[med-svn] [r-bioc-edger] 02/04: Stick to old version since new upstream versions need non-free locfit

[Andreas Tille]

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

commit e9d58fa9f4355acb76949a3b36c7e8a82b759bf4
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 8 22:25:38 2017 +0200

    Stick to old version since new upstream versions need non-free locfit
---
 debian/changelog                                |  6 ++--
 debian/patches/do_not_attempt_locfit_test.patch | 38 ++++++++++++-------------
 2 files changed, 21 insertions(+), 23 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 173baab..51c5b30 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,6 @@
-r-bioc-edger (3.18.1+dfsg-1) UNRELEASED; urgency=medium
+r-bioc-edger (3.14.0+dfsg-2) UNRELEASED; urgency=medium
 
-  TODO: this version really seems to need locfit - do we want to do
-        another try to free this code?
-  * New upstream version
+  * Stick to old version since new upstream versions need non-free locfit
   * Switch to dh-r
   * Generic BioConductor homepage
   * debhelper 10
diff --git a/debian/patches/do_not_attempt_locfit_test.patch b/debian/patches/do_not_attempt_locfit_test.patch
index 181b890..ac3cd89 100644
--- a/debian/patches/do_not_attempt_locfit_test.patch
+++ b/debian/patches/do_not_attempt_locfit_test.patch
@@ -39,22 +39,22 @@ Description: r-cran-locfit has a non-free license and thus can not be packaged
 --- 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$tagwise.dispersion)
--   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-- 0.1423  0.1618  0.1788  0.1863  0.2015  0.2692 
--> dglm2 <- estimateDisp(dglm, design, prior.df=20)
--> summary(dglm2$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$tagwise.dispersion)
--   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-- 0.1423  0.1605  0.1783  0.1867  0.2031  0.2740 
--> 
- > # Continuous trend
- > nlibs <- 3
- > ntags <- 1000
+    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+  0.1385  0.1792  0.1964  0.1935  0.2026  0.2709 
+ > 
+-> dglm2 <- estimateDisp(dglm, design)
+-> summary(dglm2$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

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