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 
+  * 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
@@ -19,7 +19,7 @@ Architecture: any
 Section: libdevel
 Depends: libbpp-popgen8 (= ${binary:Version}),
          ${misc:Depends},
-	 ${devlibs:Depends},
+         ${devlibs:Depends},
          libbpp-core-dev (>= 2.4.1),
          libbpp-seq-dev (>= 2.4.1)
 Description: Bio++ Population Genetics library development files

debian/copyright

@@ -19,7 +19,7 @@ License: GPL-2+
     it under the terms of the GNU General Public License as published by
     the Free Software Foundation; either version 2 of the License, or
     (at your option) any later version.
- . 
+ .
     This package is distributed in the hope that it will be useful,
     but WITHOUT ANY WARRANTY; without even the implied warranty of
     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
@@ -159,7 +159,7 @@ License: CeCILL
  .
  The purpose of the Agreement is the grant by the Licensor to the
  Licensee of a non-exclusive, transferable and worldwide license for the
- Software as set forth in Article 5 hereinafter for the whole term of the 
+ Software as set forth in Article 5 hereinafter for the whole term of the
  protection granted by the rights over said Software.
  .
  .
@@ -179,7 +179,7 @@ License: CeCILL
  characteristics of the Software, to the limited warranty, and to the
  fact that its use is restricted to experienced users has been provided
  to the Licensee prior to its acceptance as set forth in Article 3.1
- hereinabove, and the Licensee hereby acknowledges that it has read and 
+ hereinabove, and the Licensee hereby acknowledges that it has read and
  understood it.
  .
  .
@@ -427,7 +427,7 @@ License: CeCILL
  9.3 The Licensee acknowledges that the Software is supplied "as is" by
  the Licensor without any other express or tacit warranty, other than
  that provided for in Article 9.2 and, in particular, without any warranty
- as to its commercial value, its secured, safe, innovative or relevant 
+ as to its commercial value, its secured, safe, innovative or relevant
  nature.
  .
  Specifically, the Licensor does not warrant that the Software is free

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>