[med-svn] [r-bioc-limma] 01/03: Drop code from unit test that is using locfit since it is not packaged for Debian (and probably can not become part of Debian)

[Andreas Tille]

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

commit a52062c4ad5529f0ff9fcddf6753efb159de022b
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 27 21:19:24 2014 +0200

    Drop code from unit test that is using locfit since it is not packaged for Debian (and probably can not become part of Debian)
---
 debian/patches/do_not_attempt_locfit_test.patch | 66 +++++++++++++++++++++++++
 debian/patches/series                           |  1 +
 debian/tests/control                            |  4 +-
 debian/tests/{upstream => run-unit-test}        | 15 +++---
 4 files changed, 77 insertions(+), 9 deletions(-)

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..498fe39
--- /dev/null
+++ b/debian/patches/do_not_attempt_locfit_test.patch
@@ -0,0 +1,66 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Fri, 27 Jun 2014 19:02:17 +0200
+Description: r-cran-locfit has a non-free license and thus can not be packaged
+ for Debian.  So we have to skip this test.  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.
+ 
+
+--- r-bioc-limma.orig/tests/limma-Tests.R
++++ r-bioc-limma/tests/limma-Tests.R
+@@ -48,19 +48,6 @@
+ out <- loessFit(y,x,weights=w,method="weightedLowess")
+ f2 <- quantile(out$fitted)
+ r2 <- quantile(out$residual)
+-out <- loessFit(y,x,weights=w,method="locfit")
+-f3 <- quantile(out$fitted)
+-r3 <- quantile(out$residual)
+-out <- loessFit(y,x,weights=w,method="loess")
+-f4 <- quantile(out$fitted)
+-r4 <- quantile(out$residual)
+-w <- rep(1,100)
+-w[2*(1:50)] <- 0
+-out <- loessFit(y,x,weights=w,method="weightedLowess")
+-f5 <- quantile(out$fitted)
+-r5 <- quantile(out$residual)
+-data.frame(f1,f2,f3,f4,f5)
+-data.frame(r1,r2,r3,r4,r5)
+ 
+ ### normalizeWithinArrays
+ 
+--- r-bioc-limma.orig/tests/limma-Tests.Rout.save
++++ r-bioc-limma/tests/limma-Tests.Rout.save
+@@ -594,32 +594,6 @@
+ > out <- loessFit(y,x,weights=w,method="weightedLowess")
+ > f2 <- quantile(out$fitted)
+ > r2 <- quantile(out$residual)
+-> out <- loessFit(y,x,weights=w,method="locfit")
+-> f3 <- quantile(out$fitted)
+-> r3 <- quantile(out$residual)
+-> out <- loessFit(y,x,weights=w,method="loess")
+-> f4 <- quantile(out$fitted)
+-> r4 <- quantile(out$residual)
+-> w <- rep(1,100)
+-> w[2*(1:50)] <- 0
+-> out <- loessFit(y,x,weights=w,method="weightedLowess")
+-> f5 <- quantile(out$fitted)
+-> r5 <- quantile(out$residual)
+-> data.frame(f1,f2,f3,f4,f5)
+-              f1           f2          f3          f4          f5
+-0%   -0.78835384 -0.687432210 -0.78957137 -0.76756060 -0.63778292
+-25%  -0.18340154 -0.179683572 -0.18979269 -0.16773223 -0.38064318
+-50%  -0.11492924 -0.114796040 -0.12087983 -0.07185314 -0.15971879
+-75%   0.01507921 -0.008145125 -0.01857508  0.04030634  0.07839396
+-100%  0.21653837  0.145106033  0.19214597  0.21417361  0.51836274
+-> data.frame(r1,r2,r3,r4,r5)
+-              r1          r2          r3           r4          r5
+-0%   -2.04434053 -2.05132680 -2.02404318 -2.101242874 -2.22280633
+-25%  -0.59321065 -0.57200209 -0.58975649 -0.577887481 -0.71037756
+-50%   0.05874864  0.04514326  0.08335198 -0.001769806  0.06785517
+-75%   0.56010750  0.55124530  0.57618740  0.561454370  0.65383830
+-100%  2.57936026  2.64549799  2.57549257  2.402324533  2.28648835
+-> 
+ > ### normalizeWithinArrays
+ > 
+ > RG <- new("RGList",list())
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
diff --git a/debian/tests/control b/debian/tests/control
index f08221c..d2aa55a 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1 +1,3 @@
-Tests: upstream
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/upstream b/debian/tests/run-unit-test
old mode 100755
new mode 100644
similarity index 58%
rename from debian/tests/upstream
rename to debian/tests/run-unit-test
index d11cae7..2aeec4a
--- a/debian/tests/upstream
+++ b/debian/tests/run-unit-test
@@ -1,10 +1,11 @@
 #!/bin/sh -e
 
-TEMPORARY_DIR=$(mktemp -d)
-
-cd $TEMPORARY_DIR
-
-cp /usr/share/doc/r-bioc-limma/tests/* .
+pkg=r-bioc-limma
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
 for test in *R.gz
 do
   zcat ${test} > `basename ${test} .gz`
@@ -12,7 +13,5 @@ do
   R CMD Rdiff `basename ${test} .gz`out.save* `basename ${test} .gz`out
   rm `basename ${test} .gz`out .RData
 done
+rm -f $ADTTMP/*
 
-cd -
-
-rm -rf $TEMPORARY_DIR

-- 
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