches/do_not_attempt_locfit_test.patch b/debian/patches/do_not_attempt_locfit_test.patch
index 98653d5..ac3cd89 100644
--- a/debian/patches/do_not_attempt_locfit_test.patch
+++ b/debian/patches/do_not_attempt_locfit_test.patch
@@ -23,7 +23,7 @@ Description: r-cran-locfit has a non-free license and thus can not be packaged
  nlibs <- 3
  ntags <- 1000
 @@ -104,13 +97,6 @@ topTags(results)
- d <- estimateGLMCommonDisp(d, design, verbose=TRUE)
+ d1 <- estimateGLMCommonDisp(d, design, verbose=TRUE)
  glmFit(d,design,dispersion=dispersion.true, prior.count=0.5/3)
  
 -d2 <- estimateDisp(d, design)
@@ -38,7 +38,7 @@ Description: r-cran-locfit has a non-free license and thus can not be packaged
  group <- factor(c(1,1,2,2))
 --- a/tests/edgeR-Tests.Rout.save
 +++ b/tests/edgeR-Tests.Rout.save
-@@ -296,17 +296,6 @@ Loading required package: splines
+@@ -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 
  > 
@@ -48,11 +48,13 @@ Description: r-cran-locfit has a non-free license and thus can not be packaged
 - 0.1766  0.1789  0.1814  0.1846  0.1870  0.2119 
 -> dglm2 <- estimateDisp(dglm, design, prior.df=20)
 -> summary(dglm2$tagwise.dispersion)
--   Min. 1st Qu.  Median    Mean 3rd Qu.    .6684268  0.7357761 17.33529  1.7309951 0.420842115 0.90967967
--2  1.2080938 -0.1660740 18.24544  1.0496688 0.591653347 0.90967967
--4  0.5416704 -0.6923084 17.57744  0.3958596 0.820427427 0.90967967
--3  0.2876249 -0.4884392 18.06216  0.1893255 0.909679672 0.90967967
+-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+- 0.1527  0.1669  0.1814  0.1858  0.1951  0.2497 
+-> dglm2 <- estimateDisp(dglm, design, robust=TRUE)
+-> summary(dglm2$tagwise.dispersion)
+-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+- 0.1766  0.1789  0.1814  0.1846  0.1870  0.2119 
 -> 
- > # spliceVariants
- > z = matrix(c(2,0,4,6,4,3,7,1,1,0,1,1,0,3,1,2,0,1,2,1,0,3,1,0), 8, 3)
- > gz = c(1,2,2,2,2,2,2,2)
+ > # Continuous trend
+ > nlibs <- 3
+ > ntags <- 1000

-- 
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