debian/changelog

+libbpp-seq (2.4.1-4) unstable; urgency=medium
+
+  * Rebuild for new version of gcc to fix symbols
+    Closes: #925736
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Set upstream metadata fields: Contact, Name.
+
+ -- Andreas Tille <tille@debian.org>  Tue, 20 Aug 2019 16:07:58 +0200
+
 libbpp-seq (2.4.1-3) unstable; urgency=medium
 
   * Rebuild for new version of gcc to fix symbols

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 (>= 0.80),
                libbpp-core-dev (>= 2.4.1)
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq
 Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

debian/libbpp-seq12.symbols.amd64

@@ -10,7 +10,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp10MultiRangeImED2Ev@Base 2.4.1
  _ZN3bpp10NexusTools14getNextCommandERSiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_b@Base 2.4.1
  _ZN3bpp10NexusTools21getNextNonCommentLineB5cxx11ERSi@Base 2.4.1
- _ZN3bpp11AAMassIndexC1Ev@Base 2.4.1
  _ZN3bpp11AAMassIndexD0Ev@Base 2.4.1
  _ZN3bpp11AAMassIndexD1Ev@Base 2.4.1
  _ZN3bpp11GeneticCodeD2Ev@Base 2.4.1
@@ -172,6 +171,7 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp13SequenceTools4RNY_E@Base 2.4.1
  _ZN3bpp13SequenceTools6getCDSERNS_8SequenceERKNS_11GeneticCodeEbbbb@Base 2.4.1
  _ZN3bpp13SequenceTools6invertERNS_8SequenceE@Base 2.4.1
+ _ZN3bpp13SequenceTools6subseqERKNS_8SequenceEmmRS1_@Base 2.4.1
  _ZN3bpp13SequenceTools7DNARep_E@Base 2.4.1
  _ZN3bpp13SequenceTools7RNARep_E@Base 2.4.1
  _ZN3bpp13SequenceTools7transc_E@Base 2.4.1
@@ -300,7 +300,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp15SequenceQuality25beforeSequenceSubstitutedERKNS_27SymbolListSubstitutionEventE@Base 2.4.1
  _ZN3bpp15SequenceQuality4initERKNS_8SequenceE@Base 2.4.1
  _ZN3bpp15SequenceQuality5mergeERKNS_18SequenceAnnotationE@Base 2.4.1
- _ZN3bpp15SequenceQuality9setScoresEmRKSt6vectorIiSaIiEE@Base 2.4.1
  _ZN3bpp15SequenceQualityD0Ev@Base 2.4.1
  _ZN3bpp15SequenceQualityD1Ev@Base 2.4.1
  _ZN3bpp15StringTokenizer9nextTokenB5cxx11Ev@Base 2.4.1
@@ -328,6 +327,7 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp16AbstractAlphabet8getStateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
  _ZN3bpp16AbstractAlphabet8getStateEi@Base 2.4.1
  _ZN3bpp16AbstractAlphabet8setStateEmPNS_13AlphabetStateE@Base 2.4.1
+ _ZN3bpp16AbstractAlphabetC2ERKS0_@Base 2.4.1
  _ZN3bpp16AbstractAlphabetD2Ev@Base 2.4.1
  _ZN3bpp16AbstractCoreSite11setPositionEi@Base 2.4.1
  _ZN3bpp16ApplicationTools12getParameterIjEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS9_S8_EEES2_SA_bi@Base 2.4.1
@@ -507,6 +507,8 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp20EmptyVectorExceptionIdED0Ev@Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionIdED1Ev@Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionIdED2Ev@Base 2.4.1
+ _ZN3bpp20EmptyVectorExceptionImEC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKSt6vectorImSaImEE@Base 2.4.1
+ _ZN3bpp20EmptyVectorExceptionImEC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKSt6vectorImSaImEE@Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionImED0Ev@Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionImED1Ev@Base 2.4.1
  _ZN3bpp20EmptyVectorExceptionImED2Ev@Base 2.4.1
@@ -682,8 +684,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp24AlignedSequenceContainer7addSiteERKNS_4SiteEmb@Base 2.4.1
  _ZN3bpp24AlignedSequenceContainer7addSiteERKNS_4SiteEmib@Base 2.4.1
  _ZN3bpp24AlignedSequenceContainer7setSiteEmRKNS_4SiteEb@Base 2.4.1
- _ZN3bpp24AlignedSequenceContainerC1EPKNS_8AlphabetE@Base 2.4.1
- _ZN3bpp24AlignedSequenceContainerC1ERKNS_13SiteContainerE@Base 2.4.1
  _ZN3bpp24AlignedSequenceContainerC1ERKNS_24OrderedSequenceContainerE@Base 2.4.1
  _ZN3bpp24AlignedSequenceContainerC2ERKNS_24OrderedSequenceContainerE@Base 2.4.1
  _ZN3bpp24AlignedSequenceContainerD0Ev@Base 2.4.1
@@ -741,7 +741,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp25AbstractSequenceContainer11setCommentsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIS6_SaIS6_EE@Base 2.4.1
  _ZN3bpp25AbstractSequenceContainer18setGeneralCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE@Base 2.4.1
  _ZN3bpp25AbstractSequenceContainer21deleteGeneralCommentsEv@Base 2.4.1
- _ZN3bpp25AbstractSequenceContainerC2ERKNS_17SequenceContainerE@Base 2.4.1
  _ZN3bpp25AbstractSequenceContainerD2Ev@Base 2.4.1
  _ZN3bpp25AlphabetMismatchExceptionC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_8AlphabetESB_@Base 2.4.1
  _ZN3bpp25AlphabetMismatchExceptionC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_8AlphabetESB_@Base 2.4.1
@@ -903,7 +902,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp3RNYD1Ev@Base 2.4.1
  _ZN3bpp4DCSED0Ev@Base 2.4.1
  _ZN3bpp4DCSED1Ev@Base 2.4.1
- _ZN3bpp4MaseC1Ejb@Base 2.4.1
  _ZN3bpp4MaseD0Ev@Base 2.4.1
  _ZN3bpp4MaseD1Ev@Base 2.4.1
  _ZN3bpp4Site11setPositionEi@Base 2.4.1
@@ -931,7 +929,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp5Fasta9FileIndexD0Ev@Base 2.4.1
  _ZN3bpp5Fasta9FileIndexD1Ev@Base 2.4.1
  _ZN3bpp5Fasta9FileIndexD2Ev@Base 2.4.1
- _ZN3bpp5FastaC1Ejbbb@Base 2.4.1
  _ZN3bpp5FastaD0Ev@Base 2.4.1
  _ZN3bpp5FastaD1Ev@Base 2.4.1
  _ZN3bpp5RangeImED0Ev@Base 2.4.1
@@ -942,7 +939,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp5RangeImEplERKm@Base 2.4.1
  _ZN3bpp6MatrixIcE6equalsERKS1_d@Base 2.4.1
  _ZN3bpp6MatrixIdE6equalsERKS1_d@Base 2.4.1
- _ZN3bpp6PhylipC1EbbjbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
  _ZN3bpp6PhylipD0Ev@Base 2.4.1
  _ZN3bpp6PhylipD1Ev@Base 2.4.1
  _ZN3bpp7ClustalD0Ev@Base 2.4.1
@@ -977,8 +973,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZN3bpp9RowMatrixIcED2Ev@Base 2.4.1
  _ZN3bpp9RowMatrixIcEclEmm@Base 2.4.1
  _ZN3bpp9RowMatrixIdE6resizeEmm@Base 2.4.1
- _ZN3bpp9RowMatrixIdEC1Emm@Base 2.4.1
- _ZN3bpp9RowMatrixIdEC2Emm@Base 2.4.1
  _ZN3bpp9RowMatrixIdED0Ev@Base 2.4.1
  _ZN3bpp9RowMatrixIdED1Ev@Base 2.4.1
  _ZN3bpp9RowMatrixIdED2Ev@Base 2.4.1
@@ -1709,8 +1703,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZNKSt5ctypeIcE8do_widenEc@Base 2.4.1
  _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE4findERS7_@Base 2.4.1
  _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE4findERS7_@Base 2.4.1
- _ZNSt11_Deque_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.1
- _ZNSt11_Deque_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.1
  _ZNSt11_Deque_baseIiSaIiEE17_M_initialize_mapEm@Base 2.4.1
  _ZNSt11_Deque_baseIiSaIiEED1Ev@Base 2.4.1
  _ZNSt11_Deque_baseIiSaIiEED2Ev@Base 2.4.1
@@ -1732,9 +1724,7 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS5_S7_EERSA_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS5_S7_EE@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC1ERKS7_@Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC1EmRKS6_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC2ERKS7_@Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC2EmRKS6_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_@Base 2.4.1
@@ -1760,13 +1750,9 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZNSt6vectorIPN3bpp8SequenceESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp8SequenceESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPN3bpp8SequenceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE@Base 2.4.1
- _ZNSt6vectorIPN3bpp8SequenceESaIS2_EEC1EmRKS3_@Base 2.4.1
- _ZNSt6vectorIPN3bpp8SequenceESaIS2_EEC2EmRKS3_@Base 2.4.1
  _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EE17_M_default_appendEm@Base 2.4.1
  _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EE17_M_realloc_insertIJS8_EEEvN9__gnu_cxx17__normal_iteratorIPS8_SA_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS8_SA_EE@Base 2.4.1
- _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EEC1EmRKS9_@Base 2.4.1
- _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EEC2EmRKS9_@Base 2.4.1
  _ZNSt6vectorIS_IcSaIcEESaIS1_EE17_M_default_appendEm@Base 2.4.1
  _ZNSt6vectorIS_IcSaIcEESaIS1_EED1Ev@Base 2.4.1
  _ZNSt6vectorIS_IcSaIcEESaIS1_EED2Ev@Base 2.4.1
@@ -1791,8 +1777,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZNSt6vectorIiSaIiEE6insertEN9__gnu_cxx17__normal_iteratorIPKiS1_EERS4_@Base 2.4.1
  _ZNSt6vectorIiSaIiEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPiS1_EE@Base 2.4.1
  _ZNSt6vectorIiSaIiEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPiS1_EES5_@Base 2.4.1
- _ZNSt6vectorIiSaIiEEC1ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_@Base 2.4.1
- _ZNSt6vectorIiSaIiEEC2ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_@Base 2.4.1
  _ZNSt6vectorIiSaIiEEaSERKS1_@Base 2.4.1
  _ZNSt6vectorImSaImEE12emplace_backIJmEEEvDpOT_@Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_default_appendEm@Base 2.4.1
@@ -1866,6 +1850,7 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E@Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_@Base 2.4.1
@@ -1880,6 +1865,7 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EEaSERKS8_@Base 2.4.1
+ _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_@Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_@Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_@Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E@Base 2.4.1
@@ -1892,7 +1878,6 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEENS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_@Base 2.4.1
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_@Base 2.4.1
  _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops16_Iter_equals_valIKS7_EEET_SH_SH_T0_St26random_access_iterator_tag@Base 2.4.1
- _ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_@Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_@Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_@Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_@Base 2.4.1
@@ -2460,6 +2445,7 @@ libbpp-seq.so.12 libbpp-seq12 #MINVER#
  _ZTVN3bpp7ClustalE@Base 2.4.1
  _ZTVN3bpp7GenBankE@Base 2.4.1
  _ZTVN3bpp8BLOSUM50E@Base 2.4.1
+ _ZTVN3bpp8ClonableE@Base 2.4.1
  _ZTVN3bpp8DNAToRNAE@Base 2.4.1
  _ZTVN3bpp8PhredPhdE@Base 2.4.1
  _ZTVN3bpp9PhredPolyE@Base 2.4.1

debian/upstream/metadata

+Name: Bpp-Seq
+Contact: Julien Yann Dutheil <julien.dutheil@univ-montp2.fr>