[med-svn] [libbpp-phyl] 01/01: Some more fixes to try resolving failure on some architectures.

[Julien Dutheil]

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jdutheil-guest pushed a commit to branch master
in repository libbpp-phyl.

commit 6ea191a808f5b6a52d66f8a2ccda1e93fc0e920a
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date:   Fri Jul 14 14:40:55 2017 +0200

    Some more fixes to try resolving failure on some architectures.
---
 ...hreshold-for-application-to-a-broader-ran.patch | 22 ++++++++++++----------
 debian/patches/more_verbose_clock_test.patch       | 22 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 3 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch b/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch
index 4ed4a7c..9f46d12 100644
--- a/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch
+++ b/debian/patches/0001-Decreased-threshold-for-application-to-a-broader-ran.patch
@@ -1,15 +1,17 @@
-From: "Julien Y. Dutheil" <dutheil at evolbio.mpg.de>
-Date: Mon, 26 Jun 2017 21:00:35 +0200
-Subject: [PATCH 1/2] Decreased threshold for application to a broader range of
- architecture.
-
----
- test/test_likelihood_clock.cpp | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
+diff --git a/test/test_likelihood_clock.cpp b/test/test_likelihood_clock.cpp
+index fa70e89..03f6f74 100644
 --- a/test/test_likelihood_clock.cpp
 +++ b/test/test_likelihood_clock.cpp
-@@ -69,7 +69,7 @@ void fitModelH(SubstitutionModel* model,
+@@ -60,7 +60,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
+   ApplicationTools::displayResult("Test model", model->getName());
+   cout << setprecision(20) << tl.getValue() << endl;
+   ApplicationTools::displayResult("* initial likelihood", tl.getValue());
+-  if (abs(tl.getValue() - initialValue) > 0.0001)
++  if (abs(tl.getValue() - initialValue) > 0.001)
+     throw Exception("Incorrect initial value.");
+   unique_ptr<OutputStream> messenger(new StlOutputStream(new ofstream("messages.txt", ios::out)));
+   unique_ptr<OutputStream> profiler(new StlOutputStream(new ofstream("profile.txt", ios::out)));
+@@ -69,7 +69,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
    cout << setprecision(20) << tl.getValue() << endl;
    ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
    tl.getParameters().printParameters(cout);
diff --git a/debian/patches/more_verbose_clock_test.patch b/debian/patches/more_verbose_clock_test.patch
new file mode 100644
index 0000000..1f6f796
--- /dev/null
+++ b/debian/patches/more_verbose_clock_test.patch
@@ -0,0 +1,22 @@
+diff --git a/test/test_likelihood_clock.cpp b/test/test_likelihood_clock.cpp
+index fa70e89..fa5a005 100644
+--- a/test/test_likelihood_clock.cpp
++++ b/test/test_likelihood_clock.cpp
+@@ -70,7 +70,7 @@ void fitModelH(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree
+   ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
+   tl.getParameters().printParameters(cout);
+   if (abs(tl.getValue() - finalValue) > 0.001)
+-    throw Exception("Incorrect final value.");
++    throw Exception("Incorrect final value:" + TextTools::toString(tl.getValue()) + "<>" + TextTools::toString(finalValue));
+ }
+ 
+ void fitModelHClock(SubstitutionModel* model, DiscreteDistribution* rdist, const Tree& tree, const SiteContainer& sites,
+@@ -92,7 +92,7 @@ void fitModelHClock(SubstitutionModel* model, DiscreteDistribution* rdist, const
+   ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue());
+   tl.getParameters().printParameters(cout);
+   if (abs(tl.getValue() - finalValue) > 0.001)
+-    throw Exception("Incorrect final value.");
++    throw Exception("Incorrect final value:" + TextTools::toString(tl.getValue()) + "<>" + TextTools::toString(finalValue));
+ }
+ 
+ int main() {
diff --git a/debian/patches/series b/debian/patches/series
index 771eb4d..b0c2c8c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ relax_test_timeout.patch
 0001-Decreased-threshold-for-application-to-a-broader-ran.patch
 0002-Fixed-unit-tests-compilation-on-some-platforms.patch
 remove_deprecated_warnings.patch
+more_verbose_clock_test.patch

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