debian/changelog

+libbpp-seq-omics (2.4.1-4) unstable; urgency=medium
+
+  * Rebuild for new version of gcc to fix symbols
+    Closes: #925737
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Trim trailing whitespace.
+
+ -- Andreas Tille <tille@debian.org>  Tue, 20 Aug 2019 18:20:38 +0200
+
 libbpp-seq-omics (2.4.1-3) unstable; urgency=medium
 
   * Rebuild for new version of gcc to fix symbols
@@ -131,4 +141,3 @@ libbpp-seq-omics (2.0.3-1) unstable; urgency=low
   * Initial release, forking from bpp-seq.
 
  -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Tue, 06 Nov 2012 14:05:00 +0100
-

debian/compat

-11

debian/control

@@ -4,11 +4,11 @@ Uploaders: Julien Dutheil <julien.dutheil@univ-montp2.fr>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                cmake,
                d-shlibs (>= 0.82),
                libbpp-seq-dev (>= 2.4.1)
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq-omics
 Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq-omics.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

debian/libbpp-seq-omics3.symbols.amd64

@@ -22,8 +22,8 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZN3bpp11MafSequenceC1ERKS0_@Base 2.4.1
  _ZN3bpp11MafSequenceD0Ev@Base 2.4.1
  _ZN3bpp11MafSequenceD1Ev@Base 2.4.1
- _ZN3bpp11VectorTools11vectorUnionINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIT_SaIS9_EERKS8_ISB_SaISB_EE@Base 2.4.1
  _ZN3bpp11VectorTools18vectorIntersectionINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIT_SaIS9_EERKSB_SD_@Base 2.4.1
+ _ZN3bpp11VectorTools6uniqueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIT_SaIS9_EERKSB_@Base 2.4.1
  _ZN3bpp12EdSymbolList11getListenerEm@Base 2.4.1
  _ZN3bpp12EdSymbolList20afterSequenceChangedERKNS_22SymbolListEditionEventE@Base 2.4.1
  _ZN3bpp12EdSymbolList20afterSequenceDeletedERKNS_23SymbolListDeletionEventE@Base 2.4.1
@@ -37,11 +37,11 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZN3bpp12EdSymbolList25beforeSequenceSubstitutedERKNS_27SymbolListSubstitutionEventE@Base 2.4.1
  _ZN3bpp12EdSymbolList7shuffleEv@Base 2.4.1
  _ZN3bpp12EdSymbolListixEm@Base 2.4.1
- _ZN3bpp12SequenceMaskC1ERKSt6vectorIbSaIbEEb@Base 2.4.1
  _ZN3bpp12SequenceMaskD0Ev@Base 2.4.1
  _ZN3bpp13AlphabetStateD0Ev@Base 2.4.1
  _ZN3bpp13AlphabetStateD1Ev@Base 2.4.1
  _ZN3bpp13BasicSequenceD0Ev@Base 2.4.1
+ _ZN3bpp13SequenceTools6subseqERKNS_8SequenceEmmRS1_@Base 2.4.1
  _ZN3bpp14LetterAlphabet13registerStateEPNS_13AlphabetStateE@Base 2.4.1
  _ZN3bpp14LetterAlphabet8setStateEmPNS_13AlphabetStateE@Base 2.4.1
  _ZN3bpp14SequenceWalkerC1ERKNS_8SequenceE@Base 2.4.1
@@ -181,7 +181,6 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZN3bpp22WindowSplitMafIteratorD0Ev@Base 2.4.1
  _ZN3bpp22WindowSplitMafIteratorD1Ev@Base 2.4.1
  _ZN3bpp23VectorSequenceContainerD2Ev@Base 2.4.1
- _ZN3bpp24AlignedSequenceContainerC1ERKS0_@Base 2.4.1
  _ZN3bpp24EntropyFilterMafIterator16nextRemovedBlockEv@Base 2.4.1
  _ZN3bpp24EntropyFilterMafIterator20analyseCurrentBlock_Ev@Base 2.4.1
  _ZN3bpp24EntropyFilterMafIteratorD0Ev@Base 2.4.1
@@ -323,6 +322,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZN3bpp9MafParserD0Ev@Base 2.4.1
  _ZN3bpp9MafParserD1Ev@Base 2.4.1
  _ZN3bpp9TextTools2toIjEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
+ _ZN3bpp9TextTools8toStringIcEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 2.4.1
  _ZN3bpp9TextTools8toStringIdEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 2.4.1
  _ZN3bpp9TextTools8toStringIiEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 2.4.1
  _ZN3bpp9TextTools8toStringIjEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_@Base 2.4.1
@@ -340,6 +340,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNK3bpp11MafSequence4stopEv@Base 2.4.1
  _ZNK3bpp11MafSequence5cloneEv@Base 2.4.1
  _ZNK3bpp11MafSequence5startEv@Base 2.4.1
+ _ZNK3bpp11MafSequence8getRangeEb@Base 2.4.1
  _ZNK3bpp12EdSymbolList10getContentEv@Base 2.4.1
  _ZNK3bpp12EdSymbolList11getAlphabetEv@Base 2.4.1
  _ZNK3bpp12EdSymbolList11getListenerEm@Base 2.4.1
@@ -462,7 +463,6 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNK3bpp6NumberIiE8toStringB5cxx11Ev@Base 2.4.1
  _ZNK3bpp6NumberIjE5cloneEv@Base 2.4.1
  _ZNK3bpp6NumberIjE8toStringB5cxx11Ev@Base 2.4.1
- _ZNK3bpp8MafBlock11getSequenceEm@Base 2.4.1
  _ZNK3bpp8MafBlock14getDescriptionB5cxx11Ev@Base 2.4.1
  _ZNK3bpp8MafBlock21getSequenceForSpeciesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
  _ZNK3bpp8MafBlock5cloneEv@Base 2.4.1
@@ -476,7 +476,6 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNK3bpp8SeqRange5cloneEv@Base 2.4.1
  _ZNK3bpp8SeqRange9getStrandEv@Base 2.4.1
  _ZNK3bpp9BppDouble5cloneEv@Base 2.4.1
- _ZNKSt15_Deque_iteratorISt6vectorIbSaIbEERS2_PS2_EplEl@Base 2.4.1
  _ZNKSt5ctypeIcE8do_widenEc@Base 2.4.1
  _ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED1Ev@Base 2.4.1
  _ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED2Ev@Base 2.4.1
@@ -486,9 +485,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv@Base 2.4.1
  _ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv@Base 2.4.1
  _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv@Base 2.4.1
- _ZNSt20__uninitialized_copyILb0EE13__uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS9_SaIS9_EEEEPS9_EET0_T_SI_SH_@Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_@Base 2.4.1
- _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_@Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.1
  _ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base 2.4.1
@@ -497,6 +494,7 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_@Base 2.4.1
  _ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE19_M_destroy_data_auxESt15_Deque_iteratorIS2_RS2_PS2_ES8_@Base 2.4.1
  _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_@Base 2.4.1
+ _ZNSt5dequeImSaImEE17_M_push_front_auxIJmEEEvDpOT_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_@Base 2.4.1
@@ -507,7 +505,6 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNSt6vectorIPKN3bpp11MafSequenceESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp13AlphabetStateESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp13SiteContainerESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
- _ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp18SymbolListListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
@@ -523,21 +520,14 @@ libbpp-seq-omics.so.3 libbpp-seq-omics3 #MINVER#
  _ZNSt6vectorIS_IiSaIiEESaIS1_EED2Ev@Base 2.4.1
  _ZNSt6vectorIS_ImSaImEESaIS1_EED1Ev@Base 2.4.1
  _ZNSt6vectorIS_ImSaImEESaIS1_EED2Ev@Base 2.4.1
- _ZNSt6vectorIbSaIbEEC1ERKS1_@Base 2.4.1
- _ZNSt6vectorIbSaIbEEC2ERKS1_@Base 2.4.1
  _ZNSt6vectorIiSaIiEE17_M_default_appendEm@Base 2.4.1
  _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJRKiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_@Base 2.4.1
- _ZNSt6vectorIiSaIiEEC1ERKS1_@Base 2.4.1
- _ZNSt6vectorIiSaIiEEC2ERKS1_@Base 2.4.1
  _ZNSt6vectorIiSaIiEEaSERKS1_@Base 2.4.1
  _ZNSt6vectorIjSaIjEE14_M_fill_assignEmRKj@Base 2.4.1
  _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base 2.4.1
  _ZNSt6vectorImSaImEE12emplace_backIJmEEEvDpOT_@Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_@Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_@Base 2.4.1
- _ZNSt6vectorImSaImEE9push_backERKm@Base 2.4.1
- _ZNSt6vectorImSaImEEC1ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_@Base 2.4.1
- _ZNSt6vectorImSaImEEC2ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_@Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIN9__gnu_cxx17__normal_iteratorIPcS4_EEEEvT_SA_St20forward_iterator_tag@Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag@Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag@Base 2.4.1