[med-svn] [r-bioc-edger] 05/06: remove tests requiring locfit from the test suite

[Andreas Tille]

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

commit acba84b962c046c07e0580c494feb9e456b49da2
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 16 15:02:49 2014 +0200

    remove tests requiring locfit from the test suite
---
 debian/changelog                                |  1 +
 debian/patches/do_not_attempt_locfit_test.patch | 81 +++++++++++++++++++++++++
 debian/patches/series                           |  1 +
 3 files changed, 83 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index b28b753..c8a85f5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ r-bioc-edger (3.8.0+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
   * cme fix dpkg-control
+  * remove tests requiring locfit from the test suite
 
  -- Andreas Tille <tille at debian.org>  Thu, 16 Oct 2014 13:46:33 +0200
 
diff --git a/debian/patches/do_not_attempt_locfit_test.patch b/debian/patches/do_not_attempt_locfit_test.patch
new file mode 100644
index 0000000..fbab05c
--- /dev/null
+++ b/debian/patches/do_not_attempt_locfit_test.patch
@@ -0,0 +1,81 @@
+Author: Andreas Tille <tille at 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$tagwise.dispersion)
+-
+ # Continuous trend
+ nlibs <- 3
+ ntags <- 1000
+@@ -104,13 +97,6 @@ topTags(results)
+ d <- estimateGLMCommonDisp(d, design, verbose=TRUE)
+ glmFit(d,design,dispersion=dispersion.true, prior.count=0.5/3)
+ 
+-d2 <- estimateDisp(d, design)
+-summary(d2$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
+@@ -296,20 +296,6 @@ Loading required package: splines
+    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)
+-Loading required package: statmod
+-> 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
+@@ -434,19 +420,6 @@ $AveLogCPM
+ 995 more elements ...
+ 
+ > 
+-> d2 <- estimateDisp(d, design)
+-> summary(d2$tagwise.dispersion)
+-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+-0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
+-> d2 <- estimateDisp(d, design, prior.df=20)
+-> summary(d2$tagwise.dispersion)
+-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+-0.04203 0.08587 0.11280 0.11010 0.12370 0.37410 
+-> d2 <- estimateDisp(d, design, robust=TRUE)
+-> summary(d2$tagwise.dispersion)
+-   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
+-0.05545 0.09511 0.11620 0.11010 0.13330 0.16860 
+-> 
+ > # Exact tests
+ > y <- matrix(rnbinom(20,mu=10,size=3/2),5,4)
+ > group <- factor(c(1,1,2,2))
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..d4944cc
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+do_not_attempt_locfit_test.patch

-- 
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