[med-svn] [Git][med-team/libbpp-popgen][master] 4 commits: d/patches/unforce-cxxflags.patch: merge upstream's flags, and forward the patch to them.

Michael R. Crusoe (@crusoe) gitlab at salsa.debian.org
Mon Mar 25 23:48:02 GMT 2024 


Michael R. Crusoe pushed to branch master at Debian Med / libbpp-popgen


Commits:
1f2c1c8b by Michael R. Crusoe at 2024-03-25T14:23:33+01:00
d/patches/unforce-cxxflags.patch: merge upstream's flags, and forward the patch to them.

- - - - -
5911ee81 by Michael R. Crusoe at 2024-03-25T14:23:33+01:00
Forwarded the spelling patch upstream.

- - - - -
13aea93f by Michael R. Crusoe at 2024-03-25T14:23:34+01:00
Silence a false-positive Lintian error from the t64 transition.

- - - - -
fd30a638 by Michael R. Crusoe at 2024-03-25T16:12:32+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/libbpp-popgen8t64.lintian-overrides
- debian/libbpp-popgen8t64.symbols.amd64
- debian/patches/spelling
- debian/patches/unforce-cxxflags.patch
- + debian/source/lintian-overrides


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,13 @@
-libbpp-popgen (2.4.1-10) UNRELEASED; urgency=medium
+libbpp-popgen (2.4.1-10) unstable; urgency=medium
 
   * Team upload.
   * d/patches/spelling: fix typos.
+  * d/patches/unforce-cxxflags.patch: merge upstream's flags, and
+    forward the patch to them.
+  * Forwarded the spelling patch upstream.
+  * Silence a false-positive Lintian error from the t64 transition.
 
- -- Michael R. Crusoe <crusoe at debian.org>  Mon, 14 Aug 2023 15:33:50 +0200
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 25 Mar 2024 16:12:32 +0100
 
 libbpp-popgen (2.4.1-9.1) unstable; urgency=medium
 


=====================================
debian/libbpp-popgen8t64.lintian-overrides
=====================================
@@ -1 +1,2 @@
 libbpp-popgen8t64: package-name-doesnt-match-sonames libbpp-popgen8
+libbpp-popgen8t64: conflicts-with-version libbpp-popgen8 (<< 2.4.1-10)


=====================================
debian/libbpp-popgen8t64.symbols.amd64
=====================================
@@ -78,7 +78,6 @@ libbpp-popgen.so.8 libbpp-popgen8t64 #MINVER#
  _ZN3bpp12DataSetTools12buildDataSetERKNS_24OrderedSequenceContainerE at Base 2.4.1
  _ZN3bpp12DataSetTools12buildDataSetERKNS_29PolymorphismSequenceContainerE at Base 2.4.1
  _ZN3bpp13BasicSequenceD0Ev at Base 2.4.1
- _ZN3bpp13BasicSequenceD1Ev at Base 2.4.1
  _ZN3bpp13SiteContainerD2Ev at Base 2.4.1
  _ZN3bpp14DistanceMatrix8asMatrixEv at Base 2.4.1
  _ZN3bpp14DistanceMatrixD0Ev at Base 2.4.1
@@ -938,6 +937,7 @@ libbpp-popgen.so.8 libbpp-popgen8t64 #MINVER#
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
  _ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1-10~
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm 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
@@ -971,6 +971,7 @@ libbpp-popgen.so.8 libbpp-popgen8t64 #MINVER#
  _ZNSt6vectorISt3setINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4lessIS6_ESaIS6_EESaISA_EE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorISt3setINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4lessIS6_ESaIS6_EESaISA_EED1Ev at Base 2.4.1
  _ZNSt6vectorISt3setINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4lessIS6_ESaIS6_EESaISA_EED2Ev at Base 2.4.1
+ _ZNSt6vectorIbSaIbEE13_M_insert_auxESt13_Bit_iteratorb at Base 2.4.1-10~
  _ZNSt6vectorIbSaIbEE14_M_fill_insertESt13_Bit_iteratormb 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
@@ -986,8 +987,6 @@ libbpp-popgen.so.8 libbpp-popgen8t64 #MINVER#
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEED1Ev at Base 2.4.1
  _ZNSt6vectorImSaImEED2Ev 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
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 2.4.1
@@ -1273,7 +1272,6 @@ libbpp-popgen.so.8 libbpp-popgen8t64 #MINVER#
  _ZTv0_n24_N3bpp11PopgenlibIOD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp11PopgenlibIOD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
- _ZTv0_n24_N3bpp13BasicSequenceD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp15BasicAlleleInfoD0Ev at Base 2.4.1


=====================================
debian/patches/spelling
=====================================
@@ -1,5 +1,6 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: fix spelling typos
+Forwarded: https://github.com/BioPP/bpp-popgen/pull/6
 --- libbpp-popgen.orig/src/Bpp/PopGen/DataSet/DataSet.cpp
 +++ libbpp-popgen/src/Bpp/PopGen/DataSet/DataSet.cpp
 @@ -388,7 +388,7 @@


=====================================
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
+Subject: Do not override user-provided CXX flags
+Forwarded: https://github.com/BioPP/bpp-popgen/pull/7
 
 --- 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/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# false positive from the t64 transition
+libbpp-popgen source: version-substvar-for-external-package Conflicts ${source:Version} libbpp-popgen8t64 -> libbpp-popgen8 [debian/control:38]



View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/-/compare/be3f1bb0c25b9ac515edfccba55abd0def1bca47...fd30a638017a4d36f264d3de3892022bed834613

-- 
View it on GitLab: https://salsa.debian.org/med-team/libbpp-popgen/-/compare/be3f1bb0c25b9ac515edfccba55abd0def1bca47...fd30a638017a4d36f264d3de3892022bed834613
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