[med-svn] [Git][med-team/libbpp-phyl-omics][master] 4 commits: d/patches/unforce-cxxflags.patch: update to unhide upstream's flags; forward the patch to them.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Mar 25 23:51:37 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / libbpp-phyl-omics
Commits:
2873a95e by Michael R. Crusoe at 2024-03-25T12:45:12+01:00
d/patches/unforce-cxxflags.patch: update to unhide upstream's flags; forward the patch to them.
- - - - -
c683c739 by Michael R. Crusoe at 2024-03-25T18:56:05+01:00
silence a false-positive lintian error from the t64 transition.
- - - - -
7ab473f8 by Michael R. Crusoe at 2024-03-25T18:56:05+01:00
d/rules: simply arch-specific symbol management.
- - - - -
f0c264d1 by Michael R. Crusoe at 2024-03-25T18:56:06+01:00
removed unused "-DBUILD_TESTING=OFF"
- - - - -
6 changed files:
- debian/changelog
- debian/libbpp-phyl-omics3t64.lintian-overrides
- debian/libbpp-phyl-omics3t64.symbols → debian/libbpp-phyl-omics3t64.symbols.amd64
- debian/patches/unforce-cxxflags.patch
- debian/rules
- + debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+libbpp-phyl-omics (2.4.1-6) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * d/patches/unforce-cxxflags.patch: update to unhide upstream's flags;
+ forward the patch to them.
+ * silence a false-positive lintian error from the t64 transition.
+ * d/rules: simply arch-specific symbol management.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 25 Mar 2024 12:38:47 +0100
+
libbpp-phyl-omics (2.4.1-5.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/libbpp-phyl-omics3t64.lintian-overrides
=====================================
@@ -1 +1,2 @@
libbpp-phyl-omics3t64: package-name-doesnt-match-sonames libbpp-phyl-omics3
+libbpp-phyl-omics3t64: conflicts-with-version libbpp-phyl-omics3 (<< 2.4.1-6)
=====================================
debian/libbpp-phyl-omics3t64.symbols → debian/libbpp-phyl-omics3t64.symbols.amd64
=====================================
@@ -144,7 +144,6 @@ libbpp-phyl-omics.so.3 libbpp-phyl-omics3t64 #MINVER#
_ZN3bpp4Node10deleteNameEv at Base 2.4.1
_ZN3bpp4Node10removeSonsEv at Base 2.4.1
_ZN3bpp4Node12removeFatherEv at Base 2.4.1
- _ZN3bpp4Node15getNodePropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
_ZN3bpp4Node17getBranchPropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
_ZN3bpp4Node17setBranchPropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8ClonableE at Base 2.4.1
_ZN3bpp4Node19setDistanceToFatherEd at Base 2.4.1
@@ -252,10 +251,8 @@ libbpp-phyl-omics.so.3 libbpp-phyl-omics3t64 #MINVER#
_ZNK3bpp46MaximumLikelihoodDistanceEstimationMafIterator15getPropertyNameB5cxx11Ev at Base 2.4.1
_ZNK3bpp47DistanceBasedPhylogenyReconstructionMafIterator15getPropertyNameB5cxx11Ev at Base 2.4.1
_ZNK3bpp4Node11getFatherIdEv at Base 2.4.1
- _ZNK3bpp4Node15getNodePropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
_ZNK3bpp4Node15getNumberOfSonsEv at Base 2.4.1
_ZNK3bpp4Node15hasNodePropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZNK3bpp4Node17getBranchPropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
_ZNK3bpp4Node17hasBranchPropertyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
_ZNK3bpp4Node19hasDistanceToFatherEv at Base 2.4.1
_ZNK3bpp4Node20getNodePropertyNamesB5cxx11Ev at Base 2.4.1
@@ -283,48 +280,45 @@ libbpp-phyl-omics.so.3 libbpp-phyl-omics3t64 #MINVER#
_ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.1
_ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
_ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
- _ZNSt12_Vector_baseIPKN3bpp4NodeESaIS3_EED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseIPKN3bpp4NodeESaIS3_EED2Ev at Base 2.4.1
- _ZNSt12_Vector_baseIPN3bpp4NodeESaIS2_EED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseIPN3bpp4NodeESaIS2_EED2Ev at Base 2.4.1
_ZNSt12_Vector_baseISt6vectorIdSaIdEESaIS2_EED1Ev at Base 2.4.1
_ZNSt12_Vector_baseISt6vectorIdSaIdEESaIS2_EED2Ev at Base 2.4.1
- _ZNSt12_Vector_baseIdSaIdEED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseIdSaIdEED2Ev at Base 2.4.1
- _ZNSt12_Vector_baseIiSaIiEED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseIiSaIiEED2Ev at Base 2.4.1
_ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv at Base 2.4.1
_ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv at Base 2.4.1
_ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE24_M_release_last_use_coldEv at Base 2.4.1
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.1
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp8ClonableESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1-6~
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
_ZNSt6vectorIPKN3bpp4NodeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorIPKN3bpp4NodeESaIS3_EED1Ev at Base 2.4.1-6~
+ _ZNSt6vectorIPKN3bpp4NodeESaIS3_EED2Ev at Base 2.4.1-6~
_ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
_ZNSt6vectorIPN3bpp4NodeESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorIPN3bpp4NodeESaIS2_EED1Ev at Base 2.4.1-6~
+ _ZNSt6vectorIPN3bpp4NodeESaIS2_EED2Ev at Base 2.4.1-6~
_ZNSt6vectorIS_IdSaIdEESaIS1_EE17_M_default_appendEm at Base 2.4.1
_ZNSt6vectorIS_IdSaIdEESaIS1_EED1Ev at Base 2.4.1
_ZNSt6vectorIS_IdSaIdEESaIS1_EED2Ev at Base 2.4.1
_ZNSt6vectorIdSaIdEE17_M_default_appendEm at Base 2.4.1
- _ZNSt6vectorIdSaIdEE17_M_realloc_insertIJRKdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorIdSaIdEED1Ev at Base 2.4.1-6~
+ _ZNSt6vectorIdSaIdEED2Ev at Base 2.4.1-6~
+ _ZNSt6vectorIiSaIiEE12emplace_backIJiEEEvDpOT_ at Base 2.4.1-6~
_ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
- _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1
- _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1
+ _ZNSt6vectorIiSaIiEED1Ev at Base 2.4.1-6~
+ _ZNSt6vectorIiSaIiEED2Ev at Base 2.4.1-6~
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.1
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeIPKN3bpp4NodeESt4pairIKS3_dESt10_Select1stIS6_ESt4lessIS3_ESaIS6_EE24_M_get_insert_unique_posERS5_ at Base 2.4.1
- _ZNSt8_Rb_treeIPKN3bpp4NodeESt4pairIKS3_dESt10_Select1stIS6_ESt4lessIS3_ESaIS6_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS6_ERS5_ at Base 2.4.1
_ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1
_ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1
_ZSt18uninitialized_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1
+ _ZSteqIcSt11char_traitsIcESaIcEEbRKNSt7__cxx1112basic_stringIT_T0_T1_EESA_ at Base 2.4.1-6~
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
_ZTIN3bpp10BppIntegerE at Base 2.4.1
_ZTIN3bpp10BppNumberIE at Base 2.4.1
_ZTIN3bpp10SymbolListE at Base 2.4.1
@@ -540,4 +534,3 @@ libbpp-phyl-omics.so.3 libbpp-phyl-omics3t64 #MINVER#
_ZTv0_n56_N3bpp25SimpleMafStatisticsResult8setValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj at Base 2.4.1
_ZTv0_n56_N3bpp38MaximumLikelihoodModelFitMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
_ZTv0_n64_NK3bpp38MaximumLikelihoodModelFitMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
- _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 2.4.1
=====================================
debian/patches/unforce-cxxflags.patch
=====================================
@@ -1,8 +1,7 @@
From: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed, 29 Jun 2014 16:52:43 +0200
Subject: Do not override Debian CXX flags
-Comment: Upstream version 2.3.0 now has additional -std=c++11 which might
- be needed to be added explicitly
+Forwarded: https://github.com/BioPP/bpp-phyl-omics/pull/6
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,7 +10,7 @@ Comment: Upstream version 2.3.0 now has additional -std=c++11 which might
# Compile options
-set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
-+#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
++add_compile_options(-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion)
IF(NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
=====================================
debian/rules
=====================================
@@ -4,28 +4,9 @@
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-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 \
@@ -36,6 +17,3 @@ override_dh_install:
--movedev debian/tmp/usr/include/* usr/include \
--movedev debian/tmp/usr/lib/*/cmake usr/lib/$(DEB_HOST_MULTIARCH) \
debian/tmp/usr/lib/*/*.so
-
-override_dh_makeshlibs:
- dh_makeshlibs 2>&1 | tee > ../dh_makeshlibs.diff
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# false positive from the t64 transition
+libbpp-phyl-omics source: version-substvar-for-external-package Conflicts ${source:Version} libbpp-phyl-omics3t64 -> libbpp-phyl-omics3 [debian/control:38]
View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/-/compare/73eaa8b36c863780676adfc616c2f5bc43b4d53e...f0c264d18ad28b2fdafa2506f3a6d12c0064974c
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-phyl-omics/-/compare/73eaa8b36c863780676adfc616c2f5bc43b4d53e...f0c264d18ad28b2fdafa2506f3a6d12c0064974c
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