debian/changelog

-libbpp-popgen (2.4.1-2) UNRELEASED; urgency=medium
+libbpp-popgen (2.4.1-2) unstable; urgency=medium
 
   [ Jelmer Vernooij]
   * Use secure copyright file specification URI.
   * Trim trailing whitespace.
 
   [ Julien Dutheil ]
-  * Standards-Version: 4.3.0
   * d-shlibs (>= 0.82)
   * Easier amd64 symbol file management
 
- -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Mon, 11 Mar 2019 08:54:44 +0200
+  [ Andreas Tille ]
+  * Rebuild for new version of gcc to fix symbols
+    Closes: #925733
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+  * Set upstream metadata fields: Contact, Name.
+
+ -- Andreas Tille <tille@debian.org>  Wed, 21 Aug 2019 08:20:43 +0200
 
 libbpp-popgen (2.4.1-1) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -4,12 +4,12 @@ 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-core-dev (>= 2.4.1),
                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-popgen
 Vcs-Git: https://salsa.debian.org/med-team/libbpp-popgen.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

debian/libbpp-popgen8.symbols.amd64

@@ -61,6 +61,7 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZN3bpp11PopgenlibIOD1Ev@Base 2.4.1
  _ZN3bpp11PopgenlibIOD2Ev@Base 2.4.1
  _ZN3bpp11VectorTools3covIddEET0_RKSt6vectorIT_SaIS4_EES8_b@Base 2.4.1
+ _ZN3bpp11VectorTools6uniqueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIT_SaIS9_EERKSB_@Base 2.4.1
  _ZN3bpp12AnalyzedLoci12setLocusInfoEmRKNS_9LocusInfoE@Base 2.4.1
  _ZN3bpp12AnalyzedLoci24addAlleleInfoByLocusNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_10AlleleInfoE@Base 2.4.1
  _ZN3bpp12AnalyzedLoci28addAlleleInfoByLocusPositionEmRKNS_10AlleleInfoE@Base 2.4.1
@@ -73,7 +74,6 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZN3bpp12DataSetTools12buildDataSetERKNS_24OrderedSequenceContainerE@Base 2.4.1
  _ZN3bpp12DataSetTools12buildDataSetERKNS_29PolymorphismSequenceContainerE@Base 2.4.1
  _ZN3bpp13BasicSequenceD0Ev@Base 2.4.1
- _ZN3bpp13BasicSequenceD1Ev@Base 2.4.1
  _ZN3bpp14DistanceMatrix8asMatrixEv@Base 2.4.1
  _ZN3bpp14DistanceMatrixD0Ev@Base 2.4.1
  _ZN3bpp14DistanceMatrixD1Ev@Base 2.4.1
@@ -99,7 +99,6 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZN3bpp15StringTokenizerD0Ev@Base 2.4.1
  _ZN3bpp15StringTokenizerD1Ev@Base 2.4.1
  _ZN3bpp15StringTokenizerD2Ev@Base 2.4.1
- _ZN3bpp15SymbolListTools9getCountsERKNS_10SymbolListERSt3mapIimSt4lessIiESaISt4pairIKimEEE@Base 2.4.1
  _ZN3bpp15VectorExceptionINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEED0Ev@Base 2.4.1
  _ZN3bpp15VectorExceptionINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEED1Ev@Base 2.4.1
  _ZN3bpp15VectorExceptionINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEED2Ev@Base 2.4.1
@@ -268,6 +267,8 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZN3bpp19VectorSiteContainerclEmm@Base 2.4.1
  _ZN3bpp20AbstractOutputStream12setPrecisionEi@Base 2.4.1
  _ZN3bpp20AbstractOutputStream24enableScientificNotationEb@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
@@ -528,7 +529,6 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZN3bpp4Site11setPositionEi@Base 2.4.1
  _ZN3bpp4SiteD0Ev@Base 2.4.1
  _ZN3bpp4SiteD1Ev@Base 2.4.1
- _ZN3bpp5FastaC1Ejbbb@Base 2.4.1
  _ZN3bpp5FastaD1Ev@Base 2.4.1
  _ZN3bpp5Group10setGroupIdEm@Base 2.4.1
  _ZN3bpp5Group12setGroupNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE@Base 2.4.1
@@ -904,21 +904,18 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZNK3bpp9RowMatrixIdEclEmm@Base 2.4.1
  _ZNKSt5ctypeIcE8do_widenEc@Base 2.4.1
  _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_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
  _ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv@Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS5_ESaISt4pairIKS5_dEEEixEOS5_@Base 2.4.1
- _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixEOi@Base 2.4.1
- _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixERS3_@Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev@Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev@Base 2.4.1
  _ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_@Base 2.4.1
  _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base 2.4.1
+ _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED1Ev@Base 2.4.1
+ _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED2Ev@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_@Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm@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
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE9push_backERKS5_@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
@@ -957,7 +954,6 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _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
  _ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE@Base 2.4.1
- _ZNSt6vectorImSaImEE9push_backERKm@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
@@ -988,6 +984,7 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E@Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_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_treeIiSt4pairIKidESt10_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_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_@Base 2.4.1
  _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
@@ -1025,7 +1022,6 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElNS0_5__ops15_Iter_less_iterEEvT_S9_T0_T1_@Base 2.4.1
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_@Base 2.4.1
  _ZSt5fixedRSt8ios_base@Base 2.4.1
- _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops16_Iter_equals_valIKmEEET_SB_SB_T0_St26random_access_iterator_tag@Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_@Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_@Base 2.4.1
  _ZTIN3bpp10AlleleInfoE@Base 2.4.1
@@ -1292,7 +1288,6 @@ libbpp-popgen.so.8 libbpp-popgen8 #MINVER#
  _ZTv0_n24_N3bpp11PopgenlibIOD0Ev@Base 2.4.1
  _ZTv0_n24_N3bpp11PopgenlibIOD1Ev@Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev@Base 2.4.1
- _ZTv0_n24_N3bpp13BasicSequenceD1Ev@Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD0Ev@Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD1Ev@Base 2.4.1
  _ZTv0_n24_N3bpp15BasicAlleleInfoD0Ev@Base 2.4.1

debian/upstream/metadata

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