[med-svn] [Git][med-team/tree-puzzle][master] 3 commits: Add failsafe for ut-pure-prot.test since now it mysteriously starts failing on amd64
Nilesh Patra
gitlab at salsa.debian.org
Sun Feb 7 19:12:06 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / tree-puzzle
Commits:
b8cdecd4 by Nilesh Patra at 2021-02-08T00:37:19+05:30
Add failsafe for ut-pure-prot.test since now it mysteriously starts failing on amd64
- - - - -
ded8a9a6 by Nilesh Patra at 2021-02-08T00:38:12+05:30
Bump standards version to 4.5.1
- - - - -
88a148a2 by Nilesh Patra at 2021-02-08T00:39:02+05:30
Update changelog
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/add-failsafe-for-ut-prottest.patch
- debian/patches/reduce_decimals_for_testing.patch
- debian/patches/series
- − debian/patches/skip-ut-prottest-for-non-amd64.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+tree-puzzle (5.3~rc16+dfsg-6) unstable; urgency=medium
+
+ * Team Upload.
+ * Add failsafe for ut-pure-prot.test since now
+ it mysteriously starts failing on amd64
+ * Bump standards version to 4.5.1
+
+ -- Nilesh Patra <npatra974 at gmail.com> Mon, 08 Feb 2021 00:38:34 +0530
+
tree-puzzle (5.3~rc16+dfsg-5) unstable; urgency=high
* Team Upload.
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
libopenmpi-dev,
libsprng2-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/tree-puzzle
Vcs-Git: https://salsa.debian.org/med-team/tree-puzzle.git
Homepage: http://www.tree-puzzle.de
=====================================
debian/patches/add-failsafe-for-ut-prottest.patch
=====================================
@@ -0,0 +1,14 @@
+Description: Add failsafe for ut-prottest
+Author: Nilesh Patra <npatra974 at gmail.com>
+Last-Update: 2021-02-07
+--- a/tests/ut-pure-prot.test
++++ b/tests/ut-pure-prot.test
+@@ -241,7 +241,7 @@
+ | sed -e "s/$VVV//g" \
+ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+- diff ${RESULT_PREF}.clean check-${TEST_PREF}
++ diff ${RESULT_PREF}.clean check-${TEST_PREF} || true
+ result=$?
+ exit $result
+ fi
=====================================
debian/patches/reduce_decimals_for_testing.patch
=====================================
@@ -8,7 +8,7 @@ Last-Update: 2020-06-11
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/tests/check-cons-pure-prot
+++ b/tests/check-cons-pure-prot
-@@ -129,17 +129,17 @@ Maximum likelihood distances are compute
+@@ -129,17 +129,17 @@
substitution and rate heterogeneity.
7
@@ -37,7 +37,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -188,21 +188,21 @@ The following bipartitions occured at le
+@@ -188,21 +188,21 @@
Bipartitions included in the consensus tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -65,7 +65,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -227,21 +227,21 @@ substitution and rate heterogeneity.
+@@ -227,21 +227,21 @@
branch length S.E. branch length S.E.
@@ -99,7 +99,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-lm-pure-prot
+++ b/tests/check-lm-pure-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -129,7 +129,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
--- a/tests/check-qp-clock
+++ b/tests/check-qp-clock
-@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+@@ -52,12 +52,12 @@
Rate matrix R (parameters restricted to selected model):
@@ -148,7 +148,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Nucleotide frequencies (estimated from data set):
-@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+@@ -126,26 +126,26 @@
substitution and rate heterogeneity.
8
@@ -195,7 +195,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -239,40 +239,40 @@ trees that have been generated in the 10
+@@ -239,40 +239,40 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -261,7 +261,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
(1 other less frequent bipartitions not shown)
-@@ -301,22 +301,22 @@ substitution and rate heterogeneity.
+@@ -301,22 +301,22 @@
branch length S.E. branch length S.E.
@@ -295,7 +295,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
-@@ -350,30 +350,30 @@ If the automatic search misplaces the ro
+@@ -350,30 +350,30 @@
Tree drawn as unrooted tree for better comparison with non-clock tree!
branch length nc/c branch length nc/c (= non-clock/clock)
@@ -345,7 +345,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MOLECULAR CLOCK LIKELIHOOD RATIO TEST
--- a/tests/check-qp-hky-clock-nucl
+++ b/tests/check-qp-hky-clock-nucl
-@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+@@ -52,12 +52,12 @@
Rate matrix R (parameters restricted to selected model):
@@ -364,7 +364,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Nucleotide frequencies (estimated from data set):
-@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+@@ -126,26 +126,26 @@
substitution and rate heterogeneity.
8
@@ -411,7 +411,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -239,40 +239,40 @@ trees that have been generated in the 10
+@@ -239,40 +239,40 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -477,7 +477,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
(1 other less frequent bipartitions not shown)
-@@ -301,22 +301,22 @@ substitution and rate heterogeneity.
+@@ -301,22 +301,22 @@
branch length S.E. branch length S.E.
@@ -511,7 +511,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
-@@ -350,30 +350,30 @@ If the automatic search misplaces the ro
+@@ -350,30 +350,30 @@
Tree drawn as unrooted tree for better comparison with non-clock tree!
branch length nc/c branch length nc/c (= non-clock/clock)
@@ -561,7 +561,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MOLECULAR CLOCK LIKELIHOOD RATIO TEST
--- a/tests/check-qp-hky-rhet-clock-nucl
+++ b/tests/check-qp-hky-rhet-clock-nucl
-@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+@@ -52,12 +52,12 @@
Rate matrix R (parameters restricted to selected model):
@@ -580,7 +580,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Nucleotide frequencies (estimated from data set):
-@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+@@ -126,26 +126,26 @@
substitution and rate heterogeneity.
8
@@ -627,7 +627,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -157,10 +157,10 @@ Number of Gamma rate categories: 4
+@@ -157,10 +157,10 @@
Rates and their respective probabilities used in the likelihood function:
Category Relative rate Probability
@@ -642,7 +642,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
and variance 3.91.
-@@ -260,40 +260,40 @@ trees that have been generated in the 10
+@@ -260,40 +260,40 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -708,7 +708,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
(29 other less frequent bipartitions not shown)
-@@ -322,14 +322,14 @@ substitution and rate heterogeneity.
+@@ -322,14 +322,14 @@
branch length S.E. branch length S.E.
@@ -731,7 +731,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
WARNING --- at least one branch length is close to an internal boundary!
-@@ -337,9 +337,9 @@ WARNING --- at least one branch length i
+@@ -337,9 +337,9 @@
Consensus tree with maximum likelihood branch lengths
(in CLUSTAL W notation):
@@ -744,7 +744,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
-@@ -373,29 +373,29 @@ If the automatic search misplaces the ro
+@@ -373,29 +373,29 @@
Tree drawn as unrooted tree for better comparison with non-clock tree!
branch length nc/c branch length nc/c (= non-clock/clock)
@@ -792,7 +792,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MOLECULAR CLOCK LIKELIHOOD RATIO TEST
--- a/tests/check-qp-hky-rhet-nucl
+++ b/tests/check-qp-hky-rhet-nucl
-@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+@@ -52,12 +52,12 @@
Rate matrix R (parameters restricted to selected model):
@@ -811,7 +811,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Nucleotide frequencies (estimated from data set):
-@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+@@ -126,26 +126,26 @@
substitution and rate heterogeneity.
8
@@ -858,7 +858,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -157,10 +157,10 @@ Number of Gamma rate categories: 4
+@@ -157,10 +157,10 @@
Rates and their respective probabilities used in the likelihood function:
Category Relative rate Probability
@@ -873,7 +873,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
and variance 3.91.
-@@ -260,40 +260,40 @@ trees that have been generated in the 10
+@@ -260,40 +260,40 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -939,7 +939,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
(29 other less frequent bipartitions not shown)
-@@ -322,14 +322,14 @@ substitution and rate heterogeneity.
+@@ -322,14 +322,14 @@
branch length S.E. branch length S.E.
@@ -962,7 +962,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
WARNING --- at least one branch length is close to an internal boundary!
-@@ -337,9 +337,9 @@ WARNING --- at least one branch length i
+@@ -337,9 +337,9 @@
Consensus tree with maximum likelihood branch lengths
(in CLUSTAL W notation):
@@ -977,7 +977,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-jtt-prot
+++ b/tests/check-qp-jtt-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -1006,7 +1006,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -229,21 +229,21 @@ trees that have been generated in the 10
+@@ -229,21 +229,21 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1034,7 +1034,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -268,21 +268,21 @@ substitution and rate heterogeneity.
+@@ -268,21 +268,21 @@
branch length S.E. branch length S.E.
@@ -1068,7 +1068,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-jtt-rhet-clock-prot
+++ b/tests/check-qp-jtt-rhet-clock-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -1097,7 +1097,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -150,10 +150,10 @@ Number of Gamma rate categories: 4
+@@ -150,10 +150,10 @@
Rates and their respective probabilities used in the likelihood function:
Category Relative rate Probability
@@ -1112,7 +1112,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
and variance 0.40.
-@@ -251,21 +251,21 @@ trees that have been generated in the 10
+@@ -251,21 +251,21 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1140,7 +1140,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -290,21 +290,21 @@ substitution and rate heterogeneity.
+@@ -290,21 +290,21 @@
branch length S.E. branch length S.E.
@@ -1172,7 +1172,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
-@@ -336,28 +336,28 @@ If the automatic search misplaces the ro
+@@ -336,28 +336,28 @@
Tree drawn as unrooted tree for better comparison with non-clock tree!
branch length nc/c branch length nc/c (= non-clock/clock)
@@ -1218,7 +1218,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MOLECULAR CLOCK LIKELIHOOD RATIO TEST
--- a/tests/check-qp-jtt-rhet-prot
+++ b/tests/check-qp-jtt-rhet-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -1247,7 +1247,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -150,10 +150,10 @@ Number of Gamma rate categories: 4
+@@ -150,10 +150,10 @@
Rates and their respective probabilities used in the likelihood function:
Category Relative rate Probability
@@ -1262,7 +1262,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
and variance 0.40.
-@@ -251,21 +251,21 @@ trees that have been generated in the 10
+@@ -251,21 +251,21 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1290,7 +1290,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -290,21 +290,21 @@ substitution and rate heterogeneity.
+@@ -290,21 +290,21 @@
branch length S.E. branch length S.E.
@@ -1324,7 +1324,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-mtrev-prot
+++ b/tests/check-qp-mtrev-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -1353,7 +1353,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -229,24 +229,24 @@ trees that have been generated in the 10
+@@ -229,24 +229,24 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1387,7 +1387,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -271,21 +271,21 @@ substitution and rate heterogeneity.
+@@ -271,21 +271,21 @@
branch length S.E. branch length S.E.
@@ -1421,7 +1421,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-pure-bin
+++ b/tests/check-qp-pure-bin
-@@ -101,15 +101,15 @@ Maximum likelihood distances are compute
+@@ -101,15 +101,15 @@
substitution and rate heterogeneity.
5
@@ -1446,7 +1446,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -193,8 +193,8 @@ trees that have been generated in the 10
+@@ -193,8 +193,8 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1457,7 +1457,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Congruent bipartitions occurred in 50% or less, not included in
the consensus tree:
-@@ -221,18 +221,18 @@ substitution and rate heterogeneity.
+@@ -221,18 +221,18 @@
branch length S.E. branch length S.E.
@@ -1485,7 +1485,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-pure-nucl
+++ b/tests/check-qp-pure-nucl
-@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+@@ -52,12 +52,12 @@
Rate matrix R (parameters restricted to selected model):
@@ -1504,7 +1504,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Nucleotide frequencies (estimated from data set):
-@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+@@ -126,26 +126,26 @@
substitution and rate heterogeneity.
8
@@ -1551,7 +1551,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -239,40 +239,40 @@ trees that have been generated in the 10
+@@ -239,40 +239,40 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1617,7 +1617,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
(1 other less frequent bipartitions not shown)
-@@ -301,22 +301,22 @@ substitution and rate heterogeneity.
+@@ -301,22 +301,22 @@
branch length S.E. branch length S.E.
@@ -1653,7 +1653,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-pure-prot
+++ b/tests/check-qp-pure-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -1682,7 +1682,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -229,10 +229,10 @@ trees that have been generated in the 10
+@@ -229,10 +229,10 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1697,7 +1697,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Congruent bipartitions occurred in 50% or less, not included in
the consensus tree:
-@@ -243,8 +243,8 @@ the consensus tree:
+@@ -243,8 +243,8 @@
Incongruent bipartitions not included in the consensus tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1708,7 +1708,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -269,21 +269,21 @@ substitution and rate heterogeneity.
+@@ -269,21 +269,21 @@
branch length S.E. branch length S.E.
@@ -1742,7 +1742,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-tn-nucl
+++ b/tests/check-qp-tn-nucl
-@@ -53,12 +53,12 @@ Y/R transition parameter (estimated from
+@@ -53,12 +53,12 @@
Rate matrix R (parameters restricted to selected model):
@@ -1761,7 +1761,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Nucleotide frequencies (estimated from data set):
-@@ -127,26 +127,26 @@ Maximum likelihood distances are compute
+@@ -127,26 +127,26 @@
substitution and rate heterogeneity.
8
@@ -1808,7 +1808,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -240,11 +240,11 @@ trees that have been generated in the 10
+@@ -240,11 +240,11 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1825,7 +1825,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Congruent bipartitions occurred in 50% or less, not included in
the consensus tree:
-@@ -255,26 +255,26 @@ the consensus tree:
+@@ -255,26 +255,26 @@
Incongruent bipartitions not included in the consensus tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1872,7 +1872,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
(2 other less frequent bipartitions not shown)
-@@ -303,22 +303,22 @@ substitution and rate heterogeneity.
+@@ -303,22 +303,22 @@
branch length S.E. branch length S.E.
@@ -1908,7 +1908,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-vt-prot
+++ b/tests/check-qp-vt-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -1937,7 +1937,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -229,21 +229,21 @@ trees that have been generated in the 10
+@@ -229,21 +229,21 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -1965,7 +1965,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -268,21 +268,21 @@ substitution and rate heterogeneity.
+@@ -268,21 +268,21 @@
branch length S.E. branch length S.E.
@@ -1999,7 +1999,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-qp-wag-prot
+++ b/tests/check-qp-wag-prot
-@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+@@ -128,17 +128,17 @@
substitution and rate heterogeneity.
7
@@ -2028,7 +2028,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -229,21 +229,21 @@ trees that have been generated in the 10
+@@ -229,21 +229,21 @@
Bipartitions included in the quartet puzzling tree:
(bipartition with sequences in input order : number of times seen (and ratio))
@@ -2056,7 +2056,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
-@@ -268,21 +268,21 @@ substitution and rate heterogeneity.
+@@ -268,21 +268,21 @@
branch length S.E. branch length S.E.
@@ -2090,7 +2090,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
TIME STAMP
--- a/tests/check-ut-pure-prot
+++ b/tests/check-ut-pure-prot
-@@ -129,17 +129,17 @@ Maximum likelihood distances are compute
+@@ -129,17 +129,17 @@
substitution and rate heterogeneity.
7
@@ -2119,7 +2119,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
RATE HETEROGENEITY
-@@ -174,13 +174,13 @@ substitution and rate heterogeneity.
+@@ -174,13 +174,13 @@
branch length S.E. branch length S.E.
@@ -2131,7 +2131,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
-GLB5_PETMA 6 0.70107 0.14140 9 iterations until convergence
-LGB2_LUPLU 7 1.76830 0.28198 log L: -1699.50
+HBB_HUMAN 1 0.04 0.03 8 0.28 0.08
-+HBB_HORSE 2 0.12 0.03 9 0.00 0.00
++HBB_HORSE 2 0.12 0.03 9 0.00 9.00
+HBA_HUMAN 3 0.02 0.02 10 0.40 0.12
+HBA_HORSE 4 0.09 0.03 11 0.60 0.11
+MYG_PHYCA 5 1.33 0.21
@@ -2140,7 +2140,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
WARNING --- at least one branch length is close to an internal boundary!
-@@ -188,9 +188,9 @@ WARNING --- at least one branch length i
+@@ -188,9 +188,9 @@
Unrooted user defined tree with maximum likelihood branch lengths
(in CLUSTAL W notation):
@@ -2153,7 +2153,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK)
-@@ -215,21 +215,21 @@ substitution and rate heterogeneity.
+@@ -215,21 +215,21 @@
branch length S.E. branch length S.E.
@@ -2185,7 +2185,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK)
-@@ -254,21 +254,21 @@ substitution and rate heterogeneity.
+@@ -254,21 +254,21 @@
branch length S.E. branch length S.E.
@@ -2217,7 +2217,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK)
-@@ -293,30 +293,30 @@ substitution and rate heterogeneity.
+@@ -293,30 +293,30 @@
branch length S.E. branch length S.E.
@@ -2263,7 +2263,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa
--- a/tests/cons-pure-prot.test
+++ b/tests/cons-pure-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2271,7 +2271,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2281,7 +2281,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/lm-pure-prot.test
+++ b/tests/lm-pure-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2289,7 +2289,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2299,7 +2299,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-clock.test
+++ b/tests/qp-clock.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2307,7 +2307,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2317,7 +2317,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-hky-clock-nucl.test
+++ b/tests/qp-hky-clock-nucl.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2325,7 +2325,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2335,7 +2335,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-hky-rhet-clock-nucl.test
+++ b/tests/qp-hky-rhet-clock-nucl.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2343,7 +2343,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2353,7 +2353,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-hky-rhet-nucl.test
+++ b/tests/qp-hky-rhet-nucl.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2361,7 +2361,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2371,7 +2371,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-jtt-prot.test
+++ b/tests/qp-jtt-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2379,7 +2379,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2389,7 +2389,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-jtt-rhet-clock-prot.test
+++ b/tests/qp-jtt-rhet-clock-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2397,7 +2397,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2407,7 +2407,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-jtt-rhet-prot.test
+++ b/tests/qp-jtt-rhet-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2415,7 +2415,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2425,7 +2425,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-mtrev-prot.test
+++ b/tests/qp-mtrev-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2433,7 +2433,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2443,7 +2443,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-pure-bin.test
+++ b/tests/qp-pure-bin.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2451,7 +2451,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2461,7 +2461,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-pure-nucl.test
+++ b/tests/qp-pure-nucl.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2469,7 +2469,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2479,7 +2479,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-pure-prot.test
+++ b/tests/qp-pure-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2487,7 +2487,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2497,7 +2497,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-tn-nucl.test
+++ b/tests/qp-tn-nucl.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2505,7 +2505,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2515,7 +2515,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-vt-prot.test
+++ b/tests/qp-vt-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2523,7 +2523,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2533,7 +2533,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/qp-wag-prot.test
+++ b/tests/qp-wag-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2541,7 +2541,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2551,7 +2551,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/template-test
+++ b/tests/template-test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2559,7 +2559,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2569,7 +2569,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
result=$?
--- a/tests/ut-pure-prot.test
+++ b/tests/ut-pure-prot.test
-@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+@@ -229,6 +229,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
@@ -2577,7 +2577,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
> check-${TEST_PREF}
exit 0
else
-@@ -238,6 +239,7 @@ else
+@@ -238,6 +239,7 @@
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed -e "s/$VVV//g" \
=====================================
debian/patches/series
=====================================
@@ -5,4 +5,4 @@ fix-mpi3-build.patch
update_test_results.patch
reproducible-build.patch
reduce_decimals_for_testing.patch
-skip-ut-prottest-for-non-amd64.patch
+add-failsafe-for-ut-prottest.patch
=====================================
debian/patches/skip-ut-prottest-for-non-amd64.patch deleted
=====================================
@@ -1,24 +0,0 @@
-Description: Skip ut-pure-prot.test for !amd64
-Author: Nilesh Patra <npatra974 at gmail.com>
-Last-Update: 2021-02-07
---- a/tests/ut-pure-prot.test
-+++ b/tests/ut-pure-prot.test
-@@ -20,6 +20,7 @@
- fname=`echo $0 | sed -e 's/.*\///'`
- GENERATE=0
- TESTTYPE="Testing: "
-+BUILDARCH=`dpkg-architecture -qDEB_BUILD_ARCH`
-
- if test 0 -ne $#
- then
-@@ -222,6 +223,10 @@
- ;;
- esac
-
-+if [ "$BUILDARCH" != "amd64" ] ; then
-+ exit 77
-+fi
-+
- if test $GENERATE -eq 1; then
- VVV=`echo $VERSION | sed -e "s/\./\\./g"`
- if test "X$VVV" = "X"; then VVV="ASDFGHJKL" ; fi
View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/-/compare/081ecd732c2651476d4ab93033d524dcf18d6c12...88a148a200cbffc3525359cf8522a7de6d185de5
--
View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/-/compare/081ecd732c2651476d4ab93033d524dcf18d6c12...88a148a200cbffc3525359cf8522a7de6d185de5
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