[med-svn] [r-bioc-limma] 03/03: New upstream version 3.32-7
Steffen Möller
moeller at moszumanska.debian.org
Mon Sep 25 21:14:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository r-bioc-limma.
commit 68f6f2696e8133d9f337d4d30b57e32c08d3138a
Author: Steffen Moeller <moeller at debian.org>
Date: Mon Sep 25 23:13:06 2017 +0200
New upstream version 3.32-7
---
debian/changelog | 8 ++++
debian/control | 2 +-
debian/patches/do_not_attempt_GO.db_test.patch | 52 ++++++++++++++------------
3 files changed, 37 insertions(+), 25 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index ded14a7..60c5f0a 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+r-bioc-limma (3.32.7+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Bumped policy to 4.1.0 (no changes required)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 25 Sep 2017 23:04:35 +0200
+
r-bioc-limma (3.30.8+dfsg-1) unstable; urgency=medium
* New upstream version
diff --git a/debian/control b/debian/control
index 9dfe18e..ec53eac 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 10),
dh-r,
r-base-dev
-Standards-Version: 3.9.8
+Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-bioc-limma.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/r-bioc-limma.git
Homepage: https://bioconductor.org/packages/limma/
diff --git a/debian/patches/do_not_attempt_GO.db_test.patch b/debian/patches/do_not_attempt_GO.db_test.patch
index ac89138..d934f35 100644
--- a/debian/patches/do_not_attempt_GO.db_test.patch
+++ b/debian/patches/do_not_attempt_GO.db_test.patch
@@ -5,58 +5,62 @@ Description: the test is usin GO.db which is not yet packaged
http://www.bioconductor.org/packages/release/data/annotation/html/GO.db.html
for Jessie this part of the test suite will be skipped
---- a/tests/limma-Tests.R
-+++ b/tests/limma-Tests.R
-@@ -274,6 +274,3 @@ EB <- c("133746","1339","134","1340","13
+Index: r-bioc-limma/tests/limma-Tests.R
+===================================================================
+--- r-bioc-limma.orig/tests/limma-Tests.R
++++ r-bioc-limma/tests/limma-Tests.R
+@@ -278,6 +278,3 @@ 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")
-go <- goana(fit,FDR=0.8,geneid=EB)
-topGO(go,n=10,truncate.term=30)
-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 @@ set1 5 Up 7.3344e-12
+Index: r-bioc-limma/tests/limma-Tests.Rout.save
+===================================================================
+--- r-bioc-limma.orig/tests/limma-Tests.Rout.save
++++ r-bioc-limma/tests/limma-Tests.Rout.save
+@@ -1336,43 +1336,4 @@ Gene50 1.034777 0.01608433 2.063663 0
+ "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:0009653 anatomical structure morpho... BP 10 1 4 0.936627742
--GO:0048856 anatomical structure develo... BP 23 4 6 0.844070086
-GO:0032502 developmental process BP 23 4 6 0.844070086
-GO:0055082 cellular chemical homeostas... BP 2 0 2 1.000000000
-GO:0006915 apoptotic process BP 5 4 1 0.009503355
+-GO:0098609 cell-cell adhesion BP 5 4 0 0.009503355
+-GO:0040011 locomotion BP 5 4 0 0.009503355
-GO:0012501 programmed cell death BP 5 4 1 0.009503355
--GO:0006897 endocytosis BP 3 3 0 0.010952381
--GO:0031988 membrane-bounded vesicle CC 19 4 5 0.691026648
--GO:0016485 protein processing BP 7 1 3 0.849770470
--GO:0005615 extracellular space CC 13 5 4 0.143422146
+-GO:0042981 regulation of apoptotic pro... BP 5 4 1 0.009503355
+-GO:0043067 regulation of programmed ce... BP 5 4 1 0.009503355
+-GO:0097190 apoptotic signaling pathway BP 3 3 0 0.010952381
+-GO:0031252 cell leading edge CC 3 3 0 0.010952381
- P.Down
--GO:0009653 0.008224876
--GO:0048856 0.009014340
-GO:0032502 0.009014340
-GO:0055082 0.009090909
-GO:0006915 0.416247633
+-GO:0098609 1.000000000
+-GO:0040011 1.000000000
-GO:0012501 0.416247633
--GO:0006897 1.000000000
--GO:0031988 0.020081679
--GO:0016485 0.020760307
--GO:0005615 0.023836810
+-GO:0042981 0.416247633
+-GO:0043067 0.416247633
+-GO:0097190 1.000000000
+-GO:0031252 1.000000000
-> topGO(go,n=10,truncate.term=30,sort="down")
- Term Ont N Up Down P.Up P.Down
--GO:0009653 anatomical structure morpho... BP 10 1 4 0.9366277 0.008224876
--GO:0048856 anatomical structure develo... BP 23 4 6 0.8440701 0.009014340
-GO:0032502 developmental process BP 23 4 6 0.8440701 0.009014340
-GO:0055082 cellular chemical homeostas... BP 2 0 2 1.0000000 0.009090909
--GO:0031988 membrane-bounded vesicle CC 19 4 5 0.6910266 0.020081679
-GO:0016485 protein processing BP 7 1 3 0.8497705 0.020760307
-GO:0005615 extracellular space CC 13 5 4 0.1434221 0.023836810
--GO:0031982 vesicle CC 20 4 5 0.7361976 0.025464546
-GO:0009887 animal organ morphogenesis BP 3 0 2 1.0000000 0.025788497
-GO:0019725 cellular homeostasis BP 3 0 2 1.0000000 0.025788497
-->
+-GO:0072359 circulatory system developm... BP 3 0 2 1.0000000 0.025788497
+-GO:0007507 heart development BP 3 0 2 1.0000000 0.025788497
+-GO:0048232 male gamete generation BP 3 0 2 1.0000000 0.025788497
+-GO:0007283 spermatogenesis BP 3 0 2 1.0000000 0.025788497
+ >
-> proc.time()
- user system elapsed
-- 3.13 0.26 4.14
+- 3.46 0.12 3.62
--
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