[med-svn] [Git][med-team/libbpp-core][master] 4 commits: Forward the gcc11 patch upstream.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Mar 25 17:39:21 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / libbpp-core
Commits:
fdb868bf by Michael R. Crusoe at 2024-03-25T16:50:48+01:00
Forward the gcc11 patch upstream.
- - - - -
df4edba0 by Michael R. Crusoe at 2024-03-25T17:11:47+01:00
d/patches/unforce-cxxflags.patch: merge with upstream's flags; especially -std=c++11; forward our patch to upstream.
- - - - -
ccdd92e9 by Michael R. Crusoe at 2024-03-25T17:18:47+01:00
Silence some false-positive Lintian errors and warnings related to the t64 transition.
- - - - -
6e0da471 by Michael R. Crusoe at 2024-03-25T17:28:19+01:00
routine-update: Ready to upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/libbpp-core4t64.lintian-overrides
- debian/libbpp-core4t64.symbols.amd64
- debian/patches/gcc11.patch
- debian/patches/unforce-cxxflags.patch
- + debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,14 @@
-libbpp-core (2.4.1-12) UNRELEASED; urgency=medium
+libbpp-core (2.4.1-12) unstable; urgency=medium
* Team upload.
* d/control: use ${devlibs:Depends} for the -dev package
+ * Forward the gcc11 patch upstream.
+ * d/patches/unforce-cxxflags.patch: merge with upstream's flags;
+ especially -std=c++11; forward our patch to upstream.
+ * Silence some false-positive Lintian errors and warnings related to
+ the t64 transition.
- -- Michael R. Crusoe <crusoe at debian.org> Sun, 13 Aug 2023 13:48:47 +0200
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 25 Mar 2024 17:28:19 +0100
libbpp-core (2.4.1-11.1) unstable; urgency=medium
=====================================
debian/libbpp-core4t64.lintian-overrides
=====================================
@@ -1 +1,2 @@
libbpp-core4t64: package-name-doesnt-match-sonames libbpp-core4
+libbpp-core4t64: conflicts-with-version libbpp-core4 (<< 2.4.1-12)
=====================================
debian/libbpp-core4t64.symbols.amd64
=====================================
@@ -2155,6 +2155,7 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_ at Base 2.4.1
_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixERS9_ at Base 2.4.1
_ZNSt3mapImSt6vectorIdSaIdEESt4lessImESaISt4pairIKmS2_EEEixEOm at Base 2.4.1
+ _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1-12~
_ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_eraseESt15_Deque_iteratorIS5_RS5_PS5_E at Base 2.4.1
_ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
_ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
@@ -2170,6 +2171,8 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt6vectorIN3bpp8RGBColorESaIS1_EED1Ev at Base 2.4.1
_ZNSt6vectorIN3bpp8RGBColorESaIS1_EED2Ev at Base 2.4.1
_ZNSt6vectorIN3bpp9StatTools7PValue_ESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJN9__gnu_cxx17__normal_iteratorIPKcS5_EESD_EEEvDpOT_ at Base 2.4.1-12~
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1-12~
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm at Base 2.4.1
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJN9__gnu_cxx17__normal_iteratorIPKcS5_EESD_EEEvNSA_IPS5_S7_EEDpOT_ 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
@@ -2216,6 +2219,7 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt6vectorISt10shared_ptrIN3bpp8OperatorEESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.1
_ZNSt6vectorISt10shared_ptrIN3bpp8OperatorEESaIS3_EED1Ev at Base 2.4.1
_ZNSt6vectorISt10shared_ptrIN3bpp8OperatorEESaIS3_EED2Ev at Base 2.4.1
+ _ZNSt6vectorISt10shared_ptrIN3bpp9ParameterEESaIS3_EE12emplace_backIJS3_EEEvDpOT_ at Base 2.4.1-12~
_ZNSt6vectorISt10shared_ptrIN3bpp9ParameterEESaIS3_EE17_M_default_appendEm at Base 2.4.1
_ZNSt6vectorISt10shared_ptrIN3bpp9ParameterEESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.1
_ZNSt6vectorISt10shared_ptrIN3bpp9ParameterEESaIS3_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS3_S5_EE at Base 2.4.1
@@ -2223,6 +2227,8 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt6vectorISt10shared_ptrIsESaIS1_EE17_M_realloc_insertIJRKS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
_ZNSt6vectorISt10shared_ptrIsESaIS1_EED1Ev at Base 2.4.1
_ZNSt6vectorISt10shared_ptrIsESaIS1_EED2Ev at Base 2.4.1
+ _ZNSt6vectorIbSaIbEE13_M_insert_auxESt13_Bit_iteratorb at Base 2.4.1-12~
+ _ZNSt6vectorIdSaIdEE12emplace_backIJdEEEvDpOT_ at Base 2.4.1-12~
_ZNSt6vectorIdSaIdEE17_M_default_appendEm at Base 2.4.1
_ZNSt6vectorIdSaIdEE17_M_realloc_insertIJRKdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
_ZNSt6vectorIdSaIdEE17_M_realloc_insertIJdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
@@ -2233,6 +2239,7 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
_ZNSt6vectorIiSaIiEED1Ev at Base 2.4.1
_ZNSt6vectorIiSaIiEED2Ev at Base 2.4.1
+ _ZNSt6vectorIjSaIjEE12emplace_backIJjEEEvDpOT_ at Base 2.4.1-12~
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
_ZNSt6vectorIjSaIjEED1Ev at Base 2.4.1
@@ -2242,8 +2249,6 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt6vectorImSaImEED1Ev at Base 2.4.1
_ZNSt6vectorImSaImEED2Ev at Base 2.4.1
_ZNSt6vectorItSaItEE17_M_realloc_insertIJRKtEEEvN9__gnu_cxx17__normal_iteratorIPtS1_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
_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
@@ -2267,7 +2272,7 @@ libbpp-core.so.4 libbpp-core4t64 #MINVER#
_ZNSt8_Rb_treeISt10shared_ptrIsESt4pairIKS1_jESt10_Select1stIS4_ESt4lessIS1_ESaIS4_EE24_M_get_insert_unique_posERS3_ at Base 2.4.1
_ZNSt8_Rb_treeISt10shared_ptrIsESt4pairIKS1_jESt10_Select1stIS4_ESt4lessIS1_ESaIS4_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS4_ERS3_ at Base 2.4.1
_ZNSt8_Rb_treeISt4pairIjjES1_St9_IdentityIS1_ESt4lessIS1_ESaIS1_EE4findERKS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIjSt4pairIKjjESt10_Select1stIS2_ESt4lessIjESaIS2_EE22_M_emplace_hint_uniqueIJS0_IjjEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIjSt4pairIKjjESt10_Select1stIS2_ESt4lessIjESaIS2_EE17_M_emplace_uniqueIJS0_IjjEEEES0_ISt17_Rb_tree_iteratorIS2_EbEDpOT_ at Base 2.4.1-12~
_ZSt10scientificRSt8ios_base at Base 2.4.1
_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEEliNS0_5__ops15_Iter_comp_iterIPFbiiEEEEvT_T0_SD_T1_T2_ at Base 2.4.1
_ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_SF_T0_ at Base 2.4.1
=====================================
debian/patches/gcc11.patch
=====================================
@@ -1,5 +1,6 @@
-Description: Including limits lib to fix gcc-11 FTBFS
-Author: Nilesh Patra <nilesh at debian.org>
+From: Nilesh Patra <nilesh at debian.org>
+Subject: Including limits header to fix gcc-11 FTBFS
+Forwarded: https://github.com/BioPP/bpp-core/pull/28
Last-Update: 2021-04-15
--- a/src/Bpp/Graph/GlobalGraph.cpp
+++ b/src/Bpp/Graph/GlobalGraph.cpp
=====================================
debian/patches/unforce-cxxflags.patch
=====================================
@@ -1,17 +1,38 @@
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 the user-provided CXX flags
+Forwarded: https://github.com/BioPP/bpp-core/pull/29
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
+--- libbpp-core.orig/CMakeLists.txt
++++ libbpp-core/CMakeLists.txt
@@ -9,7 +9,7 @@
project (bpp-core CXX)
# 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
+--- libbpp-core.orig/cmake/doc-cmake-for-developpers.cmake
++++ libbpp-core/cmake/doc-cmake-for-developpers.cmake
+@@ -23,7 +23,7 @@
+ # - the CMake package
+ # Do not change it unless there is a good reason...
+
+-set (CMAKE_CXX_FLAGS "std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
++add_compile_options(std=c++11 -Wall -Weffc++ -Wshadow -Wconversion)
+ # Define compile options to be used for all C++ targets.
+ # NOTES for the future:
+ # -> CMake >= 2.8.12 adds per target COMPILE_OPTIONS by using target_compile_options (<target> [PRIVATE|PUBLIC] <opt1> ... <optN>)
+--- libbpp-core.orig/cmake/project-template-for-users.cmake
++++ libbpp-core/cmake/project-template-for-users.cmake
+@@ -21,7 +21,7 @@
+
+ # Bio++ REQUIRES using at least the C++11 standard.
+ # This line specifies options passed to the compiler (you can add your own).
+-set (CMAKE_CXX_FLAGS "-std=c++11")
++add_compile_options(-std=c++11)
+
+ # Tells CMake to create a binary from dummy.cpp (replace with your .cpp file(s))
+ add_executable (myprogram dummy.cpp other.cpp)
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# false-positive related to the t64 transition
+libbpp-core source: version-substvar-for-external-package Conflicts ${source:Version} libbpp-core4t64 -> libbpp-core4 [debian/control:36]
View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/-/compare/4ddbe526864fe254ebd88c18c42acf652519a66b...6e0da471eeae8f3b02d4dc8cd37d3085e569d2c3
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-core/-/compare/4ddbe526864fe254ebd88c18c42acf652519a66b...6e0da471eeae8f3b02d4dc8cd37d3085e569d2c3
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