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commit 7679d3fb7d17dedc04a70828d3fc31e7037a73af Author: Gordon Ball <[email protected]> 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 <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
