[med-svn] [r-bioc-limma] 05/06: Adapt patch
Andreas Tille
tille at debian.org
Fri Oct 28 07:47:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-limma.
commit 938714fe3ab295b280f96cbb27763799d8c9a1ca
Author: Andreas Tille <tille at debian.org>
Date: Fri Oct 28 09:40:58 2016 +0200
Adapt patch
---
debian/patches/do_not_attempt_GO.db_test.patch | 58 +++++++++++++-------------
1 file changed, 29 insertions(+), 29 deletions(-)
diff --git a/debian/patches/do_not_attempt_GO.db_test.patch b/debian/patches/do_not_attempt_GO.db_test.patch
index 86214ad..5dd0d8a 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
-@@ -274,6 +274,3 @@
+@@ -274,6 +274,3 @@ EB <- c("133746","1339","134","1340","13
"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")
@@ -16,47 +16,47 @@ 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
-@@ -1317,43 +1317,3 @@
+@@ -1317,43 +1317,3 @@ set1 5 Up 7.3344e-12
+ "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
--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:0048856 anatomical structure develo... BP 23 3 5 0.845083285
--GO:0044767 single-organism development... BP 23 3 5 0.845083285
--GO:1902589 single-organism organelle o... BP 7 1 3 0.762502428
+-GO:0032502 developmental process BP 23 3 5 0.845083285
-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:0048856 0.0066515474
--GO:0044767 0.0066515474
--GO:1902589 0.0066732856
--GO:0008219 0.3605604217
--GO:0016265 0.3605604217
+-GO:0019725 cellular homeostasis BP 3 0 2 1.000000000
+-GO:0048232 male gamete generation BP 3 0 2 1.000000000
+-GO:0007283 spermatogenesis BP 3 0 2 1.000000000
+- P.Down
+-GO:0006915 0.309695910
+-GO:0012501 0.309695910
+-GO:0055082 0.004242424
+-GO:0006897 1.000000000
+-GO:0048856 0.006651547
+-GO:0032502 0.006651547
+-GO:0008219 0.360560422
+-GO:0019725 0.012294372
+-GO:0048232 0.012294372
+-GO:0007283 0.012294372
-> topGO(go,n=10,truncate.term=30,sort="down")
-- 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:0048856 anatomical structure develo... BP 23 3 5 0.8450833 0.0066515474
--GO:0044767 single-organism development... BP 23 3 5 0.8450833 0.0066515474
--GO:1902589 single-organism organelle o... BP 7 1 3 0.7625024 0.0066732856
--GO:0031225 anchored component of membr... CC 3 0 2 1.0000000 0.0122943723
--GO:0019725 cellular homeostasis BP 3 0 2 1.0000000 0.0122943723
--GO:0061008 hepaticobiliary system deve... BP 3 0 2 1.0000000 0.0122943723
--GO:0001889 liver development BP 3 0 2 1.0000000 0.0122943723
--GO:0048232 male gamete generation BP 3 0 2 1.0000000 0.0122943723
+- Term Ont N Up Down P.Up P.Down
+-GO:0055082 cellular chemical homeostas... BP 2 0 2 1.0000000 0.004242424
+-GO:0048856 anatomical structure develo... BP 23 3 5 0.8450833 0.006651547
+-GO:0032502 developmental process BP 23 3 5 0.8450833 0.006651547
+-GO:0019725 cellular homeostasis BP 3 0 2 1.0000000 0.012294372
+-GO:0048232 male gamete generation BP 3 0 2 1.0000000 0.012294372
+-GO:0007283 spermatogenesis BP 3 0 2 1.0000000 0.012294372
+-GO:0009653 anatomical structure morpho... BP 10 0 3 1.0000000 0.020760307
+-GO:0031988 membrane-bounded vesicle CC 19 1 4 0.9851064 0.023153004
+-GO:0007276 gamete generation BP 4 0 2 1.0000000 0.023749721
+-GO:0032504 multicellular organism repr... BP 4 0 2 1.0000000 0.023749721
->
-> proc.time()
- user system elapsed
-- 2.77 0.23 3.04
+- 2.88 0.18 3.08
--
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