[med-svn] [Git][med-team/libbpp-seq-omics][master] 5 commits: d/patches/unforce-cxxflags.patch: merge with upstream's flag,
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Mar 25 23:51:52 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / libbpp-seq-omics
Commits:
40b6d830 by Michael R. Crusoe at 2024-03-25T16:32:51+01:00
d/patches/unforce-cxxflags.patch: merge with upstream's flag,
especially -std=c++11; forward our patch to upstream.
- - - - -
a8a72094 by Michael R. Crusoe at 2024-03-25T16:38:56+01:00
Silence some false-positive Lintian errors and overrides related to the t64 transition.
- - - - -
fd10cb1b by Michael R. Crusoe at 2024-03-25T16:48:00+01:00
Add patch to fix a typo.
- - - - -
fab46eb3 by Michael R. Crusoe at 2024-03-25T18:55:34+01:00
remove unused BUILD_TESTING=off
- - - - -
6b70e2dc by Michael R. Crusoe at 2024-03-25T19:02:40+01:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/libbpp-seq-omics3t64.lintian-overrides
- debian/libbpp-seq-omics3t64.symbols.amd64
- debian/patches/series
- + debian/patches/spelling
- debian/patches/unforce-cxxflags.patch
- debian/rules
- + debian/source/lintian-overrides
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+libbpp-seq-omics (2.4.1-11) unstable; urgency=medium
+
+ * Team upload.
+ * d/patches/unforce-cxxflags.patch: merge with upstream's flag,
+ especially -std=c++11; forward our patch to upstream.
+ * Silence some false-positive Lintian errors and overrides related to
+ the t64 transition.
+ * Add patch to fix a typo.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 25 Mar 2024 19:02:40 +0100
+
libbpp-seq-omics (2.4.1-10.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/libbpp-seq-omics3t64.lintian-overrides
=====================================
@@ -1 +1,2 @@
libbpp-seq-omics3t64: package-name-doesnt-match-sonames libbpp-seq-omics3
+libbpp-seq-omics3t64: conflicts-with-version libbpp-seq-omics3 (<< 2.4.1-11)
=====================================
debian/libbpp-seq-omics3t64.symbols.amd64
=====================================
@@ -1,4 +1,5 @@
libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
+* Build-Depends-Package: libbpp-seq-omics-dev
_ZN3bpp10BppIntegerD0Ev at Base 2.4.1
_ZN3bpp10BppIntegerD1Ev at Base 2.4.1
_ZN3bpp10MultiRangeImE10restrictToERKNS_5RangeImEE at Base 2.4.1
@@ -40,6 +41,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
_ZN3bpp12EdSymbolList25beforeSequenceSubstitutedERKNS_27SymbolListSubstitutionEventE at Base 2.4.1
_ZN3bpp12EdSymbolList7shuffleEv at Base 2.4.1
_ZN3bpp12EdSymbolListixEm at Base 2.4.1
+ _ZN3bpp12SequenceMaskC1ERKSt6vectorIbSaIbEEb at Base 2.4.1-11~
_ZN3bpp12SequenceMaskD0Ev at Base 2.4.1
_ZN3bpp13AlphabetStateD0Ev at Base 2.4.1
_ZN3bpp13AlphabetStateD1Ev at Base 2.4.1
@@ -58,6 +60,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
_ZN3bpp15StringTokenizerD0Ev at Base 2.4.1
_ZN3bpp15StringTokenizerD1Ev at Base 2.4.1
_ZN3bpp15StringTokenizerD2Ev at Base 2.4.1
+ _ZN3bpp15SymbolListTools9getCountsERKNS_10SymbolListERSt3mapIimSt4lessIiESaISt4pairIKimEEE at Base 2.4.1-11~
_ZN3bpp16AbstractAlphabetC2ERKS0_ at Base 2.4.1
_ZN3bpp16AbstractAlphabetD2Ev at Base 2.4.1
_ZN3bpp16BadCharExceptionD0Ev at Base 2.4.1
@@ -487,8 +490,6 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
_ZNSt10unique_ptrIN3bpp18SequenceFeatureSetESt14default_deleteIS1_EED2Ev at Base 2.4.1
_ZNSt10unique_ptrIN3bpp8MafBlockESt14default_deleteIS1_EED1Ev at Base 2.4.1
_ZNSt10unique_ptrIN3bpp8MafBlockESt14default_deleteIS1_EED2Ev at Base 2.4.1
- _ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED1Ev at Base 2.4.1
- _ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED2Ev at Base 2.4.1
_ZNSt11_Deque_baseImSaImEE17_M_initialize_mapEm at Base 2.4.1
_ZNSt11_Deque_baseImSaImEED1Ev at Base 2.4.1
_ZNSt11_Deque_baseImSaImEED2Ev at Base 2.4.1
@@ -508,6 +509,8 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
_ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
_ZNSt5dequeISt6vectorIbSaIbEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
_ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
+ _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_ 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_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
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC1ERKS7_ at Base 2.4.1
@@ -549,12 +552,8 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
_ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
_ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorImSaImEEC1ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_ at Base 2.4.1
- _ZNSt6vectorImSaImEEC2ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_ 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
@@ -574,6 +573,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3t64 #MINVER#
_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
_ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1
_ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_ at Base 2.4.1
+ _ZSteqIbSaIbEEbRKSt6vectorIT_T0_ES6_ at Base 2.4.1-11~
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_ at Base 2.4.1
_ZTIN3bpp10BppIntegerE at Base 2.4.1
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
+spelling
unforce-cxxflags.patch
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,14 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Fix spelling typo
+Forwarded: https://github.com/BioPP/bpp-seq-omics/pull/13
+--- libbpp-seq-omics.orig/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp
++++ libbpp-seq-omics/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp
+@@ -119,7 +119,7 @@
+ } else if (s == 10) {
+ qualStr += "F";
+ } else {
+- throw Exception("MafAlignmentParser::writeBlock. Unsuported score value: " + TextTools::toString(s));
++ throw Exception("MafAlignmentParser::writeBlock. Unsupported score value: " + TextTools::toString(s));
+ }
+ }
+ out << qualStr << endl;
=====================================
debian/patches/unforce-cxxflags.patch
=====================================
@@ -1,17 +1,15 @@
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
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11)
+Subject: Do not override user-provided CXX flags
+Forwarded: https://github.com/BioPP/bpp-seq-omics/pull/12
+--- libbpp-seq-omics.orig/CMakeLists.txt
++++ libbpp-seq-omics/CMakeLists.txt
+@@ -9,7 +9,7 @@
project (bpp-seq-omics 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 $@
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# false-positive from the t64 transition
+libbpp-seq-omics source: version-substvar-for-external-package Conflicts ${source:Version} libbpp-seq-omics3t64 -> libbpp-seq-omics3 [debian/control:37]
View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/-/compare/4e7e625d42cedf236148583df4af9e0252a2f7e2...6b70e2dcdd0ab180768ef8cc05306f6cec7c98af
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/-/compare/4e7e625d42cedf236148583df4af9e0252a2f7e2...6b70e2dcdd0ab180768ef8cc05306f6cec7c98af
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