[med-svn] [Git][med-team/libbpp-seq][master] 5 commits: quiet a t64-transition related false-positive.

Michael R. Crusoe (@crusoe) gitlab at salsa.debian.org
Mon Mar 25 18:41:46 GMT 2024 


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


Commits:
eb91cd87 by Michael R. Crusoe at 2024-03-25T19:38:23+01:00
quiet a t64-transition related false-positive.

- - - - -
5aaee895 by Michael R. Crusoe at 2024-03-25T19:38:50+01:00
d/patches/spelling: forward upstream

- - - - -
35b37e8d by Michael R. Crusoe at 2024-03-25T19:39:12+01:00
d/patches/unforce-cxxflags.patch: improve and forward upstream

- - - - -
92c7db2c by Michael R. Crusoe at 2024-03-25T19:39:19+01:00
remove unused "-DBUILD_TESTING=OFF"

- - - - -
f64bc36b by Michael R. Crusoe at 2024-03-25T19:39:39+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/libbpp-seq12t64.lintian-overrides
- debian/libbpp-seq12t64.symbols.amd64
- debian/patches/spelling
- debian/patches/unforce-cxxflags.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libbpp-seq (2.4.1-12) unstable; urgency=medium
+
+  * Team upload.
+  * Silence another lintian warning
+  * d/patches/spelling: forward upstream
+  * d/patches/unforce-cxxflags.patch: improve and forward upstream.
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 25 Mar 2024 19:38:05 +0100
+
 libbpp-seq (2.4.1-11) unstable; urgency=medium
 
   [ Dann Frazier ]


=====================================
debian/libbpp-seq12t64.lintian-overrides
=====================================
@@ -1 +1,2 @@
 libbpp-seq12t64: package-name-doesnt-match-sonames libbpp-seq12
+libbpp-seq12t64: conflicts-with-version libbpp-seq12 (<< 2.4.1-11)


=====================================
debian/libbpp-seq12t64.symbols.amd64
=====================================
@@ -98,7 +98,7 @@ libbpp-seq.so.12 libbpp-seq12t64 #MINVER#
  _ZN3bpp13AAVolumeIndexD0Ev at Base 2.4.1
  _ZN3bpp13AAVolumeIndexD1Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
- _ZN3bpp13AlphabetStateC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
+ (optional)_ZN3bpp13AlphabetStateC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
  _ZN3bpp13AlphabetStateD0Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateD1Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateD2Ev at Base 2.4.1
@@ -512,6 +512,8 @@ libbpp-seq.so.12 libbpp-seq12t64 #MINVER#
  _ZN3bpp20EmptyVectorExceptionIdED0Ev at Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionIdED1Ev at Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionIdED2Ev at Base 2.4.1
+ _ZN3bpp20EmptyVectorExceptionImEC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKSt6vectorImSaImEE at Base 2.4.1-11~
+ _ZN3bpp20EmptyVectorExceptionImEC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKSt6vectorImSaImEE at Base 2.4.1-11~
  _ZN3bpp20EmptyVectorExceptionImED0Ev at Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionImED1Ev at Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionImED2Ev at Base 2.4.1
@@ -1731,17 +1733,21 @@ libbpp-seq.so.12 libbpp-seq12t64 #MINVER#
  _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_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_baseIcSaIcEED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseIcSaIcEED2Ev at Base 2.4.1
+ (optional)_ZNSt12_Vector_baseIcSaIcEED1Ev at Base 2.4.1
+ (optional)_ZNSt12_Vector_baseIcSaIcEED2Ev at Base 2.4.1
  _ZNSt12_Vector_baseIiSaIiEED1Ev at Base 2.4.1
  _ZNSt12_Vector_baseIiSaIiEED2Ev at Base 2.4.1
  _ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_ 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
+ _ZNSt5dequeIiSaIiEE13emplace_frontIJiEEEvDpOT_ at Base 2.4.1-11~
  _ZNSt5dequeIiSaIiEE17_M_push_front_auxIJRKiEEEvDpOT_ at Base 2.4.1
  _ZNSt5dequeIiSaIiEE17_M_reallocate_mapEmb at Base 2.4.1
  _ZNSt6vectorIN3bpp13BasicSequenceESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorIN3bpp13BasicSequenceESaIS1_EED1Ev at Base 2.4.1-11~
+ _ZNSt6vectorIN3bpp13BasicSequenceESaIS1_EED2Ev at Base 2.4.1-11~
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1-11~
  _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
@@ -1801,8 +1807,8 @@ libbpp-seq.so.12 libbpp-seq12t64 #MINVER#
  _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJRKiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEE6insertEN9__gnu_cxx17__normal_iteratorIPKiS1_EERS4_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEEC1ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEEC2ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
+ (optional)_ZNSt6vectorIiSaIiEEC1ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
+ (optional)_ZNSt6vectorIiSaIiEEC2ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEED1Ev at Base 2.4.1
  _ZNSt6vectorIiSaIiEED2Ev at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_default_appendEm at Base 2.4.1
@@ -1811,8 +1817,8 @@ libbpp-seq.so.12 libbpp-seq12t64 #MINVER#
  _ZNSt6vectorImSaImEE9push_backERKm 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
+ (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1
+ (optional)_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


=====================================
debian/patches/spelling
=====================================
@@ -1,5 +1,6 @@
 From: Michael R. Crusoe <crusoe at debian.org>
 Subject: fix a typo
+Forwarded: https://github.com/BioPP/bpp-seq/pull/16
 --- libbpp-seq.orig/src/Bpp/Seq/StringSequenceTools.cpp
 +++ libbpp-seq/src/Bpp/Seq/StringSequenceTools.cpp
 @@ -332,7 +332,7 @@
@@ -18,7 +19,7 @@ Subject: fix a typo
      const std::string getFormatDescription() const
      {
 -      return "Optional file comments (preceeded by ;;), sequence comments (preceeded by ;), sequence name, sequence";
-+      return "Optional file comments (pprecede by ;;), sequence comments (pprecede by ;), sequence name, sequence";
++      return "Optional file comments (preceded by ;;), sequence comments (preceded by ;), sequence name, sequence";
      }
      /** @} */
  


=====================================
debian/patches/unforce-cxxflags.patch
=====================================
@@ -1,17 +1,16 @@
 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-seq/pull/17
 
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11)
+--- libbpp-seq.orig/CMakeLists.txt
++++ libbpp-seq/CMakeLists.txt
+@@ -9,7 +9,7 @@
  project (bpp-seq 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


=====================================
debian/rules
=====================================
@@ -4,8 +4,6 @@
 
 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/-/compare/95d3fad4b8d298903d42fd6847e3254db03da6ec...f64bc36b6d2e544a4bfe407bd8647ced86627cee

-- 
View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq/-/compare/95d3fad4b8d298903d42fd6847e3254db03da6ec...f64bc36b6d2e544a4bfe407bd8647ced86627cee
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