[med-svn] [Git][med-team/libbpp-seq][master] Better platform-specific symbol file management.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq Commits: 03768bc3 by Julien Y. Dutheil at 2019-03-11T20:52:28Z Better platform-specific symbol file management. - - - - - 2 changed files: - debian/libbpp-seq12.symbols → debian/libbpp-seq12.symbols.amd64 - debian/rules Changes: = debian/libbpp-seq12.symbols → debian/libbpp-seq12.symbols.amd64 = = debian/rules = @@ -9,23 +9,6 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF %: dh $@ -override_dh_makeshlibs: -ifeq ($(DEB_BUILD_ARCH),amd64) - echo "Architecture amd64 is the only one where a symbols file is provided" -else - echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" - mkdir -p debian/hidesymbols - mv debian/*.symbols debian/hidesymbols -endif - dh_makeshlibs -ifeq ($(DEB_BUILD_ARCH),amd64) - echo "dh_makeshlibs for architecture amd64 including symbols done" -else - # restore original debian/ dir to enable building twice in a row - mv debian/hidesymbols/*.symbols debian - rmdir debian/hidesymbols -endif - override_dh_install: dh_install d-shlibmove --commit \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/03768bc30f93d72d4491d1e62a7d047d71596008 -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/03768bc30f93d72d4491d1e62a7d047d71596008 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][master] Updated symbols file.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-popgen
Commits:
d733b8fb by Julien Y. Dutheil at 2019-03-11T20:51:52Z
Updated symbols file.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/libbpp-popgen8.symbols → debian/libbpp-popgen8.symbols.amd64
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,9 +1,15 @@
libbpp-popgen (2.4.1-2) UNRELEASED; urgency=medium
+ [ Jelmer Vernooij]
* Use secure copyright file specification URI.
* Trim trailing whitespace.
- -- Jelmer Vernooij Wed, 24 Oct 2018 22:53:39 +
+ [ Julien Dutheil ]
+ * Standards-Version: 4.3.0
+ * d-shlibs (>= 0.82)
+ * Easier amd64 symbol file management
+
+ -- Julien Dutheil Mon, 11 Mar 2019 08:54:44
+0200
libbpp-popgen (2.4.1-1) unstable; urgency=medium
=
debian/control
=
@@ -6,10 +6,10 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 11~),
cmake,
- d-shlibs (>= 0.80),
+ d-shlibs (>= 0.82),
libbpp-core-dev (>= 2.4.1),
libbpp-seq-dev (>= 2.4.1)
-Standards-Version: 4.2.0
+Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-popgen
Vcs-Git: https://salsa.debian.org/med-team/libbpp-popgen.git
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
@@ -19,6 +19,7 @@ Architecture: any
Section: libdevel
Depends: libbpp-popgen8 (= ${binary:Version}),
${misc:Depends},
+${devlibs:Depends},
libbpp-core-dev (>= 2.4.1),
libbpp-seq-dev (>= 2.4.1)
Description: Bio++ Population Genetics library development files
=
debian/libbpp-popgen8.symbols → debian/libbpp-popgen8.symbols.amd64
=
@@ -756,6 +756,7 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
_ZNK3bpp19VectorSiteContainer7valueAtEmm@Base 2.4.1
_ZNK3bpp19VectorSiteContainerclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm@Base
2.4.1
_ZNK3bpp19VectorSiteContainerclEmm@Base 2.4.1
+ _ZNK3bpp20AbstractCoreSequence7getNameB5cxx11Ev@Base 2.4.1
_ZNK3bpp20AbstractOutputStream12getPrecisionEv@Base 2.4.1
_ZNK3bpp20AbstractOutputStream27isScientificNotationEnabledEv@Base 2.4.1
_ZNK3bpp20MapSequenceContainer20getNumberOfSequencesEv@Base 2.4.1
@@ -903,6 +904,8 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
_ZNK3bpp9RowMatrixIdEclEmm@Base 2.4.1
_ZNKSt5ctypeIcE8do_widenEc@Base 2.4.1
_ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_@Base
2.4.1
+
_ZNSt11_Deque_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base
2.4.1
+
_ZNSt11_Deque_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base
2.4.1
_ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv@Base 2.4.1
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS5_ESaISt4pairIKS5_dEEEixEOS5_@Base
2.4.1
_ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixEOi@Base 2.4.1
@@ -915,6 +918,7 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base
2.4.1
+
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE9push_backERKS5_@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base
2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_@Base
2.4.1
@@ -983,6 +987,7 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_@Base
2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E@Base
2.4.1
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E@Base
2.4.1
+
_ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iterat
[med-svn] [Git][med-team/bppphyview][master] 3 commits: New upstream version 0.6.1
Julien Y. Dutheil pushed to branch master at Debian Med / bppphyview
Commits:
890fa115 by Julien Y. Dutheil at 2018-08-27T06:56:51Z
New upstream version 0.6.1
- - - - -
557379fe by Julien Y. Dutheil at 2018-08-27T06:56:51Z
Update upstream source from tag 'upstream/0.6.1'
Update to upstream version '0.6.1'
with Debian dir 954143223d1d66a063b26a5a663b4055add0e901
- - - - -
f7bab19d by Julien Y. Dutheil at 2018-08-27T07:00:31Z
Version 0.6.1.
- - - - -
5 changed files:
- CMakeLists.txt
- bppPhyView/PhyView.cpp
- bppphyview.spec
- debian/changelog
- debian/control
Changes:
=
CMakeLists.txt
=
@@ -93,10 +93,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppphyview")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "0.6.0")
+SET(CPACK_PACKAGE_VERSION "0.6.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "0")
SET(CPACK_PACKAGE_VERSION_MINOR "6")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetic Viewer")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
bppPhyView/PhyView.cpp
=
@@ -1038,15 +1038,15 @@ void PhyView::exit()
void PhyView::aboutBpp()
{
QMessageBox msgBox;
- msgBox.setText("Bio++ 2.4.0.");
- msgBox.setInformativeText("bpp-core 2.4.0\nbpp-seq 2.4.0.\nbpp-phyl
2.4.0.\nbpp-qt 2.4.0");
+ msgBox.setText("Bio++ 2.4.1.");
+ msgBox.setInformativeText("bpp-core 2.4.1\nbpp-seq 2.4.1.\nbpp-phyl
2.4.1.\nbpp-qt 2.4.1");
msgBox.exec();
}
void PhyView::about()
{
QMessageBox msgBox;
- msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.6.0.");
+ msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.6.1.");
msgBox.setInformativeText("Julien Dutheil .");
msgBox.exec();
}
=
bppphyview.spec
=
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bppphyview
Name: bppphyview
-Version: 0.6.0
+Version: 0.6.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -11,9 +11,9 @@ Source: %{name}-%{version}.tar.gz
Summary: Bio++ Phylogenetic Viewer
Group: Productivity/Scientific/Other
-Requires: libbpp-phyl12 = 2.4.0
-Requires: libbpp-core4 = 2.4.0
-Requires: libbpp-qt2 = 2.4.0
+Requires: libbpp-phyl12 = 2.4.1
+Requires: libbpp-core4 = 2.4.1
+Requires: libbpp-qt2 = 2.4.1
%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} ||
0%{?scientificlinux_version}
Requires: libqt5core5 >= 5.0.0
@@ -47,12 +47,12 @@ BuildRoot: %{_builddir}/%{name}-root
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: groff
-BuildRequires: libbpp-core4 = 2.4.0
-BuildRequires: libbpp-core-devel = 2.4.0
-BuildRequires: libbpp-phyl12 = 2.4.0
-BuildRequires: libbpp-phyl-devel = 2.4.0
-BuildRequires: libbpp-qt2 = 2.4.0
-BuildRequires: libbpp-qt-devel = 2.4.0
+BuildRequires: libbpp-core4 = 2.4.1
+BuildRequires: libbpp-core-devel = 2.4.1
+BuildRequires: libbpp-phyl12 = 2.4.1
+BuildRequires: libbpp-phyl-devel = 2.4.1
+BuildRequires: libbpp-qt2 = 2.4.1
+BuildRequires: libbpp-qt-devel = 2.4.1
%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} ||
0%{?scientificlinux_version}
BuildRequires: qt >= 5.0.0
@@ -132,6 +132,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/phyview.1*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 0.6.1-1
+- Compatibility update with Bio++ 2.4.1.
* Mon Mar 12 2018 Julien Dutheil 0.6.0-1
- Compatibility update with Bio++ 2.4.0.
- More options in branch lengths panel.
=
debian/changelog
=
@@ -1,3 +1,10 @@
+bppphyview (0.6.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Compatibility with Bio++ 2.4.1.
+
+ -- Julien Dutheil Mon, 27 Aug 2018 08:57:24
+0200
+
bppphyview (0.6.0-1) unstable; urgency=medium
* New upstream version
=
debian/control
=
@@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 11~),
cmake,
qt5-qmake,
qtdeclarative5-dev,
- libbpp-qt-dev (>= 2.4.0)
+ libbpp-qt-dev (>= 2.4.1)
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/bppphyview
Vcs-Git: https://salsa.debian.org/med-team/bppphyview.git
View it on GitLab:
https://salsa.debian.org/med-team/bppphyview/compare/85d0469d006a02050d4542e1ec8e5b66c6962f15...f7bab19d712c0e048f8237a31dd176fb313d841d
--
View it
[med-svn] [Git][med-team/bppphyview] Pushed new tag upstream/0.6.1
Julien Y. Dutheil pushed new tag upstream/0.6.1 at Debian Med / bppphyview -- View it on GitLab: https://salsa.debian.org/med-team/bppphyview/tree/upstream/0.6.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppphyview][upstream] New upstream version 0.6.1
Julien Y. Dutheil pushed to branch upstream at Debian Med / bppphyview
Commits:
890fa115 by Julien Y. Dutheil at 2018-08-27T06:56:51Z
New upstream version 0.6.1
- - - - -
3 changed files:
- CMakeLists.txt
- bppPhyView/PhyView.cpp
- bppphyview.spec
Changes:
=
CMakeLists.txt
=
@@ -93,10 +93,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppphyview")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "0.6.0")
+SET(CPACK_PACKAGE_VERSION "0.6.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "0")
SET(CPACK_PACKAGE_VERSION_MINOR "6")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogenetic Viewer")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
bppPhyView/PhyView.cpp
=
@@ -1038,15 +1038,15 @@ void PhyView::exit()
void PhyView::aboutBpp()
{
QMessageBox msgBox;
- msgBox.setText("Bio++ 2.4.0.");
- msgBox.setInformativeText("bpp-core 2.4.0\nbpp-seq 2.4.0.\nbpp-phyl
2.4.0.\nbpp-qt 2.4.0");
+ msgBox.setText("Bio++ 2.4.1.");
+ msgBox.setInformativeText("bpp-core 2.4.1\nbpp-seq 2.4.1.\nbpp-phyl
2.4.1.\nbpp-qt 2.4.1");
msgBox.exec();
}
void PhyView::about()
{
QMessageBox msgBox;
- msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.6.0.");
+ msgBox.setText("This is Bio++ Phylogenetic Viewer version 0.6.1.");
msgBox.setInformativeText("Julien Dutheil .");
msgBox.exec();
}
=
bppphyview.spec
=
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bppphyview
Name: bppphyview
-Version: 0.6.0
+Version: 0.6.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -11,9 +11,9 @@ Source: %{name}-%{version}.tar.gz
Summary: Bio++ Phylogenetic Viewer
Group: Productivity/Scientific/Other
-Requires: libbpp-phyl12 = 2.4.0
-Requires: libbpp-core4 = 2.4.0
-Requires: libbpp-qt2 = 2.4.0
+Requires: libbpp-phyl12 = 2.4.1
+Requires: libbpp-core4 = 2.4.1
+Requires: libbpp-qt2 = 2.4.1
%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} ||
0%{?scientificlinux_version}
Requires: libqt5core5 >= 5.0.0
@@ -47,12 +47,12 @@ BuildRoot: %{_builddir}/%{name}-root
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: groff
-BuildRequires: libbpp-core4 = 2.4.0
-BuildRequires: libbpp-core-devel = 2.4.0
-BuildRequires: libbpp-phyl12 = 2.4.0
-BuildRequires: libbpp-phyl-devel = 2.4.0
-BuildRequires: libbpp-qt2 = 2.4.0
-BuildRequires: libbpp-qt-devel = 2.4.0
+BuildRequires: libbpp-core4 = 2.4.1
+BuildRequires: libbpp-core-devel = 2.4.1
+BuildRequires: libbpp-phyl12 = 2.4.1
+BuildRequires: libbpp-phyl-devel = 2.4.1
+BuildRequires: libbpp-qt2 = 2.4.1
+BuildRequires: libbpp-qt-devel = 2.4.1
%if 0%{?fedora} || 0%{?rhel_version} || 0%{?centos_version} ||
0%{?scientificlinux_version}
BuildRequires: qt >= 5.0.0
@@ -132,6 +132,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/phyview.1*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 0.6.1-1
+- Compatibility update with Bio++ 2.4.1.
* Mon Mar 12 2018 Julien Dutheil 0.6.0-1
- Compatibility update with Bio++ 2.4.0.
- More options in branch lengths panel.
View it on GitLab:
https://salsa.debian.org/med-team/bppphyview/commit/890fa115f6d02096c22a09dea3bf501fcebd94e6
--
View it on GitLab:
https://salsa.debian.org/med-team/bppphyview/commit/890fa115f6d02096c22a09dea3bf501fcebd94e6
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/bppphyview][pristine-tar] pristine-tar data for bppphyview_0.6.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / bppphyview Commits: f1840e34 by Julien Y. Dutheil at 2018-08-27T06:56:51Z pristine-tar data for bppphyview_0.6.1.orig.tar.gz - - - - - 2 changed files: - + bppphyview_0.6.1.orig.tar.gz.delta - + bppphyview_0.6.1.orig.tar.gz.id Changes: = bppphyview_0.6.1.orig.tar.gz.delta = Binary files /dev/null and b/bppphyview_0.6.1.orig.tar.gz.delta differ = bppphyview_0.6.1.orig.tar.gz.id = @@ -0,0 +1 @@ +66b3063f24f07f60fc708eb528fc3d4436e49910 View it on GitLab: https://salsa.debian.org/med-team/bppphyview/commit/f1840e347a5103da0f541bf0bbad3f8af15ff273 -- View it on GitLab: https://salsa.debian.org/med-team/bppphyview/commit/f1840e347a5103da0f541bf0bbad3f8af15ff273 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/maffilter][pristine-tar] pristine-tar data for maffilter_1.3.1+dfsg.orig.tar.xz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / maffilter Commits: e379e7de by Julien Y. Dutheil at 2018-08-22T09:39:07Z pristine-tar data for maffilter_1.3.1+dfsg.orig.tar.xz - - - - - 2 changed files: - + maffilter_1.3.1+dfsg.orig.tar.xz.delta - + maffilter_1.3.1+dfsg.orig.tar.xz.id Changes: = maffilter_1.3.1+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/maffilter_1.3.1+dfsg.orig.tar.xz.delta differ = maffilter_1.3.1+dfsg.orig.tar.xz.id = --- /dev/null +++ b/maffilter_1.3.1+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +3c843be6d7820d5e8d5aab42fbb4057d5c24be46 View it on GitLab: https://salsa.debian.org/med-team/maffilter/commit/e379e7ded83cde55a2a9c32f8d26d4c89931f607 -- View it on GitLab: https://salsa.debian.org/med-team/maffilter/commit/e379e7ded83cde55a2a9c32f8d26d4c89931f607 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/maffilter] Pushed new tag upstream/1.3.1+dfsg
Julien Y. Dutheil pushed new tag upstream/1.3.1+dfsg at Debian Med / maffilter -- View it on GitLab: https://salsa.debian.org/med-team/maffilter/tree/upstream/1.3.1+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/maffilter][upstream] New upstream version 1.3.1+dfsg
Julien Y. Dutheil pushed to branch upstream at Debian Med / maffilter Commits: 42965fb6 by Julien Y. Dutheil at 2018-08-22T09:37:23Z New upstream version 1.3.1+dfsg - - - - - 30 changed files: - CMakeLists.txt - MafFilter/MafFilter.cpp - buildBin.sh - doc/CMakeLists.txt - doc/maffilter.texi - + docs/Manual/AlnFilter.html - + docs/Manual/AlnFilter2.html - + docs/Manual/AlnScore.html - + docs/Manual/Analyzing.html - + docs/Manual/BlockCounts.html - + docs/Manual/BlockLength.html - + docs/Manual/BlockSize.html - + docs/Manual/Cleaning.html - + docs/Manual/Concatenate.html - + docs/Manual/CountClusters.html - + docs/Manual/Description.html - + docs/Manual/Descriptive.html - + docs/Manual/DistanceBasedPhylogeny.html - + docs/Manual/DistanceEstimation.html - + docs/Manual/DiversityStatistics.html - + docs/Manual/DropSpecies.html - + docs/Manual/EntropyFilter.html - + docs/Manual/Exporting.html - + docs/Manual/ExtractFeature.html - + docs/Manual/Extracting.html - + docs/Manual/FeatureFilter.html - + docs/Manual/Filters.html - + docs/Manual/FourSpeciesSitePatternCounts.html - + docs/Manual/General.html - + docs/Manual/Introduction.html The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/maffilter/commit/42965fb6c194389d92407c58b15b267660e7d987 -- View it on GitLab: https://salsa.debian.org/med-team/maffilter/commit/42965fb6c194389d92407c58b15b267660e7d987 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl-omics][pristine-tar] pristine-tar data for libbpp-phyl-omics_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-phyl-omics Commits: e8ba0f67 by Julien Y. Dutheil at 2018-08-20T07:06:33Z pristine-tar data for libbpp-phyl-omics_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-phyl-omics_2.4.1.orig.tar.gz.delta - + libbpp-phyl-omics_2.4.1.orig.tar.gz.id Changes: = libbpp-phyl-omics_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-phyl-omics_2.4.1.orig.tar.gz.delta differ = libbpp-phyl-omics_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-phyl-omics_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +fdb8daaa5f1649dfa62636873ff87960e4fc4b2f View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/e8ba0f675ca0ed02b714777f657dde946a340751 -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/e8ba0f675ca0ed02b714777f657dde946a340751 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite][upstream] New upstream version 2.4.1
Julien Y. Dutheil pushed to branch upstream at Debian Med / bppsuite
Commits:
5524c887 by Julien Y. Dutheil at 2018-08-22T07:18:03Z
New upstream version 2.4.1
- - - - -
4 changed files:
- CMakeLists.txt
- README.md
- bppsuite.spec
- doc/bppsuite.texi
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ IF(NOT NO_DEP_CHECK)
ENDIF(NOT NO_DEP_CHECK)
IF(NO_DEP_CHECK)
- MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+ MESSAGE(STATUS "Dependencies checking disabled. Only distribution can be
built.")
ELSE(NO_DEP_CHECK)
@@ -34,7 +34,7 @@ IF(NOT BUILD_STATIC)
FORCE)
ENDIF()
IF(BUILD_STATIC)
- MESSAGE("-- Static linkage requested.")
+ MESSAGE(STATUS "Static linkage requested.")
SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
ENDIF()
@@ -88,10 +88,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppsuite")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
README.md
=
--- a/README.md
+++ b/README.md
@@ -78,5 +78,8 @@ Many examples are available in the subdirectory of
Examples.
### Documentation
-Documentation can be found at
https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
+
+Documentation can be found in one page at: http://bioweb.me/bppsuite-doc
+
+Or on github: https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or
html.
\ No newline at end of file
=
bppsuite.spec
=
--- a/bppsuite.spec
+++ b/bppsuite.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP
Name: bppsuite
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -88,6 +88,7 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/*.1*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 2.4.1-1
* Mon Mar 12 2018 Julien Dutheil 2.4.0-1
* Tue Jun 06 2017 Julien Dutheil 2.3.1-1
* Wed May 10 2017 Julien Dutheil 2.3.0-1
=
doc/bppsuite.texi
=
--- a/doc/bppsuite.texi
+++ b/doc/bppsuite.texi
@@ -1667,8 +1667,34 @@ Concerning the optimization procedure, this choice may
entail the non-
identifiability of several parameters (here the probabilities in model
3), so the user should be careful about this.
+
+When the submodel is aliased behind a model name, the paths should be
+defined as combinations of the model that is mixed. For example,
+YNGP_M2 is made of 3 YN98 models, depending of three @var{omega}
+values: <1, =1, >1. If we want a site to switch between <1 and >1
+omega values between two sets of branches:
+
+@cartouche
+@example
+nonhomogeneous = general
+nonhomogeneous.number_of_models = 2
+
+model1=YNGP_M2(frequencies=F1X4)
+model2=YNGP_M2(frequencies=F1X4)
+
+model1.nodes_id=0:1
+model2.nodes_id=2:3
+
+site.number_of_paths=3
+site.path1=model1[YN98.omega_1] & model2[YN98.omega_3]
+site.path2=model1[YN98.omega_2] & model2[YN98.omega_2]
+site.path3=model1[YN98.omega_3] & model2[YN98.omega_1]
+
+@end example
+@end cartouche
+
Another example in the case of mixtures of mixed models, where the
-submodels are defined by their names;
+submodels are defined by their names:
@cartouche
@example
@@ -1730,6 +1756,17 @@ For nucleotides only, set the G content equal to the C
content.
Full parametrization. Contains N free parameters, where N is equal to the size
of the alphabet - 1. For codon models, N is the size of the alphabet - 1 - the
number of stop codons, whose frequencies are set to 0.
For nucleotide sequences, theta is the GC content, theta1 is the proportion of
A over A+T, and theta2 is the proportion of G over G+C.
+@item Empirical(file=@{path@} [,col=@{int@}])
+Read frequencies from a file. Each frequencies is set as plain column
+in the file. If several columns are in the file, the number of the
+column can be given with @{col@} argument (default: 1).
+
+@item Empirical+F(name=@{chars@}, file=@{path@}, [theta=@{real]0,1[@},
theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"])
+Build a protein substitution model from a file in PAML format, and use
+free equilibrium frequencies. 'name'
[med-svn] [Git][med-team/bppsuite] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / bppsuite -- View it on GitLab: https://salsa.debian.org/med-team/bppsuite/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite][pristine-tar] pristine-tar data for bppsuite_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / bppsuite Commits: 5b92ad13 by Julien Y. Dutheil at 2018-08-22T07:18:04Z pristine-tar data for bppsuite_2.4.1.orig.tar.gz - - - - - 2 changed files: - + bppsuite_2.4.1.orig.tar.gz.delta - + bppsuite_2.4.1.orig.tar.gz.id Changes: = bppsuite_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/bppsuite_2.4.1.orig.tar.gz.delta differ = bppsuite_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/bppsuite_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +802adbe45c1ffaec35d880e965525e5d8629ce2f View it on GitLab: https://salsa.debian.org/med-team/bppsuite/commit/5b92ad131c1485ca10ad5917a27ad29ae0ff83f6 -- View it on GitLab: https://salsa.debian.org/med-team/bppsuite/commit/5b92ad131c1485ca10ad5917a27ad29ae0ff83f6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl-omics][upstream] New upstream version 2.4.1
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-phyl-omics
Commits:
60ca9b85 by Julien Y. Dutheil at 2018-08-20T07:06:32Z
New upstream version 2.4.1
- - - - -
3 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-phyl-omics.spec
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -96,10 +96,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-phyl-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogen-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
Doxyfile
=
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-phyl-omics
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=
bpp-phyl-omics.spec
=
--- a/bpp-phyl-omics.spec
+++ b/bpp-phyl-omics.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-phyl-omics
Name: bpp-phyl-omics
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -94,6 +94,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Wed Aug 13 2018 Julien Dutheil 2.4.1-1
+- Compatibility update gcc8
* Mon Mar 12 2018 Julien Dutheil 2.4.0-1
- Increased interface number
- Removed dynamic exceptions specifications.
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/60ca9b857812460e670cbaa37a9d8607c4d112b5
--
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/60ca9b857812460e670cbaa37a9d8607c4d112b5
You're receiving this email because of your account on salsa.debian.org.
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[med-svn] [Git][med-team/libbpp-phyl-omics] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-phyl-omics -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][upstream] New upstream version 2.4.1
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-seq-omics
Commits:
f12fcff8 by Julien Y. Dutheil at 2018-08-20T04:40:31Z
New upstream version 2.4.1
- - - - -
7 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-seq-omics.spec
- src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
- src/Bpp/Seq/Io/Maf/MafSequence.cpp
- src/Bpp/Seq/Io/Maf/MafSequence.h
- src/Bpp/Seq/Io/Maf/MafStatistics.cpp
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
Doxyfile
=
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-seq-omics
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=
bpp-seq-omics.spec
=
--- a/bpp-seq-omics.spec
+++ b/bpp-seq-omics.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-seq-omics
Name: bpp-seq-omics
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -84,6 +84,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 2.4.1-1
+- Compatibility update gcc8
* Fri Mar 03 2018 Julien Dutheil 2.4.0-1
- Increased interface number
- Removed dynamic exceptions declarations.
=
src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
=
--- a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
@@ -60,6 +60,8 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_()
int unk = AlphabetTools::DNA_ALPHABET.getUnknownCharacterCode();
size_t nr;
size_t nc = static_cast(block->getNumberOfSites());
+ if (nc < windowSize_)
+throw Exception("AlignmentFilterMafIterator::analyseCurrentBlock_.
Block is smaller than window size: " + TextTools::toString(nc));
vector< vector > aln;
if (missingAsGap_) {
@@ -94,8 +96,6 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_()
window_.clear();
//Init window:
size_t i;
- if (nc < windowSize_)
-throw Exception("AlignmentFilterMafIterator::analyseCurrentBlock_.
Block is smaller than window size: " + TextTools::toString(nc));
for (i = 0; i < windowSize_; ++i) {
for (size_t j = 0; j < nr; ++j) {
col[j] = aln[j][i];
@@ -284,6 +284,8 @@ MafBlock*
AlignmentFilter2MafIterator::analyseCurrentBlock_()
int unk = AlphabetTools::DNA_ALPHABET.getUnknownCharacterCode();
size_t nr;
size_t nc = static_cast(block->getNumberOfSites());
+ if (nc < windowSize_)
+throw Exception("AlignmentFilter2MafIterator::analyseCurrentBlock_.
Block is smaller than window size: " + TextTools::toString(nc));
vector< vector > aln;
if (missingAsGap_) {
=
src/Bpp/Seq/Io/Maf/MafSequence.cpp
=
--- a/src/Bpp/Seq/Io/Maf/MafSequence.cpp
+++ b/src/Bpp/Seq/Io/Maf/MafSequence.cpp
@@ -50,7 +50,7 @@ MafSequence* MafSequence::subSequence(size_t startAt, size_t
length) const
string subseq = toString().substr(startAt, length);
size_t begin = begin_;
if (hasCoordinates_) {
-for (unsigned int i = 0; i < startAt; ++i) {
+for (size_t i = 0; i < startAt; ++i) {
if (! getAlphabet()->isGap(operator[](i))) begin++;
}
}
=
src/Bpp/Seq/Io/Maf/MafSequence.h
=
--- a/src/Bpp/Seq/Io/Maf/MafSequence.h
+++ b/src/Bpp/Seq/Io/Maf/MafSequence.h
@@ -64,12 +64,12 @@ class MafSequence:
{
private:
bool hasCoordinates_;
-size_t begin_;
+size_t begin_;
std::string species_;
std::string chromosome_;
char strand
[med-svn] [Git][med-team/libbpp-seq-omics] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-seq-omics -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-qt] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-qt -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][pristine-tar] pristine-tar data for libbpp-seq-omics_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-seq-omics Commits: b5a92f36 by Julien Y. Dutheil at 2018-08-20T04:40:32Z pristine-tar data for libbpp-seq-omics_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-seq-omics_2.4.1.orig.tar.gz.delta - + libbpp-seq-omics_2.4.1.orig.tar.gz.id Changes: = libbpp-seq-omics_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-seq-omics_2.4.1.orig.tar.gz.delta differ = libbpp-seq-omics_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-seq-omics_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +51ad996902842fb9ce921fc81dd2f36aad8b8657 View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/b5a92f36f23f36bf8b7d8f9b091f344a3f058adc -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/b5a92f36f23f36bf8b7d8f9b091f344a3f058adc You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-qt][pristine-tar] pristine-tar data for libbpp-qt_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-qt Commits: 50f5453d by Julien Y. Dutheil at 2018-08-22T06:41:21Z pristine-tar data for libbpp-qt_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-qt_2.4.1.orig.tar.gz.delta - + libbpp-qt_2.4.1.orig.tar.gz.id Changes: = libbpp-qt_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-qt_2.4.1.orig.tar.gz.delta differ = libbpp-qt_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-qt_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +3d3a5d00d7d95e7925e3640640682abbdc066aa2 View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/commit/50f5453d6f745987252d3245794f7baf80dbbe9b -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/commit/50f5453d6f745987252d3245794f7baf80dbbe9b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-qt][upstream] New upstream version 2.4.1
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-qt
Commits:
9a0fa62b by Julien Y. Dutheil at 2018-08-22T06:41:21Z
New upstream version 2.4.1
- - - - -
3 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-qt.spec
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -102,10 +102,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-qt")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Qt graphic library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
Doxyfile
=
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-qt
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=
bpp-qt.spec
=
--- a/bpp-qt.spec
+++ b/bpp-qt.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-qt
Name: bpp-qt
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -174,6 +174,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 2.4.1-1
+- Compatibility update gcc8
* Mon Feb 26 2018 Julien Dutheil 2.4.0-1
- Removed dynamic exception specifications
- Port to Qt5
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-qt/commit/9a0fa62ba8893cba4feaa8f7411c098b615abf93
--
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-qt/commit/9a0fa62ba8893cba4feaa8f7411c098b615abf93
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[med-svn] [Git][med-team/libbpp-raa] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-raa -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-raa][upstream] New upstream version 2.4.1
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-raa
Commits:
7506d6dd by Julien Y. Dutheil at 2018-08-22T07:04:21Z
New upstream version 2.4.1
- - - - -
5 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-raa.spec
- − header.html
- src/Bpp/Raa/RAA.cpp
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -104,10 +104,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-raa")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Remote Acnuc Access library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
Doxyfile
=
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-raa
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=
bpp-raa.spec
=
--- a/bpp-raa.spec
+++ b/bpp-raa.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-raa
Name: bpp-raa
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -90,8 +90,10 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Mon Aug 13 2018 Julien Dutheil 2.4.1-1
+- Compatibility gcc8.
* Mon Feb 26 2018 Julien Dutheil 2.4.0-1
-- Increased interface number
+- Increased interface number.
- Removed dynamic exceptions specifications.
* Tue Jun 06 2017 Julien Dutheil 2.3.1-1
- Increased interface number
=
header.html deleted
=
--- a/header.html
+++ /dev/null
@@ -1,27 +0,0 @@
-http://www.w3.org/1999/xhtml"; xml:lang="en" lang="en">
-
-
-
-
-
-
-
-
-
-
- http://kimura.univ-montp2.fr/BioPP/"; accesskey="1"
target="_top">Bio++ Class documentation
-
-
-
-
-http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Utils/html/index.html";
target="_top">Utils
-http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/NumCalc/html/index.html";
target="_top">NumCalc
-http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Seq/html/index.html";
target="_top">SeqLib
-http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Phyl/html/index.html";
target="_top">PhylLib
-http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Pop/html/index.html";
target="_top">PopGenLib
-http://kimura.univ-montp2.fr/BioPP/Documents/ClassDocumentation/Raa/html/index.html";
target="_top">Raa
-
-
-
-
-
=
src/Bpp/Raa/RAA.cpp
=
--- a/src/Bpp/Raa/RAA.cpp
+++ b/src/Bpp/Raa/RAA.cpp
@@ -262,7 +262,7 @@ Sequence* RAA::translateCDS(int seqrank)
{
Sprot = new BasicSequence(*sname, *pstring,
&AlphabetTools::PROTEIN_ALPHABET );
}
- catch (BadCharException e)
+ catch (BadCharException& e)
{
delete sname;
delete pstring;
@@ -283,14 +283,7 @@ Sequence* RAA::translateCDS(const string& name)
if (rank == 0)
return NULL;
Sequence* Sprot;
- try
- {
-Sprot = translateCDS(rank);
- }
- catch (BadCharException e)
- {
-throw e;
- }
+ Sprot = translateCDS(rank);
return Sprot;
}
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6
--
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-raa/commit/7506d6dd0e2d1ba1e3e922649c2aebe3ddd528e6
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[med-svn] [Git][med-team/libbpp-raa][pristine-tar] pristine-tar data for libbpp-raa_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-raa Commits: 894b1f16 by Julien Y. Dutheil at 2018-08-22T07:04:22Z pristine-tar data for libbpp-raa_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-raa_2.4.1.orig.tar.gz.delta - + libbpp-raa_2.4.1.orig.tar.gz.id Changes: = libbpp-raa_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-raa_2.4.1.orig.tar.gz.delta differ = libbpp-raa_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-raa_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +9092236b26fe4d4b18c1a93584ff3b3c3a4fe519 View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/894b1f1647864bb1658e95e33185cd182615962d -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/894b1f1647864bb1658e95e33185cd182615962d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-popgen -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][pristine-tar] pristine-tar data for libbpp-popgen_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-popgen Commits: 806bcb73 by Julien Y. Dutheil at 2018-08-20T10:34:19Z pristine-tar data for libbpp-popgen_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-popgen_2.4.1.orig.tar.gz.delta - + libbpp-popgen_2.4.1.orig.tar.gz.id Changes: = libbpp-popgen_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-popgen_2.4.1.orig.tar.gz.delta differ = libbpp-popgen_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-popgen_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +cf97d2ae7d1969d7cef8a9322297306f2a573d61 View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/806bcb7309f5cbf8fd14c73ac8b5d7bfabcda5d9 -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/806bcb7309f5cbf8fd14c73ac8b5d7bfabcda5d9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][pristine-tar] pristine-tar data for libbpp-phyl_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-phyl Commits: ed0228f4 by Julien Y. Dutheil at 2018-08-19T11:47:45Z pristine-tar data for libbpp-phyl_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-phyl_2.4.1.orig.tar.gz.delta - + libbpp-phyl_2.4.1.orig.tar.gz.id Changes: = libbpp-phyl_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-phyl_2.4.1.orig.tar.gz.delta differ = libbpp-phyl_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-phyl_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +9f3a0f7018b0ee95793a2cba5e2839e19e581ca3 View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/ed0228f4afa4b11b082da3e75361aa5d156a1354 -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/ed0228f4afa4b11b082da3e75361aa5d156a1354 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-phyl -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq][pristine-tar] pristine-tar data for libbpp-seq_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-seq Commits: e1d5f616 by Julien Y. Dutheil at 2018-08-19T09:45:37Z pristine-tar data for libbpp-seq_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-seq_2.4.1.orig.tar.gz.delta - + libbpp-seq_2.4.1.orig.tar.gz.id Changes: = libbpp-seq_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-seq_2.4.1.orig.tar.gz.delta differ = libbpp-seq_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-seq_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +1408755fbe9b5bc6468fc1a1f89b138ff2d5ecdb View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/e1d5f616ce757e40815719e0cee0f823cef4049c -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/e1d5f616ce757e40815719e0cee0f823cef4049c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-seq -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core] Pushed new tag upstream/2.4.1
Julien Y. Dutheil pushed new tag upstream/2.4.1 at Debian Med / libbpp-core -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/tree/upstream/2.4.1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core][pristine-tar] pristine-tar data for libbpp-core_2.4.1.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-core Commits: ddd98613 by Julien Y. Dutheil at 2018-08-18T11:31:47Z pristine-tar data for libbpp-core_2.4.1.orig.tar.gz - - - - - 2 changed files: - + libbpp-core_2.4.1.orig.tar.gz.delta - + libbpp-core_2.4.1.orig.tar.gz.id Changes: = libbpp-core_2.4.1.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-core_2.4.1.orig.tar.gz.delta differ = libbpp-core_2.4.1.orig.tar.gz.id = --- /dev/null +++ b/libbpp-core_2.4.1.orig.tar.gz.id @@ -0,0 +1 @@ +a0207aea46ef442c1fb63c34437d286583a4 View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/commit/ddd9861343d157bb32a086a23189d0c34ef2152b -- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/commit/ddd9861343d157bb32a086a23189d0c34ef2152b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/maffilter][master] 3 commits: New upstream version 1.3.1+dfsg
Julien Y. Dutheil pushed to branch master at Debian Med / maffilter Commits: 42965fb6 by Julien Y. Dutheil at 2018-08-22T09:37:23Z New upstream version 1.3.1+dfsg - - - - - c4c0255a by Julien Y. Dutheil at 2018-08-22T09:39:07Z Update upstream source from tag 'upstream/1.3.1+dfsg' Update to upstream version '1.3.1+dfsg' with Debian dir 0f1af31559e203329da5c68741b7e584920ff03d - - - - - 4fca7c1c by Julien Y. Dutheil at 2018-08-22T12:12:28Z Version 1.3.1. Compiles against Bio++ 2.4.1. - - - - - 30 changed files: - CMakeLists.txt - MafFilter/MafFilter.cpp - buildBin.sh - debian/changelog - debian/control - − debian/patches/fix_doc_compression.patch - debian/patches/series - doc/CMakeLists.txt - doc/maffilter.texi - + docs/Manual/AlnFilter.html - + docs/Manual/AlnFilter2.html - + docs/Manual/AlnScore.html - + docs/Manual/Analyzing.html - + docs/Manual/BlockCounts.html - + docs/Manual/BlockLength.html - + docs/Manual/BlockSize.html - + docs/Manual/Cleaning.html - + docs/Manual/Concatenate.html - + docs/Manual/CountClusters.html - + docs/Manual/Description.html - + docs/Manual/Descriptive.html - + docs/Manual/DistanceBasedPhylogeny.html - + docs/Manual/DistanceEstimation.html - + docs/Manual/DiversityStatistics.html - + docs/Manual/DropSpecies.html - + docs/Manual/EntropyFilter.html - + docs/Manual/Exporting.html - + docs/Manual/ExtractFeature.html - + docs/Manual/Extracting.html - + docs/Manual/FeatureFilter.html The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/maffilter/compare/daaccf9cb471fafd2bcda234cd1ceaca81a1e2de...4fca7c1ce5d99e29c9cb452aae2217a3aa152b43 -- View it on GitLab: https://salsa.debian.org/med-team/maffilter/compare/daaccf9cb471fafd2bcda234cd1ceaca81a1e2de...4fca7c1ce5d99e29c9cb452aae2217a3aa152b43 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/physamp][master] Package now builds against Bio++ 2.4.1.
Julien Y. Dutheil pushed to branch master at Debian Med / physamp Commits: c7cdad7e by Julien Y. Dutheil at 2018-08-22T07:29:41Z Package now builds against Bio++ 2.4.1. - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +physamp (1.1.0-2) UNRELEASED; urgency=medium + + * Builds against Bio++ 2.4.1. + + -- Julien Dutheil Wed, 22 Aug 2018 09:24:42 +0200 + physamp (1.1.0-1) unstable; urgency=medium [ Steffen Moeller ] = debian/control = --- a/debian/control +++ b/debian/control @@ -7,7 +7,7 @@ Priority: optional Build-Depends: debhelper (>= 11~), cmake, texinfo, - libbpp-phyl-dev (>= 2.4.0) + libbpp-phyl-dev (>= 2.4.1) Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/physamp Vcs-Git: https://salsa.debian.org/med-team/physamp.git View it on GitLab: https://salsa.debian.org/med-team/physamp/commit/c7cdad7e2f78b75448dbc900f90499f884b96c73 -- View it on GitLab: https://salsa.debian.org/med-team/physamp/commit/c7cdad7e2f78b75448dbc900f90499f884b96c73 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil pushed to branch master at Debian Med / bppsuite
Commits:
5524c887 by Julien Y. Dutheil at 2018-08-22T07:18:03Z
New upstream version 2.4.1
- - - - -
eb8c5bde by Julien Y. Dutheil at 2018-08-22T07:18:04Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir 2b388ba14be5ef280973e4479a489bca129bfcd9
- - - - -
e34c1cda by Julien Y. Dutheil at 2018-08-22T07:23:21Z
Version 2.4.1.
Compatibility update with gcc 8.
- - - - -
5 changed files:
- CMakeLists.txt
- README.md
- bppsuite.spec
- debian/changelog
- doc/bppsuite.texi
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ IF(NOT NO_DEP_CHECK)
ENDIF(NOT NO_DEP_CHECK)
IF(NO_DEP_CHECK)
- MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+ MESSAGE(STATUS "Dependencies checking disabled. Only distribution can be
built.")
ELSE(NO_DEP_CHECK)
@@ -34,7 +34,7 @@ IF(NOT BUILD_STATIC)
FORCE)
ENDIF()
IF(BUILD_STATIC)
- MESSAGE("-- Static linkage requested.")
+ MESSAGE(STATUS "Static linkage requested.")
SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
ENDIF()
@@ -88,10 +88,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppsuite")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
README.md
=
--- a/README.md
+++ b/README.md
@@ -78,5 +78,8 @@ Many examples are available in the subdirectory of
Examples.
### Documentation
-Documentation can be found at
https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
+
+Documentation can be found in one page at: http://bioweb.me/bppsuite-doc
+
+Or on github: https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or
html.
\ No newline at end of file
=
bppsuite.spec
=
--- a/bppsuite.spec
+++ b/bppsuite.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP
Name: bppsuite
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -88,6 +88,7 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/*.1*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 2.4.1-1
* Mon Mar 12 2018 Julien Dutheil 2.4.0-1
* Tue Jun 06 2017 Julien Dutheil 2.3.1-1
* Wed May 10 2017 Julien Dutheil 2.3.0-1
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bppsuite (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+
+ -- Julien Dutheil Wed, 22 Aug 2018 09:18:13
+0200
+
bppsuite (2.4.0-1) unstable; urgency=medium
[ Julien Dutheil ]
=
doc/bppsuite.texi
=
--- a/doc/bppsuite.texi
+++ b/doc/bppsuite.texi
@@ -1667,8 +1667,34 @@ Concerning the optimization procedure, this choice may
entail the non-
identifiability of several parameters (here the probabilities in model
3), so the user should be careful about this.
+
+When the submodel is aliased behind a model name, the paths should be
+defined as combinations of the model that is mixed. For example,
+YNGP_M2 is made of 3 YN98 models, depending of three @var{omega}
+values: <1, =1, >1. If we want a site to switch between <1 and >1
+omega values between two sets of branches:
+
+@cartouche
+@example
+nonhomogeneous = general
+nonhomogeneous.number_of_models = 2
+
+model1=YNGP_M2(frequencies=F1X4)
+model2=YNGP_M2(frequencies=F1X4)
+
+model1.nodes_id=0:1
+model2.nodes_id=2:3
+
+site.number_of_paths=3
+site.path1=model1[YN98.omega_1] & model2[YN98.omega_3]
+site.path2=model1[YN98.omega_2] & model2[YN98.omega_2]
+site.path3=model1[YN98.omega_3] & model2[YN98.omega_1]
+
+@end example
+@end cartouche
+
Another example in the case of mixtures of mixed models, where the
-submodels are defined by their names;
+submodels are defined by their names:
@cartouche
@example
@@ -1730,6 +1756,17 @@ For nucleotides only, set the G content equal to the C
content.
Full parametrization. Contains N free parameters, where N is equal to the size
of the alphabet - 1. For codon models, N is the size of the alphabet - 1 - t
[med-svn] [Git][med-team/libbpp-seq-omics][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq-omics
Commits:
f12fcff8 by Julien Y. Dutheil at 2018-08-20T04:40:31Z
New upstream version 2.4.1
- - - - -
50b2d0b4 by Julien Y. Dutheil at 2018-08-20T04:40:32Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir 61002ea6222bca9396a92fa710e29906f54e11a1
- - - - -
1950286d by Julien Y. Dutheil at 2018-08-20T07:04:55Z
New version 2.4.1.
Ref: #897785
- - - - -
10 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-seq-omics.spec
- debian/changelog
- debian/control
- debian/libbpp-seq-omics3.symbols
- src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
- src/Bpp/Seq/Io/Maf/MafSequence.cpp
- src/Bpp/Seq/Io/Maf/MafSequence.h
- src/Bpp/Seq/Io/Maf/MafStatistics.cpp
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
Doxyfile
=
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-seq-omics
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=
bpp-seq-omics.spec
=
--- a/bpp-seq-omics.spec
+++ b/bpp-seq-omics.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-seq-omics
Name: bpp-seq-omics
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -84,6 +84,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Wed Aug 15 2018 Julien Dutheil 2.4.1-1
+- Compatibility update gcc8
* Fri Mar 03 2018 Julien Dutheil 2.4.0-1
- Increased interface number
- Removed dynamic exceptions declarations.
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-seq-omics (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version.
+ * Addresses: #897785
+
+ -- Julien Dutheil Mon, 20 Aug 2018 08:48:12
+0200
+
libbpp-seq-omics (2.4.0-2) unstable; urgency=medium
[ Julien Dutheil ]
=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs (>= 0.82),
- libbpp-seq-dev (>= 2.4.0)
+ libbpp-seq-dev (>= 2.4.1)
Standards-Version: 4.1.3
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq-omics
Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq-omics.git
@@ -18,7 +18,7 @@ Architecture: any
Section: libdevel
Depends: libbpp-seq-omics3 (= ${binary:Version}),
${misc:Depends},
- libbpp-seq-dev (>= 2.4.0)
+ libbpp-seq-dev (>= 2.4.1)
Description: Bio++ Sequence library: genomics components (development files)
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
=
debian/libbpp-seq-omics3.symbols
=
The diff for this file was not included because it is too large.
=
src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
=
--- a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
+++ b/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
@@ -60,6 +60,8 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_()
int unk = AlphabetTools::DNA_ALPHABET.getUnknownCharacterCode();
size_t nr;
size_t nc = static_cast(block->getNumberOfSites());
+ if (nc < windowSize_)
+throw Exception("AlignmentFilterMafIterator::analyseCurrentBlock_.
Block is smaller than window size: " + TextTools::toString(nc));
vector< vector > aln;
if (missingAsGap_) {
[med-svn] [Git][med-team/libbpp-phyl-omics][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl-omics
Commits:
60ca9b85 by Julien Y. Dutheil at 2018-08-20T07:06:32Z
New upstream version 2.4.1
- - - - -
cede0eb4 by Julien Y. Dutheil at 2018-08-20T07:06:33Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir f73261816a1edfb2312254aee60813560f513a66
- - - - -
da760224 by Julien Y. Dutheil at 2018-08-22T06:34:53Z
Version 2.4.1.
Ref: #897781.
- - - - -
6 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-phyl-omics.spec
- debian/changelog
- debian/control
- debian/libbpp-phyl-omics3.symbols
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -96,10 +96,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-phyl-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Phylogen-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=
Doxyfile
=
--- a/Doxyfile
+++ b/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-phyl-omics
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = 2.4.0
+PROJECT_NUMBER = 2.4.1
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
=
bpp-phyl-omics.spec
=
--- a/bpp-phyl-omics.spec
+++ b/bpp-phyl-omics.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP/bpp-phyl-omics
Name: bpp-phyl-omics
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -94,6 +94,8 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/include/*
%changelog
+* Wed Aug 13 2018 Julien Dutheil 2.4.1-1
+- Compatibility update gcc8
* Mon Mar 12 2018 Julien Dutheil 2.4.0-1
- Increased interface number
- Removed dynamic exceptions specifications.
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-phyl-omics (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * Addresses: #897781
+
+ -- Julien Dutheil Mon, 20 Aug 2018 09:06:47
+0200
+
libbpp-phyl-omics (2.4.0-2) unstable; urgency=medium
[ Julien Dutheil ]
=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -7,8 +7,8 @@ Priority: optional
Build-Depends: debhelper (>= 11~),
cmake,
d-shlibs (>= 0.82),
- libbpp-phyl-dev (>= 2.4.0),
- libbpp-seq-omics-dev (>= 2.4.0)
+ libbpp-phyl-dev (>= 2.4.1),
+ libbpp-seq-omics-dev (>= 2.4.1)
Standards-Version: 4.1.3
Vcs-Browser: https://salsa.debian.org/med-team/libbpp-phyl-omics
Vcs-Git: https://salsa.debian.org/med-team/libbpp-phyl-omics.git
@@ -19,8 +19,8 @@ Architecture: any
Section: libdevel
Depends: libbpp-phyl-omics3 (= ${binary:Version}),
${misc:Depends},
- libbpp-phyl-dev (>= 2.4.0),
- libbpp-seq-omics-dev (>= 2.4.0)
+ libbpp-phyl-dev (>= 2.4.1),
+ libbpp-seq-omics-dev (>= 2.4.1)
Description: Bio++ Phylogenetics library: genomics components (development
files)
Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics.
=
debian/libbpp-phyl-omics3.symbols
=
The diff for this file was not included because it is too large.
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl-omics/compare/ee827f8f83abd40ae7bc72e3f27ad645fa2acf98...da760224109aafd3a4453c6b8a415e3bcb6cfb1a
--
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl-omics/compare/ee827f8f83abd40ae7bc72e3f27ad645fa2acf98...da760224109aafd3a4453c6b8a415e3bcb6cfb1a
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[med-svn] [Git][med-team/libbpp-phyl][master] Improved failing test.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl
Commits:
e988691e by Julien Y. Dutheil at 2018-05-01T15:53:06+02:00
Improved failing test.
Merged with reduce time patch.
- - - - -
3 changed files:
- debian/patches/increase_test_tolerance.patch
- − debian/patches/reduce_test_time.patch
- debian/patches/series
Changes:
=
debian/patches/increase_test_tolerance.patch
=
--- a/debian/patches/increase_test_tolerance.patch
+++ b/debian/patches/increase_test_tolerance.patch
@@ -4,7 +4,7 @@ Description: By increasing tolerance of test boundaries the
package should
build on all architectures
diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp
-index b4cd485..b8358d1 100644
+index b4cd485..c38a277 100644
--- a/test/test_likelihood_nh.cpp
+++ b/test/test_likelihood_nh.cpp
@@ -59,14 +59,14 @@ void fitModelNH(SubstitutionModelSet* model,
DiscreteDistribution* rdist, const
@@ -25,3 +25,34 @@ index b4cd485..b8358d1 100644
throw Exception("Incorrect final value.");
}
+@@ -89,14 +89,14 @@ int main() {
+ DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
+
+ size_t nsites = 1000;
+- unsigned int nrep = 20;
++ unsigned int nrep = 5;
+ size_t nmodels = modelSet->getNumberOfModels();
+ vector thetas(nmodels);
+ vector thetasEst1(nmodels);
+ vector thetasEst2(nmodels);
+
+ for (size_t i = 0; i < nmodels; ++i) {
+-double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.99) +
0.005;
++double theta = RandomTools::giveRandomNumberBetweenZeroAndEntry(0.9) +
0.05;
+ cout << "Theta" << i << " set to " << theta << endl;
+ modelSet->setParameterValue("T92.theta_" + TextTools::toString(i + 1),
theta);
+ thetas[i] = theta;
+@@ -119,11 +119,11 @@ int main() {
+ tl2.initialize();
+
+ unsigned int c1 = OptimizationTools::optimizeNumericalParameters2(
+-&tl, tl.getParameters(), 0,
++&tl, tl.getSubstitutionModelParameters(), 0,
+ 0.0001, 1, messenger, profiler, false, false, 1,
OptimizationTools::OPTIMIZATION_NEWTON);
+
+ unsigned int c2 = OptimizationTools::optimizeNumericalParameters2(
+-&tl2, tl2.getParameters(), 0,
++&tl2, tl2.getSubstitutionModelParameters(), 0,
+ 0.0001, 1, messenger, profiler, false, false, 1,
OptimizationTools::OPTIMIZATION_NEWTON);
+
+ cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " <<
tl2.getValue() << endl;
=
debian/patches/reduce_test_time.patch deleted
=
--- a/debian/patches/reduce_test_time.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Julien Y. Dutheil
-Last-Update: 2018-02-11 21:18:30 +0100
-Description: Reduce number of iterations to reduce test time
-
-diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp
-index b4cd485..97431aa 100644
a/test/test_likelihood_nh.cpp
-+++ b/test/test_likelihood_nh.cpp
-@@ -89,7 +89,7 @@ int main() {
- DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
-
- size_t nsites = 1000;
-- unsigned int nrep = 20;
-+ unsigned int nrep = 3;
- size_t nmodels = modelSet->getNumberOfModels();
- vector thetas(nmodels);
- vector thetasEst1(nmodels);
=
debian/patches/series
=
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
unforce-cxxflags.patch
-reduce_test_time.patch
increase_test_tolerance.patch
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/e988691e2c0107969c54b6d74dd4cedd7c8f53f3
---
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/e988691e2c0107969c54b6d74dd4cedd7c8f53f3
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[med-svn] [Git][med-team/libbpp-phyl][master] Fixing failing test on some archs.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl
Commits:
2b47de61 by Julien Y. Dutheil at 2018-04-30T17:48:26+02:00
Fixing failing test on some archs.
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/increase_test_tolerance.patch
- debian/patches/series
Changes:
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbpp-phyl (2.4.0-2) UNRELEASED; urgency=medium
+
+ * Increases likelihood test tolerance.
+
+ -- Julien Dutheil Mon, 30 Apr 2018 16:58:46
+0200
+
libbpp-phyl (2.4.0-1) unstable; urgency=medium
[ Julien Dutheil ]
=
debian/patches/increase_test_tolerance.patch
=
--- /dev/null
+++ b/debian/patches/increase_test_tolerance.patch
@@ -0,0 +1,22 @@
+diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp
+index b4cd485..b8358d1 100644
+--- a/test/test_likelihood_nh.cpp
b/test/test_likelihood_nh.cpp
+@@ -59,14 +59,14 @@ void fitModelNH(SubstitutionModelSet* model,
DiscreteDistribution* rdist, const
+ tl.initialize();
+ cout << setprecision(20) << tl.getValue() << endl;
+ ApplicationTools::displayResult("* initial likelihood", tl.getValue());
+- if (abs(tl.getValue() - initialValue) > 0.0001)
++ if (abs(tl.getValue() - initialValue) > 0.01)
+ throw Exception("Incorrect initial value.");
+ OptimizationTools::optimizeTreeScale(&tl);
+ ApplicationTools::displayResult("* likelihood after tree scale",
tl.getValue());
+- OptimizationTools::optimizeNumericalParameters2(&tl, tl.getParameters(), 0,
0.01, 1, 0, 0);
++ OptimizationTools::optimizeNumericalParameters2(&tl, tl.getParameters(), 0,
0.0001, 1, 0, 0);
+ cout << setprecision(20) << tl.getValue() << endl;
+ ApplicationTools::displayResult("* likelihood after full optimization",
tl.getValue());
+- if (abs(tl.getValue() - finalValue) > 0.0001)
++ if (abs(tl.getValue() - finalValue) > 0.01)
+ throw Exception("Incorrect final value.");
+ }
+
=
debian/patches/series
=
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
unforce-cxxflags.patch
reduce_test_time.patch
+increase_test_tolerance.patch
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/2b47de610eda7c3e4c3bcf4a7ee0f6f60993c3b7
---
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/2b47de610eda7c3e4c3bcf4a7ee0f6f60993c3b7
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[med-svn] [Git][med-team/maffilter] Pushed new tag upstream/1.3.0+dfsg
Julien Y. Dutheil pushed new tag upstream/1.3.0+dfsg at Debian Med / maffilter --- View it on GitLab: https://salsa.debian.org/med-team/maffilter/tree/upstream/1.3.0+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/maffilter][pristine-tar] pristine-tar data for maffilter_1.3.0+dfsg.orig.tar.xz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / maffilter Commits: a1b28742 by Julien Y. Dutheil at 2018-04-30T11:39:19+02:00 pristine-tar data for maffilter_1.3.0+dfsg.orig.tar.xz - - - - - 2 changed files: - + maffilter_1.3.0+dfsg.orig.tar.xz.delta - + maffilter_1.3.0+dfsg.orig.tar.xz.id Changes: = maffilter_1.3.0+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/maffilter_1.3.0+dfsg.orig.tar.xz.delta differ = maffilter_1.3.0+dfsg.orig.tar.xz.id = --- /dev/null +++ b/maffilter_1.3.0+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +1a41bf27cb1ef03d877704b2cb8d01af552f5849 View it on GitLab: https://salsa.debian.org/med-team/maffilter/commit/a1b2874220e0b2463526cb9478856835c4324ce8 --- View it on GitLab: https://salsa.debian.org/med-team/maffilter/commit/a1b2874220e0b2463526cb9478856835c4324ce8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppphyview][pristine-tar] pristine-tar data for bppphyview_0.6.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / bppphyview Commits: c67e4ee5 by Julien Y. Dutheil at 2018-04-18T20:58:19+02:00 pristine-tar data for bppphyview_0.6.0.orig.tar.gz - - - - - 2 changed files: - + bppphyview_0.6.0.orig.tar.gz.delta - + bppphyview_0.6.0.orig.tar.gz.id Changes: = bppphyview_0.6.0.orig.tar.gz.delta = Binary files /dev/null and b/bppphyview_0.6.0.orig.tar.gz.delta differ = bppphyview_0.6.0.orig.tar.gz.id = --- /dev/null +++ b/bppphyview_0.6.0.orig.tar.gz.id @@ -0,0 +1 @@ +0a8714b3a4f23ef36bbab743ada29a9e72ce61ad View it on GitLab: https://salsa.debian.org/med-team/bppphyview/commit/c67e4ee5885519dd50be798794d1ec928d45ef57 --- View it on GitLab: https://salsa.debian.org/med-team/bppphyview/commit/c67e4ee5885519dd50be798794d1ec928d45ef57 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppphyview] Pushed new tag upstream/0.6.0
Julien Y. Dutheil pushed new tag upstream/0.6.0 at Debian Med / bppphyview --- View it on GitLab: https://salsa.debian.org/med-team/bppphyview/tree/upstream/0.6.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/physamp] Pushed new tag v1.1.0
Julien Y. Dutheil pushed new tag v1.1.0 at Debian Med / physamp --- View it on GitLab: https://salsa.debian.org/med-team/physamp/tree/v1.1.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/physamp] Pushed new tag v1.0.3
Julien Y. Dutheil pushed new tag v1.0.3 at Debian Med / physamp --- View it on GitLab: https://salsa.debian.org/med-team/physamp/tree/v1.0.3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/physamp] Pushed new tag v1.0.2
Julien Y. Dutheil pushed new tag v1.0.2 at Debian Med / physamp --- View it on GitLab: https://salsa.debian.org/med-team/physamp/tree/v1.0.2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/physamp][upstream] New upstream version 1.1.0
Julien Y. Dutheil pushed to branch upstream at Debian Med / physamp
Commits:
62913cc6 by Julien Y. Dutheil at 2018-04-18T16:05:29+02:00
New upstream version 1.1.0
- - - - -
7 changed files:
- CMakeLists.txt
- ChangeLog
- docs/_config.yml
- docs/physamp.texi
- physamp.spec
- physamp/AlignmentOptimizer.cpp
- physamp/PhyloSampler.cpp
Changes:
=
CMakeLists.txt
=
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -59,6 +59,7 @@ else ()
# Generate command line args (always add -c to output compressed file to
stdout)
if (${COMPRESS_PROGRAM} STREQUAL "gzip")
# -n for no timestamp in files (reproducible builds)
+# -9 for maximum compression (lintian error)
set (COMPRESS_ARGS -c9n)
else ()
set (COMPRESS_ARGS -c)
@@ -73,7 +74,7 @@ IF (CMAKE_INSTALL_PREFIX)
ENDIF (CMAKE_INSTALL_PREFIX)
include (GNUInstallDirs)
-find_package (bpp-phyl 11.0.0 REQUIRED)
+find_package (bpp-phyl 12.0.0 REQUIRED)
# Subdirectories
@@ -86,10 +87,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "physamp")
SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
-SET(CPACK_PACKAGE_VERSION "1.0.3")
+SET(CPACK_PACKAGE_VERSION "1.1.0")
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "0")
-SET(CPACK_PACKAGE_VERSION_PATCH "3")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Phylogenetic Sampler package")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
=
ChangeLog
=
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,8 @@
+14/03/18 -*- Version 1.1.0 -*-
+
+14/03/18 Julien Dutheil
+* Compatibility update Bio++ 2.4.0.
+
30/03/15 -*- Version 0.2.0 -*-
30/03/15 Julien Dutheil
=
docs/_config.yml
=
--- a/docs/_config.yml
+++ b/docs/_config.yml
@@ -1 +1,5 @@
-theme: jekyll-theme-slate
\ No newline at end of file
+theme: jekyll-theme-slate
+title: PhySamp
+description: Phylogenetic Sampling and Optimization of Sequence Alignments
+show_downloads: true
+share: true
=
docs/physamp.texi
=
--- a/docs/physamp.texi
+++ b/docs/physamp.texi
@@ -1,7 +1,7 @@
\input texinfo @c -*-texinfo-*-
@c %**start of header
@setfilename physamp.info
-@settitle PhySamp Manual 1.0.3
+@settitle PhySamp Manual 1.1.0
@documentencoding UTF-8
@afourpaper
@dircategory Science Biology Genetics
@@ -13,9 +13,9 @@
@copying
-This is the manual of the PhySamp package, version 1.0.3.
+This is the manual of the PhySamp package, version 1.1.0.
-Copyright @copyright{} 2017 Julien Y. Dutheil
+Copyright @copyright{} 2018 Julien Y. Dutheil
@end copying
@titlepage
=
physamp.spec
=
--- a/physamp.spec
+++ b/physamp.spec
@@ -1,34 +1,31 @@
-%define _basename physamp
-%define _version 1.0.1
-%define _release 1
%define _prefix /usr
-URL: https://github.com/jydu/maffilter
+URL: https://github.com/jydu/physamp
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: physamp
+Version: 1.1.0
+Release: 1%{?dist}
License: GPL-3.0
Vendor: Julien Dutheil
-Source: %{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
Summary: The PhySamp package
Group: Productivity/Scientific/Other
-Requires: libbpp-phyl11 = 2.3.1
-Requires: libbpp-seq11 = 2.3.1
-Requires: libbpp-core3 = 2.3.1
+Requires: libbpp-phyl12 = 2.4.0
+Requires: libbpp-seq12 = 2.4.0
+Requires: libbpp-core4 = 2.4.0
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: groff
BuildRequires: texinfo >= 4.0.0
-BuildRequires: libbpp-core3 = 2.3.1
-BuildRequires: libbpp-core-devel = 2.3.1
-BuildRequires: libbpp-seq11 = 2.3.1
-BuildRequires: libbpp-seq-devel = 2.3.1
-BuildRequires: libbpp-phyl11 = 2.3.1
-BuildRequires: libbpp-phyl-devel = 2.3.1
+BuildRequires: libbpp-core4 = 2.4.0
+BuildRequires: libbpp-core-devel = 2.4.0
+BuildRequires: libbpp-seq12 = 2.4.0
+BuildRequires: libbpp-seq-devel = 2.4.0
+BuildRequires: libbpp-phyl12 = 2.4.0
+BuildRequires: libbpp-phyl-devel = 2.4.0
AutoReq: yes
@@ -80,6 +77,9 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/bppphysamp.1.*
%changelog
+* Wed Mar 14 2018 Julien Dutheil 1.1.0-1
+- Compatibility update with Bio++ 2.4.0
+- More options in branch panel
* Tue Jun 06 2017 Julien Dutheil 1.0.1-1
- Compatibility update with Bio++ 2.3.1
* Fri May 26 2017 Julien Dutheil 1.0.0-1
=
physamp/AlignmentOpt
[med-svn] [Git][med-team/physamp] Pushed new tag upstream/1.1.0
Julien Y. Dutheil pushed new tag upstream/1.1.0 at Debian Med / physamp --- View it on GitLab: https://salsa.debian.org/med-team/physamp/tree/upstream/1.1.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/physamp][pristine-tar] pristine-tar data for physamp_1.1.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / physamp Commits: d04718a0 by Julien Y. Dutheil at 2018-04-18T16:05:31+02:00 pristine-tar data for physamp_1.1.0.orig.tar.gz - - - - - 2 changed files: - + physamp_1.1.0.orig.tar.gz.delta - + physamp_1.1.0.orig.tar.gz.id Changes: = physamp_1.1.0.orig.tar.gz.delta = Binary files /dev/null and b/physamp_1.1.0.orig.tar.gz.delta differ = physamp_1.1.0.orig.tar.gz.id = --- /dev/null +++ b/physamp_1.1.0.orig.tar.gz.id @@ -0,0 +1 @@ +cb7fb900c8440ba93f4287884d12370e9f8cf15a View it on GitLab: https://salsa.debian.org/med-team/physamp/commit/d04718a011eca8fb50d7c374e9854e6d844019b7 --- View it on GitLab: https://salsa.debian.org/med-team/physamp/commit/d04718a011eca8fb50d7c374e9854e6d844019b7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite][master] Ran cme to fix package.
Julien Y. Dutheil pushed to branch master at Debian Med / bppsuite Commits: a40fb84d by Julien Y. Dutheil at 2018-04-09T09:42:37+02:00 Ran cme to fix package. - - - - - 3 changed files: - debian/control - debian/copyright - − debian/docs Changes: = debian/control = --- a/debian/control +++ b/debian/control @@ -4,12 +4,14 @@ Uploaders: Julien Dutheil , Andreas Tille Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper (>= 11), cmake, texinfo, libbpp-phyl-dev (>= 2.4.0), libbpp-popgen-dev (>= 2.4.0) Standards-Version: 4.1.3 +Vcs-Browser: https://salsa.debian.org/med-team/bppsuite +Vcs-Git: https://salsa.debian.org/med-team/bppsuite.git Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Package: bppsuite = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: bppsuite Upstream-Contact: Julien Yann Dutheil Source: https://github.com/BioPP/bppsuite @@ -14,24 +14,6 @@ Copyright: 2014 Julien Yann Dutheil 2017 Andreas Tille License: GPL-2+ -License: GPL-2+ -This package is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; either version 2 of the License, or -(at your option) any later version. - . -This package is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - . -You should have received a copy of the GNU General Public License -along with this package; if not, write to the Free Software -Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - . - On Debian systems, the complete text of the GNU General - Public License can be found in `/usr/share/common-licenses/GPL'. - License: CeCILL CeCILL FREE SOFTWARE LICENSE AGREEMENT . @@ -536,3 +518,21 @@ License: CeCILL . . Version 2.0 dated 2005-05-21. + +License: GPL-2+ +This package is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 2 of the License, or +(at your option) any later version. + . +This package is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + . +You should have received a copy of the GNU General Public License +along with this package; if not, write to the Free Software +Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + . + On Debian systems, the complete text of the GNU General + Public License can be found in `/usr/share/common-licenses/GPL'. = debian/docs deleted = --- a/debian/docs +++ /dev/null View it on GitLab: https://salsa.debian.org/med-team/bppsuite/commit/a40fb84dcea92b077587e8ef114e2965d518cf37 --- View it on GitLab: https://salsa.debian.org/med-team/bppsuite/commit/a40fb84dcea92b077587e8ef114e2965d518cf37 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / bppsuite --- View it on GitLab: https://salsa.debian.org/med-team/bppsuite/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/bppsuite][pristine-tar] pristine-tar data for bppsuite_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / bppsuite Commits: 2dcf778c by Julien Y. Dutheil at 2018-04-08T08:31:09+02:00 pristine-tar data for bppsuite_2.4.0.orig.tar.gz - - - - - 2 changed files: - + bppsuite_2.4.0.orig.tar.gz.delta - + bppsuite_2.4.0.orig.tar.gz.id Changes: = bppsuite_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/bppsuite_2.4.0.orig.tar.gz.delta differ = bppsuite_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/bppsuite_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +d07ea70747b504f8d8759cd2b2ea7a48ceaf77c7 View it on GitLab: https://salsa.debian.org/med-team/bppsuite/commit/2dcf778c7c28351593ab6345967b7b2f1e1baee3 --- View it on GitLab: https://salsa.debian.org/med-team/bppsuite/commit/2dcf778c7c28351593ab6345967b7b2f1e1baee3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-qt][master] Symbols for amd64 arch only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-qt Commits: 7be1b21e by Julien Y. Dutheil at 2018-04-07T22:27:00+02:00 Symbols for amd64 arch only. Updated dates in copyright file. - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -4,6 +4,7 @@ libbpp-qt (2.4.0-1) UNRELEASED; urgency=medium * Provide full license text of CeCILL license [ Julien Y. Dutheil ] + * Provide symbols file only for amd64 * New upstream version * Removed unnecessary override = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -1,10 +1,10 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: B++-Qt +Upstream-Name: Bpp-Qt Upstream-Contact: Julien Yann Dutheil -Source: http://biopp.univ-montp2.fr/Repositories/sources/ +Source: https://github.com/BioPP/bpp-qt/ Files: * -Copyright: 2010-2016 Julien Yann Dutheil +Copyright: 2010-2018 Julien Yann Dutheil Bio++ Development Team License: CeCILL = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif + override_dh_install: dh_install d-shlibmove --commit \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/commit/7be1b21e92bfbd2a64302b488b2f3ff9d2375767 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/commit/7be1b21e92bfbd2a64302b488b2f3ff9d2375767 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl-omics][master] Symbols for amd64 arch only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl-omics Commits: 30462412 by Julien Y. Dutheil at 2018-04-07T22:22:13+02:00 Symbols for amd64 arch only. Also restored CMakeList.txt file. Updated dates in copyright file. - - - - - 4 changed files: - CMakeLists.txt - debian/changelog - debian/copyright - debian/rules Changes: = CMakeLists.txt = --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11) project (bpp-phyl-omics CXX) # Compile options -#set (CMAKE_CXX_FLAGS "-std=c++11 -g") +set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion") IF(NOT CMAKE_BUILD_TYPE) SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,9 @@ libbpp-phyl-omics (2.4.0-2) UNRELEASED; urgency=medium + [ Julien Dutheil ] + * Provide symbols file only for amd64 + + [ Andreas Tille ] * Provide full license text of CeCILL license -- Andreas Tille Fri, 06 Apr 2018 07:54:46 +0200 = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil Source: https://github.com/BioPP/bpp-phyl-omics/ Files: * -Copyright: 2010-2016 Julien Yann Dutheil +Copyright: 2010-2018 Julien Yann Dutheil Bio++ Development Team License: CeCILL = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif + override_dh_install: dh_install d-shlibmove --commit \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/304624126151f5cecd0b43f5928a70aab0dd09c1 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/304624126151f5cecd0b43f5928a70aab0dd09c1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][master] Symbols for amd64 arch only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq-omics Commits: 8d9fc21e by Julien Y. Dutheil at 2018-04-07T22:18:36+02:00 Symbols for amd64 arch only. Fixed dates in copyright file. - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,7 @@ -libbpp-seq-omics (2.4.0-3) UNRELEASED; urgency=medium +libbpp-seq-omics (2.4.0-2) UNRELEASED; urgency=medium [ Julien Dutheil ] + * Provide symbols file only for amd64 * Versioned Build-Depends: d-shlibs (>= 0.82) [ Andreas Tille ] = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil Source: https://github.com/BioPP/bpp-seq-omics/ Files: * -Copyright: 2010-2016 Julien Yann Dutheil +Copyright: 2010-2018 Julien Yann Dutheil Bio++ Development Team License: CeCILL = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif + override_dh_install: dh_install d-shlibmove --commit \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/8d9fc21e0e0e3121f92d8a0c0dcb033c7f7e8890 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/8d9fc21e0e0e3121f92d8a0c0dcb033c7f7e8890 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][master] Fixed changelog.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-popgen Commits: 6466a41e by Julien Y. Dutheil at 2018-04-07T21:58:49+02:00 Fixed changelog. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,11 +1,9 @@ -libbpp-popgen (2.4.0-3) UNRELEASED; urgency=medium - - * Provide symbols file only for amd64 - - -- Julien Dutheil Sat, 07 Apr 2018 21:48:53 +0200 - libbpp-popgen (2.4.0-2) UNRELEASED; urgency=medium + [ Julien Dutheil ] + * Provide symbols file only for amd64 + + [ Andreas Tille ] * Provide full license text of CeCILL license -- Andreas Tille Fri, 06 Apr 2018 07:55:34 +0200 View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/6466a41e5c1a63cad951ef4315fdffe60e082896 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/6466a41e5c1a63cad951ef4315fdffe60e082896 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq][master] Fixed changelog.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq Commits: fe0ca09c by Julien Y. Dutheil at 2018-04-07T21:57:55+02:00 Fixed changelog. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,11 +1,9 @@ -libbpp-seq (2.4.0-3) UNRELEASED; urgency=medium - - * Provide symbols file only for amd64 - - -- Julien Dutheil Sat, 07 Apr 2018 20:37:13 +0200 - libbpp-seq (2.4.0-2) UNRELEASED; urgency=medium + [ Julien Dutheil ] + * Provide symbols file only for amd64 + + [ Andreas Tille ] * Provide full license text of CeCILL license -- Andreas Tille Fri, 06 Apr 2018 07:51:07 +0200 View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/fe0ca09c12c33f971eacc1364e01da1eb0cc29af --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/fe0ca09c12c33f971eacc1364e01da1eb0cc29af You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][master] Fixed changelog.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl Commits: 75daa418 by Julien Y. Dutheil at 2018-04-07T21:57:05+02:00 Fixed changelog. - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,11 +1,9 @@ -libbpp-phyl (2.4.0-3) UNRELEASED; urgency=medium - - * Provide symbols file only for amd64 - - -- Julien Dutheil Sat, 07 Apr 2018 21:35:24 +0200 - libbpp-phyl (2.4.0-2) UNRELEASED; urgency=medium + [ Julien Dutheil ] + * Provide symbols file only for amd64 + + [ Andreas Tille ] * Provide full license text of CeCILL license -- Andreas Tille Fri, 06 Apr 2018 07:53:20 +0200 View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/75daa418a0ccac25c0c9d35297f567589a88c3a6 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/75daa418a0ccac25c0c9d35297f567589a88c3a6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-raa][master] Symbol files for amd64 arch only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-raa Commits: 5e61f327 by Julien Y. Dutheil at 2018-04-07T21:55:52+02:00 Symbol files for amd64 arch only. Fixed dates in copyright file. - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,9 @@ libbpp-raa (2.4.0-2) UNRELEASED; urgency=medium + [ Julien Dutheil ] + * Provide symbols file only for amd64 + + [ Andreas Tille ] * Provide full license text of CeCILL license -- Andreas Tille Fri, 06 Apr 2018 07:57:17 +0200 = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil Source: https://github.com/BioPP/bpp-raa/ Files: * -Copyright: 2010-2016 Julien Yann Dutheil +Copyright: 2010-2018 Julien Yann Dutheil Bio++ Development Team License: CeCILL = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -6,6 +6,22 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif override_dh_install: dh_install View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/5e61f327e056ed1dd989654858d7b57aa0e62c98 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/5e61f327e056ed1dd989654858d7b57aa0e62c98 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][master] Symbol files for amd64 only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-popgen Commits: e4cb4464 by Julien Y. Dutheil at 2018-04-07T21:49:41+02:00 Symbol files for amd64 only. Fixed date in copyright file. - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +libbpp-popgen (2.4.0-3) UNRELEASED; urgency=medium + + * Provide symbols file only for amd64 + + -- Julien Dutheil Sat, 07 Apr 2018 21:48:53 +0200 + libbpp-popgen (2.4.0-2) UNRELEASED; urgency=medium * Provide full license text of CeCILL license = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil Source: https://github.com/BioPP/bpp-popgen/ Files: * -Copyright: 2010-2016 Julien Yann Dutheil +Copyright: 2010-2018 Julien Yann Dutheil Bio++ Development Team License: CeCILL = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -7,6 +7,23 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif + override_dh_install: dh_install d-shlibmove --commit \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/e4cb446416a332522166566a97d0b8b39055374e --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/e4cb446416a332522166566a97d0b8b39055374e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][master] Symbols for amd64 arch only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl Commits: 1b47abd0 by Julien Y. Dutheil at 2018-04-07T21:45:42+02:00 Symbols for amd64 arch only. Fixed dates in copyright file. - - - - - 3 changed files: - debian/changelog - debian/copyright - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +libbpp-phyl (2.4.0-3) UNRELEASED; urgency=medium + + * Provide symbols file only for amd64 + + -- Julien Dutheil Sat, 07 Apr 2018 21:35:24 +0200 + libbpp-phyl (2.4.0-2) UNRELEASED; urgency=medium * Provide full license text of CeCILL license = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -4,7 +4,7 @@ Upstream-Contact: Julien Yann Dutheil Source: https://github.com/BioPP/bpp-phyl/ Files: * -Copyright: 2010-2016 Julien Yann Dutheil +Copyright: 2010-2018 Julien Yann Dutheil Bio++ Development Team License: CeCILL = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -9,6 +9,23 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif + override_dh_install: dh_install d-shlibmove --commit \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/1b47abd0d35173535261eaa509bf0c39a2255bea --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/1b47abd0d35173535261eaa509bf0c39a2255bea You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq][master] Symbols file for amd64 only.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq Commits: 9f467c88 by Julien Y. Dutheil at 2018-04-07T20:38:36+02:00 Symbols file for amd64 only. - - - - - 2 changed files: - debian/changelog - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +libbpp-seq (2.4.0-3) UNRELEASED; urgency=medium + + * Provide symbols file only for amd64 + + -- Julien Dutheil Sat, 07 Apr 2018 20:37:13 +0200 + libbpp-seq (2.4.0-2) UNRELEASED; urgency=medium * Provide full license text of CeCILL license = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -9,9 +9,24 @@ CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF %: dh $@ +override_dh_makeshlibs: +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "Architecture amd64 is the only one where a symbols file is provided" +else + echo "Symbols file for architecture $(DEB_BUILD_ARCH) is not provided" + mkdir -p debian/hidesymbols + mv debian/*.symbols debian/hidesymbols +endif + dh_makeshlibs +ifeq ($(DEB_BUILD_ARCH),amd64) + echo "dh_makeshlibs for architecture amd64 including symbols done" +else + # restore original debian/ dir to enable building twice in a row + mv debian/hidesymbols/*.symbols debian + rmdir debian/hidesymbols +endif + override_dh_install: - # Broken header, don't install (if we do, the postinst will pull it - # into generic include files) dh_install d-shlibmove --commit \ --multiarch \ View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/9f467c88bd4d867c96caf18552b11142daa21a37 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/9f467c88bd4d867c96caf18552b11142daa21a37 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-qt] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-qt --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-qt][pristine-tar] pristine-tar data for libbpp-qt_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-qt Commits: 9bfbc64c by Julien Y. Dutheil at 2018-04-07T07:38:52+02:00 pristine-tar data for libbpp-qt_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-qt_2.4.0.orig.tar.gz.delta - + libbpp-qt_2.4.0.orig.tar.gz.id Changes: = libbpp-qt_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-qt_2.4.0.orig.tar.gz.delta differ = libbpp-qt_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-qt_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +c7391650f052c58887612c937e7ddb9d0656ed1c View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/commit/9bfbc64c025761f5f968038be128efe470cd6280 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-qt/commit/9bfbc64c025761f5f968038be128efe470cd6280 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core][master] 2 commits: Fixed copyright file.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-core Commits: 07f15714 by Julien Y. Dutheil at 2018-04-07T07:31:20+02:00 Fixed copyright file. - - - - - cc18852b by Julien Y. Dutheil at 2018-04-07T07:31:34+02:00 Merge branch 'master' of ssh://salsa.debian.org/med-team/libbpp-core - - - - - 1 changed file: - debian/copyright Changes: = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -1,11 +1,11 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: B++-Core +Upstream-Name: Bpp-Core Upstream-Contact: Julien Yann Dutheil -Source: http://biopp.univ-montp2.fr/Repositories/sources/ +Source: https://github.com/BioPP/bpp-core/ Files: * Copyright: 2010-2016 Julien Yann Dutheil - Bio++ Development Team + Bio++ Development Team License: CeCILL Files: debian/* View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/compare/693dbb2bf08eb91b27061507d6f10f21f074dff9...cc18852b0287f5c93c1be27c0cf9713b17fec4c6 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/compare/693dbb2bf08eb91b27061507d6f10f21f074dff9...cc18852b0287f5c93c1be27c0cf9713b17fec4c6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl-omics] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-phyl-omics --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl-omics][pristine-tar] pristine-tar data for libbpp-phyl-omics_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-phyl-omics Commits: 85de4059 by Julien Y. Dutheil at 2018-03-29T14:08:45+02:00 pristine-tar data for libbpp-phyl-omics_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-phyl-omics_2.4.0.orig.tar.gz.delta - + libbpp-phyl-omics_2.4.0.orig.tar.gz.id Changes: = libbpp-phyl-omics_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-phyl-omics_2.4.0.orig.tar.gz.delta differ = libbpp-phyl-omics_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-phyl-omics_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +8250a58368c6a64045b0ab118ad6891b6021da6b View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/85de4059f1ffb9a241ab27252ef58fd01a0d57ea --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/commit/85de4059f1ffb9a241ab27252ef58fd01a0d57ea You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][master] Fixed dh-libs version.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq-omics Commits: 9c2d0c81 by Julien Y. Dutheil at 2018-03-31T07:22:07+02:00 Fixed dh-libs version. - - - - - 3 changed files: - debian/changelog - debian/control - debian/rules Changes: = debian/changelog = --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +libbpp-seq-omics (2.4.0-2) UNRELEASED; urgency=medium + + * Versioned Build-Depends: d-shlibs (>= 0.82) + + -- Julien Dutheil Sat, 31 Mar 2018 07:21:05 +0200 + libbpp-seq-omics (2.4.0-1) unstable; urgency=medium * New upstream version. = debian/control = --- a/debian/control +++ b/debian/control @@ -6,7 +6,7 @@ Section: science Priority: optional Build-Depends: debhelper (>= 11~), cmake, - d-shlibs (>= 0.80), + d-shlibs (>= 0.82), libbpp-seq-dev (>= 2.4.0) Standards-Version: 4.1.3 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-seq-omics.git = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -4,6 +4,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all +CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF + %: dh $@ View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/9c2d0c81be930014e609cd8406ff04f9ca0aa19d --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/9c2d0c81be930014e609cd8406ff04f9ca0aa19d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][master] 2 commits: Minor fixes.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl Commits: 3750d063 by Julien Y. Dutheil at 2018-03-30T20:12:09+02:00 Minor fixes. - - - - - f818042e by Julien Y. Dutheil at 2018-03-30T20:12:31+02:00 Merge branch 'master' of ssh://salsa.debian.org/med-team/libbpp-phyl - - - - - 2 changed files: - debian/copyright - debian/rules Changes: = debian/copyright = --- a/debian/copyright +++ b/debian/copyright @@ -5,7 +5,7 @@ Source: https://github.com/BioPP/bpp-phyl/ Files: * Copyright: 2010-2016 Julien Yann Dutheil - Bio++ Development Team + Bio++ Development Team License: CeCILL The provided software is distributed under the CeCILL license: . = debian/rules = --- a/debian/rules +++ b/debian/rules @@ -4,6 +4,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all +CMAKE_EXTRA_FLAGS += -DBUILD_TESTING=OFF + %: dh $@ View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/compare/dbb1c0927c7b6e6816ef059c998feb7f57f56ebc...f818042e0f81deb54fbba41e4837b1303db08893 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/compare/dbb1c0927c7b6e6816ef059c998feb7f57f56ebc...f818042e0f81deb54fbba41e4837b1303db08893 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-seq-omics --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][upstream] New upstream version 2.4.0
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-seq-omics Commits: f1ead48d by Julien Y. Dutheil at 2018-03-28T09:57:46+02:00 New upstream version 2.4.0 - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-seq-omics.spec - src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp - src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h - src/Bpp/Seq/Feature/FeatureReader.h - src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp - src/Bpp/Seq/Feature/Gff/GffFeatureReader.h - src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp - src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h - src/Bpp/Seq/Io/Fastq.cpp - src/Bpp/Seq/Io/Fastq.h - src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp - src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h - src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp - src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.h - src/Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp - src/Bpp/Seq/Io/Maf/ChromosomeMafIterator.h - src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp - src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h - src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp - src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h - src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp - src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h - src/Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp - src/Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.h - src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp - src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h - src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/f1ead48d78b03a3e99a39fe6a231adec28b1aa96 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/f1ead48d78b03a3e99a39fe6a231adec28b1aa96 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][master] 4 commits: New upstream version 2.4.0
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq-omics Commits: f1ead48d by Julien Y. Dutheil at 2018-03-28T09:57:46+02:00 New upstream version 2.4.0 - - - - - d869f860 by Julien Y. Dutheil at 2018-03-28T09:57:46+02:00 Update upstream source from tag 'upstream/2.4.0' Update to upstream version '2.4.0' with Debian dir 562ccf7521be0dbc9e6309a54518d5f13b2a4cd4 - - - - - 0697db15 by Julien Y. Dutheil at 2018-03-28T10:02:47+02:00 Drafted version 2.4.0. - - - - - ab1916a8 by Julien Y. Dutheil at 2018-03-28T11:15:52+02:00 Added symbol file. - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-seq-omics.spec - debian/changelog - debian/control - debian/copyright - + debian/libbpp-seq-omics3.symbols - − debian/patches/fix_test_cmakelist.patch - debian/patches/series - debian/patches/unforce-cxxflags.patch - src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp - src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h - src/Bpp/Seq/Feature/FeatureReader.h - src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp - src/Bpp/Seq/Feature/Gff/GffFeatureReader.h - src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp - src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h - src/Bpp/Seq/Io/Fastq.cpp - src/Bpp/Seq/Io/Fastq.h - src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp - src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h - src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp - src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.h - src/Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp - src/Bpp/Seq/Io/Maf/ChromosomeMafIterator.h - src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp - src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h - src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp - src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/compare/fe2936147d529ca6adcab531ec957f5987809930...ab1916a84ea5017e935aff127392bb2dbc6dbb18 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/compare/fe2936147d529ca6adcab531ec957f5987809930...ab1916a84ea5017e935aff127392bb2dbc6dbb18 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq-omics][pristine-tar] pristine-tar data for libbpp-seq-omics_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-seq-omics Commits: 6be91ae3 by Julien Y. Dutheil at 2018-03-28T09:57:46+02:00 pristine-tar data for libbpp-seq-omics_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-seq-omics_2.4.0.orig.tar.gz.delta - + libbpp-seq-omics_2.4.0.orig.tar.gz.id Changes: = libbpp-seq-omics_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-seq-omics_2.4.0.orig.tar.gz.delta differ = libbpp-seq-omics_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-seq-omics_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +9260a41b17dd5a02bfe352d80cc90140d0845b07 View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/6be91ae36e0b698717fa8b109cdc48247a8fb7f1 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/commit/6be91ae36e0b698717fa8b109cdc48247a8fb7f1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-raa] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-raa --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-raa][pristine-tar] pristine-tar data for libbpp-raa_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-raa Commits: 0e554bc0 by Julien Y. Dutheil at 2018-03-28T09:31:58+02:00 pristine-tar data for libbpp-raa_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-raa_2.4.0.orig.tar.gz.delta - + libbpp-raa_2.4.0.orig.tar.gz.id Changes: = libbpp-raa_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-raa_2.4.0.orig.tar.gz.delta differ = libbpp-raa_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-raa_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +6a9f9e702bc02384201f0b580bdfcf5284fac796 View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/0e554bc0e03892887deea04b0fb4912a352da7aa --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-raa/commit/0e554bc0e03892887deea04b0fb4912a352da7aa You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][pristine-tar] pristine-tar data for libbpp-popgen_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-popgen Commits: 61c44c6b by Julien Y. Dutheil at 2018-03-27T21:43:16+02:00 pristine-tar data for libbpp-popgen_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-popgen_2.4.0.orig.tar.gz.delta - + libbpp-popgen_2.4.0.orig.tar.gz.id Changes: = libbpp-popgen_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-popgen_2.4.0.orig.tar.gz.delta differ = libbpp-popgen_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-popgen_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +068723d0a1065857ed37ec4b8965fbe6f91becfa View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/61c44c6b0254a0526c2cc140296e88c49249147c --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/61c44c6b0254a0526c2cc140296e88c49249147c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][upstream] New upstream version 2.4.0
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-popgen Commits: 6bfddcbf by Julien Y. Dutheil at 2018-03-27T21:43:15+02:00 New upstream version 2.4.0 - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-popgen.spec - src/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp - src/Bpp/PopGen/BiAlleleMonolocusGenotype.h - src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp - src/Bpp/PopGen/DataSet/AnalyzedLoci.h - src/Bpp/PopGen/DataSet/AnalyzedSequences.cpp - src/Bpp/PopGen/DataSet/AnalyzedSequences.h - src/Bpp/PopGen/DataSet/DataSet.cpp - src/Bpp/PopGen/DataSet/DataSet.h - src/Bpp/PopGen/DataSet/DataSetTools.cpp - src/Bpp/PopGen/DataSet/DataSetTools.h - src/Bpp/PopGen/DataSet/Date.cpp - src/Bpp/PopGen/DataSet/Date.h - src/Bpp/PopGen/DataSet/Group.cpp - src/Bpp/PopGen/DataSet/Group.h - src/Bpp/PopGen/DataSet/Individual.cpp - src/Bpp/PopGen/DataSet/Individual.h - src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.cpp - src/Bpp/PopGen/DataSet/Io/AbstractIDataSet.h - src/Bpp/PopGen/DataSet/Io/AbstractODataSet.cpp - src/Bpp/PopGen/DataSet/Io/AbstractODataSet.h - src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.cpp - src/Bpp/PopGen/DataSet/Io/Darwin/DarwinDon.h - src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.cpp - src/Bpp/PopGen/DataSet/Io/Darwin/DarwinVarSingle.h - src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.cpp - src/Bpp/PopGen/DataSet/Io/GeneMapper/GeneMapperCsvExport.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/6bfddcbfbb409573cfac06986afb1686c32f7141 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/commit/6bfddcbfbb409573cfac06986afb1686c32f7141 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-popgen --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-popgen][master] 4 commits: New upstream version 2.4.0
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-popgen Commits: 6bfddcbf by Julien Y. Dutheil at 2018-03-27T21:43:15+02:00 New upstream version 2.4.0 - - - - - 467d829b by Julien Y. Dutheil at 2018-03-27T21:43:16+02:00 Update upstream source from tag 'upstream/2.4.0' Update to upstream version '2.4.0' with Debian dir 78dbb1dff73d549fab58f03d69ccf4fcea3c3af7 - - - - - 05be2d18 by Julien Y. Dutheil at 2018-03-27T21:48:47+02:00 Drafted version 2.4.0. - - - - - 734f8fef by Julien Y. Dutheil at 2018-03-27T22:04:56+02:00 Added symbol file. - - - - - 16 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-popgen.spec - debian/changelog - debian/control - debian/copyright - + debian/libbpp-popgen8.symbols - debian/patches/unforce-cxxflags.patch - src/Bpp/PopGen/BiAlleleMonolocusGenotype.cpp - src/Bpp/PopGen/BiAlleleMonolocusGenotype.h - src/Bpp/PopGen/DataSet/AnalyzedLoci.cpp - src/Bpp/PopGen/DataSet/AnalyzedLoci.h - src/Bpp/PopGen/DataSet/AnalyzedSequences.cpp - src/Bpp/PopGen/DataSet/AnalyzedSequences.h - src/Bpp/PopGen/DataSet/DataSet.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/compare/15e2ef9b22335750691093fd1ba3160c1fd82fa2...734f8fef33ddc3e2d802ee6c8615730dba1430c5 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/compare/15e2ef9b22335750691093fd1ba3160c1fd82fa2...734f8fef33ddc3e2d802ee6c8615730dba1430c5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][upstream] New upstream version 2.4.0
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-phyl Commits: 0f9752d1 by Julien Y. Dutheil at 2018-03-27T09:57:49+02:00 New upstream version 2.4.0 - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-phyl.spec - src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp - src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h - src/Bpp/Phyl/BipartitionList.cpp - src/Bpp/Phyl/BipartitionList.h - src/Bpp/Phyl/BipartitionTools.cpp - src/Bpp/Phyl/BipartitionTools.h - src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp - src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h - src/Bpp/Phyl/Distance/BioNJ.cpp - src/Bpp/Phyl/Distance/BioNJ.h - src/Bpp/Phyl/Distance/DistanceEstimation.cpp - src/Bpp/Phyl/Distance/DistanceEstimation.h - src/Bpp/Phyl/Distance/DistanceMethod.h - src/Bpp/Phyl/Distance/HierarchicalClustering.cpp - src/Bpp/Phyl/Distance/HierarchicalClustering.h - src/Bpp/Phyl/Distance/NeighborJoining.cpp - src/Bpp/Phyl/Distance/NeighborJoining.h - src/Bpp/Phyl/Distance/PGMA.cpp - src/Bpp/Phyl/Distance/PGMA.h - src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp - src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h - src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp - src/Bpp/Phyl/Graphics/AbstractTreeDrawing.h - src/Bpp/Phyl/Graphics/CladogramPlot.cpp - src/Bpp/Phyl/Graphics/CladogramPlot.h - src/Bpp/Phyl/Graphics/PhylogramPlot.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/0f9752d1e4c8d08ee1b477859ef4806cac13e23e --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/0f9752d1e4c8d08ee1b477859ef4806cac13e23e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][master] 5 commits: New upstream version 2.4.0
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl Commits: 0f9752d1 by Julien Y. Dutheil at 2018-03-27T09:57:49+02:00 New upstream version 2.4.0 - - - - - 636b1e47 by Julien Y. Dutheil at 2018-03-27T09:57:59+02:00 Update upstream source from tag 'upstream/2.4.0' Update to upstream version '2.4.0' with Debian dir 2f3ac7f8d45d8c57b1116e66b8d944ceb1fa - - - - - 63091681 by Julien Y. Dutheil at 2018-03-27T11:20:25+02:00 Drafted release 2.4.0. - - - - - ff8a2106 by Julien Y. Dutheil at 2018-03-27T11:23:16+02:00 Added list of symbols. - - - - - a74622f1 by Julien Y. Dutheil at 2018-03-27T11:26:59+02:00 Merge branch 'master' of ssh://salsa.debian.org/med-team/libbpp-phyl - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-phyl.spec - debian/changelog - debian/control - debian/copyright - + debian/libbpp-phyl12.symbols - − debian/patches/correct_constructors_inheritance.patch - − debian/patches/fix_covariant_return.patch - debian/patches/series - debian/patches/unforce-cxxflags.patch - src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp - src/Bpp/Phyl/App/PhylogeneticsApplicationTools.h - src/Bpp/Phyl/BipartitionList.cpp - src/Bpp/Phyl/BipartitionList.h - src/Bpp/Phyl/BipartitionTools.cpp - src/Bpp/Phyl/BipartitionTools.h - src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp - src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h - src/Bpp/Phyl/Distance/BioNJ.cpp - src/Bpp/Phyl/Distance/BioNJ.h - src/Bpp/Phyl/Distance/DistanceEstimation.cpp - src/Bpp/Phyl/Distance/DistanceEstimation.h - src/Bpp/Phyl/Distance/DistanceMethod.h - src/Bpp/Phyl/Distance/HierarchicalClustering.cpp - src/Bpp/Phyl/Distance/HierarchicalClustering.h - src/Bpp/Phyl/Distance/NeighborJoining.cpp - src/Bpp/Phyl/Distance/NeighborJoining.h - src/Bpp/Phyl/Distance/PGMA.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/compare/5afe4850b42099c7d9d6f50213c9129a9335a7f3...a74622f14183c427e4f03c381f338d14ee06a67a --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/compare/5afe4850b42099c7d9d6f50213c9129a9335a7f3...a74622f14183c427e4f03c381f338d14ee06a67a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][pristine-tar] pristine-tar data for libbpp-phyl_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-phyl Commits: 134fe958 by Julien Y. Dutheil at 2018-03-27T09:57:59+02:00 pristine-tar data for libbpp-phyl_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-phyl_2.4.0.orig.tar.gz.delta - + libbpp-phyl_2.4.0.orig.tar.gz.id Changes: = libbpp-phyl_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-phyl_2.4.0.orig.tar.gz.delta differ = libbpp-phyl_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-phyl_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +66c2dcdca3e197894e2130b45bba5e0e4e7959e3 View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/134fe9586b8264cdd9b025e685ca8f7541612197 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/commit/134fe9586b8264cdd9b025e685ca8f7541612197 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-phyl --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq][master] 3 commits: New upstream version 2.4.0
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq Commits: 690616d6 by Julien Y. Dutheil at 2018-03-25T14:12:06+02:00 New upstream version 2.4.0 - - - - - f79c1c58 by Julien Y. Dutheil at 2018-03-25T14:12:08+02:00 Update upstream source from tag 'upstream/2.4.0' Update to upstream version '2.4.0' with Debian dir 9e7ba6c3f6aedc7c62c7dae4aed4b530c0c23c41 - - - - - 8cff27ae by Julien Y. Dutheil at 2018-03-25T20:44:33+02:00 Drafted version 2.4.0. - - - - - 30 changed files: - + .clang-format - + .gitignore - CMakeLists.txt - ChangeLog - Doxyfile - bpp-seq.spec - debian/changelog - debian/control - debian/copyright - − debian/libbpp-seq11.symbols - + debian/libbpp-seq12.symbols - debian/patches/unforce-cxxflags.patch - debian/rules - src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp - src/Bpp/Seq/Alphabet/AbstractAlphabet.h - src/Bpp/Seq/Alphabet/Alphabet.h - src/Bpp/Seq/Alphabet/AlphabetExceptions.h - src/Bpp/Seq/Alphabet/AlphabetTools.cpp - src/Bpp/Seq/Alphabet/AlphabetTools.h - src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp - src/Bpp/Seq/Alphabet/BinaryAlphabet.h - src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp - src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h - src/Bpp/Seq/Alphabet/CodonAlphabet.cpp - src/Bpp/Seq/Alphabet/CodonAlphabet.h - src/Bpp/Seq/Alphabet/DNA.cpp - src/Bpp/Seq/Alphabet/DNA.h - src/Bpp/Seq/Alphabet/DefaultAlphabet.h - src/Bpp/Seq/Alphabet/LetterAlphabet.h - src/Bpp/Seq/Alphabet/NucleicAlphabet.h The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/compare/3929f00a8f53a259683149d581f06844373677c5...8cff27aeacebc7548c2f80a7d0094845f9fb8be7 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/compare/3929f00a8f53a259683149d581f06844373677c5...8cff27aeacebc7548c2f80a7d0094845f9fb8be7 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq][pristine-tar] pristine-tar data for libbpp-seq_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-seq Commits: 4c5f725f by Julien Y. Dutheil at 2018-03-25T14:12:08+02:00 pristine-tar data for libbpp-seq_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-seq_2.4.0.orig.tar.gz.delta - + libbpp-seq_2.4.0.orig.tar.gz.id Changes: = libbpp-seq_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-seq_2.4.0.orig.tar.gz.delta differ = libbpp-seq_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-seq_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +8c74e6ef751626a213c9d57ff5d63f187889619d View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/4c5f725ff57773d910a7a4290ba12cdeffd5add8 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/4c5f725ff57773d910a7a4290ba12cdeffd5add8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-seq --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-seq][upstream] New upstream version 2.4.0
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-seq Commits: 690616d6 by Julien Y. Dutheil at 2018-03-25T14:12:06+02:00 New upstream version 2.4.0 - - - - - 30 changed files: - + .clang-format - + .gitignore - CMakeLists.txt - ChangeLog - Doxyfile - bpp-seq.spec - src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp - src/Bpp/Seq/Alphabet/AbstractAlphabet.h - src/Bpp/Seq/Alphabet/Alphabet.h - src/Bpp/Seq/Alphabet/AlphabetExceptions.h - src/Bpp/Seq/Alphabet/AlphabetTools.cpp - src/Bpp/Seq/Alphabet/AlphabetTools.h - src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp - src/Bpp/Seq/Alphabet/BinaryAlphabet.h - src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp - src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h - src/Bpp/Seq/Alphabet/CodonAlphabet.cpp - src/Bpp/Seq/Alphabet/CodonAlphabet.h - src/Bpp/Seq/Alphabet/DNA.cpp - src/Bpp/Seq/Alphabet/DNA.h - src/Bpp/Seq/Alphabet/DefaultAlphabet.h - src/Bpp/Seq/Alphabet/LetterAlphabet.h - src/Bpp/Seq/Alphabet/NucleicAlphabet.h - src/Bpp/Seq/Alphabet/NumericAlphabet.cpp - src/Bpp/Seq/Alphabet/NumericAlphabet.h - src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp - src/Bpp/Seq/Alphabet/ProteicAlphabet.h - src/Bpp/Seq/Alphabet/RNA.cpp - src/Bpp/Seq/Alphabet/RNA.h - src/Bpp/Seq/Alphabet/RNY.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/690616d6a0acfd4297c462f5f4e83f040200c15b --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/commit/690616d6a0acfd4297c462f5f4e83f040200c15b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core][upstream] New upstream version 2.4.0
Julien Y. Dutheil pushed to branch upstream at Debian Med / libbpp-core Commits: 78ac75e2 by Julien Y. Dutheil at 2018-03-21T15:51:15+01:00 New upstream version 2.4.0 - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-core.spec - cmake/doc-cmake-for-developpers.cmake - src/Bpp/App/ApplicationTools.cpp - src/Bpp/App/ApplicationTools.h - src/Bpp/App/NumCalcApplicationTools.cpp - src/Bpp/Graph/AssociationGraphImplObserver.h - src/Bpp/Graph/AssociationGraphObserver.h - src/Bpp/Graph/AssociationTreeGraphImplObserver.h - src/Bpp/Io/BppODiscreteDistributionFormat.cpp - src/Bpp/Numeric/AbstractParameterAliasable.cpp - src/Bpp/Numeric/AutoParameter.cpp - src/Bpp/Numeric/DataTable.cpp - src/Bpp/Numeric/DataTable.h - src/Bpp/Numeric/Function/AbstractOptimizer.cpp - src/Bpp/Numeric/Function/DirectionFunction.h - src/Bpp/Numeric/Function/Operators/ComputationTree.cpp - src/Bpp/Numeric/Function/Operators/ComputationTree.h - + src/Bpp/Numeric/Function/Operators/NegativeOperator.h - src/Bpp/Numeric/Matrix/MatrixTools.h - src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h - src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp - src/Bpp/Numeric/Prob/ConstantDistribution.cpp - src/Bpp/Numeric/Prob/DirichletDiscreteDistribution.cpp - src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp - src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h - src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp - src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/commit/78ac75e26cd6cb9eef768bee6900e9d62d881a21 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/commit/78ac75e26cd6cb9eef768bee6900e9d62d881a21 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core][master] 4 commits: New upstream version 2.4.0
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-core Commits: 78ac75e2 by Julien Y. Dutheil at 2018-03-21T15:51:15+01:00 New upstream version 2.4.0 - - - - - 78900e27 by Julien Y. Dutheil at 2018-03-21T15:51:17+01:00 Update upstream source from tag 'upstream/2.4.0' Update to upstream version '2.4.0' with Debian dir e5a830e5e4f95c3f9e14340b16811141f3031908 - - - - - 1ba68a84 by Julien Y. Dutheil at 2018-03-21T16:13:24+01:00 Drafted version 2.4.0. - - - - - cd13f67d by Julien Y. Dutheil at 2018-03-21T21:17:43+01:00 Updated symbol list. - - - - - 30 changed files: - CMakeLists.txt - ChangeLog - Doxyfile - bpp-core.spec - cmake/doc-cmake-for-developpers.cmake - debian/changelog - debian/libbpp-core4.symbols - − debian/patches/bump_soversion.patch - − debian/patches/gcc-7.patch - debian/patches/series - debian/patches/unforce-cxxflags.patch - src/Bpp/App/ApplicationTools.cpp - src/Bpp/App/ApplicationTools.h - src/Bpp/App/NumCalcApplicationTools.cpp - src/Bpp/Graph/AssociationGraphImplObserver.h - src/Bpp/Graph/AssociationGraphObserver.h - src/Bpp/Graph/AssociationTreeGraphImplObserver.h - src/Bpp/Io/BppODiscreteDistributionFormat.cpp - src/Bpp/Numeric/AbstractParameterAliasable.cpp - src/Bpp/Numeric/AutoParameter.cpp - src/Bpp/Numeric/DataTable.cpp - src/Bpp/Numeric/DataTable.h - src/Bpp/Numeric/Function/AbstractOptimizer.cpp - src/Bpp/Numeric/Function/DirectionFunction.h - src/Bpp/Numeric/Function/Operators/ComputationTree.cpp - src/Bpp/Numeric/Function/Operators/ComputationTree.h - + src/Bpp/Numeric/Function/Operators/NegativeOperator.h - src/Bpp/Numeric/Matrix/MatrixTools.h - src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h - src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/compare/3f14c3b0fa96c19275cb33f17a82f82386849b3d...cd13f67db30f24b69e36f21af7bb70e647ef7e87 --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/compare/3f14c3b0fa96c19275cb33f17a82f82386849b3d...cd13f67db30f24b69e36f21af7bb70e647ef7e87 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core] Pushed new tag upstream/2.4.0
Julien Y. Dutheil pushed new tag upstream/2.4.0 at Debian Med / libbpp-core --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/tree/upstream/2.4.0 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-core][pristine-tar] pristine-tar data for libbpp-core_2.4.0.orig.tar.gz
Julien Y. Dutheil pushed to branch pristine-tar at Debian Med / libbpp-core Commits: 099ac102 by Julien Y. Dutheil at 2018-03-21T15:51:17+01:00 pristine-tar data for libbpp-core_2.4.0.orig.tar.gz - - - - - 2 changed files: - + libbpp-core_2.4.0.orig.tar.gz.delta - + libbpp-core_2.4.0.orig.tar.gz.id Changes: = libbpp-core_2.4.0.orig.tar.gz.delta = Binary files /dev/null and b/libbpp-core_2.4.0.orig.tar.gz.delta differ = libbpp-core_2.4.0.orig.tar.gz.id = --- /dev/null +++ b/libbpp-core_2.4.0.orig.tar.gz.id @@ -0,0 +1 @@ +25962a5861a9c915bf53702491e935660c7b0a0f View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/commit/099ac1027ea9c4725833050f4142145541c69f7c --- View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/commit/099ac1027ea9c4725833050f4142145541c69f7c You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libbpp-phyl][master] Reduced test execution time.
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-phyl
Commits:
5afe4850 by Julien Y. Dutheil at 2018-02-11T21:18:30+01:00
Reduced test execution time.
Closesi: #890136
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/reduce_test_time.patch
- debian/patches/series
Changes:
=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-phyl (2.3.2-3) UNRELEASED; urgency=medium
+
+ * Reduced execution time of test_likelihood_nh
+Closes: #890136
+
+ -- Julien Dutheil Fri, 09 Feb 2018 09:10:11
+0200
+
libbpp-phyl (2.3.2-2) unstable; urgency=medium
* Fixed covariant return type on 32bits arch.
=
debian/patches/reduce_test_time.patch
=
--- /dev/null
+++ b/debian/patches/reduce_test_time.patch
@@ -0,0 +1,13 @@
+diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp
+index b4cd485..97431aa 100644
+--- a/test/test_likelihood_nh.cpp
b/test/test_likelihood_nh.cpp
+@@ -89,7 +89,7 @@ int main() {
+ DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0);
+
+ size_t nsites = 1000;
+- unsigned int nrep = 20;
++ unsigned int nrep = 3;
+ size_t nmodels = modelSet->getNumberOfModels();
+ vector thetas(nmodels);
+ vector thetasEst1(nmodels);
=
debian/patches/series
=
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
unforce-cxxflags.patch
correct_constructors_inheritance.patch
fix_covariant_return.patch
+reduce_test_time.patch
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/5afe4850b42099c7d9d6f50213c9129a9335a7f3
---
View it on GitLab:
https://salsa.debian.org/med-team/libbpp-phyl/commit/5afe4850b42099c7d9d6f50213c9129a9335a7f3
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