[med-svn] [r-bioc-limma] 03/03: New upstream: 3.28.10
Gordon Ball
chronitis-guest at moszumanska.debian.org
Tue Jun 21 13:32:22 UTC 2016
This is an automated email from the git hooks/post-receive script.
chronitis-guest pushed a commit to branch master
in repository r-bioc-limma.
commit 7679d3fb7d17dedc04a70828d3fc31e7037a73af
Author: Gordon Ball <gordon at chronitis.net>
Date: Tue Jun 21 15:22:00 2016 +0200
New upstream: 3.28.10
---
debian/changelog | 8 ++++
debian/patches/do_not_attempt_GO.db_test.patch | 66 +++++++++++++++-----------
2 files changed, 46 insertions(+), 28 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 927edee..234268b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+r-bioc-limma (3.28.10+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * Fix the run-unit-test script (don't check for exact stdout match)
+ and add a missing test dependency (r-cran-mass)
+
+ -- Gordon Ball <gordon at chronitis.net> Tue, 21 Jun 2016 15:17:31 +0200
+
r-bioc-limma (3.26.1+dfsg-1) unstable; urgency=medium
* New upstream version
diff --git a/debian/patches/do_not_attempt_GO.db_test.patch b/debian/patches/do_not_attempt_GO.db_test.patch
index 7005c12..7f1803c 100644
--- a/debian/patches/do_not_attempt_GO.db_test.patch
+++ b/debian/patches/do_not_attempt_GO.db_test.patch
@@ -7,7 +7,7 @@ Description: the test is usin GO.db which is not yet packaged
--- a/tests/limma-Tests.R
+++ b/tests/limma-Tests.R
-@@ -270,6 +270,3 @@ EB <- c("133746","1339","134","1340","13
+@@ -274,6 +274,3 @@
"136371","1364","1365","136541","1366","136647","1368","136853","1369","136991",
"1370","137075","1371","137209","1373","137362","1374","137492","1375","1376",
"137682","137695","137735","1378","137814","137868","137872","137886","137902","137964")
@@ -16,36 +16,46 @@ Description: the test is usin GO.db which is not yet packaged
-topGO(go,n=10,truncate.term=30,sort="down")
--- a/tests/limma-Tests.Rout.save
+++ b/tests/limma-Tests.Rout.save
-@@ -1303,32 +1303,3 @@ set1 5 -0.2481655 Up 0.0009
+@@ -1317,42 +1317,6 @@
+ "136371","1364","1365","136541","1366","136647","1368","136853","1369","136991",
+ "1370","137075","1371","137209","1373","137362","1374","137492","1375","1376",
+ "137682","137695","137735","1378","137814","137868","137872","137886","137902","137964")
-> go <- goana(fit,FDR=0.8,geneid=EB)
-> topGO(go,n=10,truncate.term=30)
-- Term Ont N Up Down P.Up P.Down
--GO:0055082 cellular chemical homeostas... BP 2 0 2 1.000000000 0.004242424
--GO:0006897 endocytosis BP 3 3 0 0.005046382 1.000000000
--GO:0019725 cellular homeostasis BP 3 0 2 1.000000000 0.012294372
--GO:0006915 apoptotic process BP 4 3 1 0.017844424 0.255402330
--GO:0012501 programmed cell death BP 4 3 1 0.017844424 0.255402330
--GO:0008283 cell proliferation BP 4 1 2 0.553950615 0.023749721
--GO:0042127 regulation of cell prolifer... BP 4 1 2 0.553950615 0.023749721
--GO:0006909 phagocytosis BP 2 2 0 0.030909091 1.000000000
--GO:0007169 transmembrane receptor prot... BP 2 2 0 0.030909091 1.000000000
--GO:0031252 cell leading edge CC 2 2 0 0.030909091 1.000000000
+- Term Ont N Up Down P.Up
+-GO:0032502 developmental process BP 24 3 6 0.868520473
+-GO:0006915 apoptotic process BP 5 4 1 0.003446627
+-GO:0012501 programmed cell death BP 5 4 1 0.003446627
+-GO:0055082 cellular chemical homeostas... BP 2 0 2 1.000000000
+-GO:0006897 endocytosis BP 3 3 0 0.005046382
+-GO:0044767 single-organism development... BP 23 3 5 0.845083285
+-GO:0048856 anatomical structure develo... BP 23 3 5 0.845083285
+-GO:1902589 single-organism organelle o... BP 7 1 3 0.762502428
+-GO:0008219 cell death BP 6 4 1 0.009129968
+-GO:0016265 death BP 6 4 1 0.009129968
+- P.Down
+-GO:0032502 0.0006606503
+-GO:0006915 0.3096959098
+-GO:0012501 0.3096959098
+-GO:0055082 0.0042424242
+-GO:0006897 1.0000000000
+-GO:0044767 0.0066515474
+-GO:0048856 0.0066515474
+-GO:1902589 0.0066732856
+-GO:0008219 0.3605604217
+-GO:0016265 0.3605604217
-> topGO(go,n=10,truncate.term=30,sort="down")
-- Term Ont N Up Down P.Up P.Down
--GO:0055082 cellular chemical homeostas... BP 2 0 2 1.0000000 0.004242424
--GO:0019725 cellular homeostasis BP 3 0 2 1.0000000 0.012294372
--GO:0008283 cell proliferation BP 4 1 2 0.5539506 0.023749721
--GO:0042127 regulation of cell prolifer... BP 4 1 2 0.5539506 0.023749721
--GO:1902589 single-organism organelle o... BP 5 1 2 0.6375849 0.038228009
--GO:0048878 chemical homeostasis BP 5 1 2 0.6375849 0.038228009
--GO:0032502 developmental process BP 22 3 4 0.8185069 0.040079017
--GO:0043230 extracellular organelle CC 14 1 3 0.9502416 0.055161144
--GO:0065010 extracellular membrane-boun... CC 14 1 3 0.9502416 0.055161144
--GO:0070062 extracellular exosome CC 14 1 3 0.9502416 0.055161144
-->
--> proc.time()
-- user system elapsed
-- 3.15 0.09 3.24
+- Term Ont N Up Down P.Up P.Down
+-GO:0032502 developmental process BP 24 3 6 0.8685205 0.0006606503
+-GO:0055082 cellular chemical homeostas... BP 2 0 2 1.0000000 0.0042424242
+-GO:0044767 single-organism development... BP 23 3 5 0.8450833 0.0066515474
+-GO:0048856 anatomical structure develo... BP 23 3 5 0.8450833 0.0066515474
+-GO:1902589 single-organism organelle o... BP 7 1 3 0.7625024 0.0066732856
+-GO:0007283 spermatogenesis BP 3 0 2 1.0000000 0.0122943723
+-GO:0048232 male gamete generation BP 3 0 2 1.0000000 0.0122943723
+-GO:0001889 liver development BP 3 0 2 1.0000000 0.0122943723
+-GO:0019725 cellular homeostasis BP 3 0 2 1.0000000 0.0122943723
+-GO:0035295 tube development BP 3 0 2 1.0000000 0.0122943723
+ >
+ > proc.time()
+ user system elapsed
--
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