[med-svn] [Git][med-team/libseqlib][master] 6 commits: Adapt symbols to new version of gcc
Andreas Tille
gitlab at salsa.debian.org
Tue Aug 20 14:56:23 BST 2019
Andreas Tille pushed to branch master at Debian Med / libseqlib
Commits:
61786a9a by Andreas Tille at 2019-08-20T13:36:53Z
Adapt symbols to new version of gcc
- - - - -
6ec29306 by Andreas Tille at 2019-08-20T13:38:52Z
debhelper-compat 12
- - - - -
d108db2a by Andreas Tille at 2019-08-20T13:38:55Z
Standards-Version: 4.4.0
- - - - -
e3c58c6e by Andreas Tille at 2019-08-20T13:45:19Z
libseqlib-dev: Depends: libssw-dev
- - - - -
aafd74f2 by Andreas Tille at 2019-08-20T13:52:07Z
Add lintian-overrides for libraries not found by pkgconfig
- - - - -
0309b8af by Andreas Tille at 2019-08-20T13:53:51Z
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/libseqlib-dev.lintian-overrides
- debian/libseqlib1.symbols
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+libseqlib (1.1.2+dfsg-4) unstable; urgency=medium
+
+ * Adapt symbols to new version of gcc
+ Closes: #925759
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * libseqlib-dev: Depends: libssw-dev
+ * Add lintian-overrides for libraries not found by pkgconfig
+
+ -- Andreas Tille <tille at debian.org> Tue, 20 Aug 2019 15:52:14 +0200
+
libseqlib (1.1.2+dfsg-3) unstable; urgency=medium
* Adapt symbols to new version of gcc
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
d-shlibs,
pkg-config,
libhts-private-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
libbwa-dev (>= 0.7.15-3),
libjsoncpp-dev,
libssw-dev
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/libseqlib
Vcs-Git: https://salsa.debian.org/med-team/libseqlib.git
Homepage: https://github.com/walaj/SeqLib
@@ -46,7 +46,9 @@ Depends: libseqlib1 (= ${binary:Version}),
libhts-private-dev,
libjsoncpp-dev,
libbwa-dev,
- libfml-dev
+ libfml-dev,
+ libssw-dev,
+ zlib1g-dev
Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
C++ API and command line tool that provides a rapid and user-friendly
interface to BAM/SAM/CRAM files, global sequence alignment operations
=====================================
debian/libseqlib-dev.lintian-overrides
=====================================
@@ -0,0 +1,5 @@
+# Libraries are specified in Depends
+libseqlib-dev: pkg-config-references-unknown-shared-library usr/lib/*/pkgconfig/libseqlib.pc -lfml (line 9)
+libseqlib-dev: pkg-config-references-unknown-shared-library usr/lib/*/pkgconfig/libseqlib.pc -lbwa (line 9)
+libseqlib-dev: pkg-config-references-unknown-shared-library usr/lib/*/pkgconfig/libseqlib.pc -lssw (line 9)
+libseqlib-dev: pkg-config-references-unknown-shared-library usr/lib/*/pkgconfig/libseqlib.pc -lz (line 9)
=====================================
debian/libseqlib1.symbols
=====================================
@@ -96,6 +96,8 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZN6SeqLib6Filter10ReadFilterD1Ev at Base 1.1.1+dfsg
_ZN6SeqLib6Filter10ReadFilterD2Ev at Base 1.1.1+dfsg
_ZN6SeqLib6Filter11AhoCorasick12TrieFromFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.1.1+dfsg
+ _ZN6SeqLib6Filter11AhoCorasickD1Ev at Base 1.1.2+dfsg
+ _ZN6SeqLib6Filter11AhoCorasickD2Ev at Base 1.1.2+dfsg
_ZN6SeqLib6Filter12AbstractRule12addMotifRuleERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb at Base 1.1.1+dfsg
_ZN6SeqLib6Filter12AbstractRule12parseSeqLineERKN4Json5ValueE at Base 1.1.1+dfsg
_ZN6SeqLib6Filter12AbstractRule12parseSubLineERKN4Json5ValueE at Base 1.1.1+dfsg
@@ -220,7 +222,6 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZNK6SeqLib9BamRecord11CountNBasesEv at Base 1.1.1+dfsg
_ZNK6SeqLib9BamRecord11PositionEndEv at Base 1.1.2+dfsg
_ZNK6SeqLib9BamRecord14GetSmartIntTagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.1.1+dfsg
- _ZNK6SeqLib9BamRecord14ParseReadGroupB5cxx11Ev at Base 1.1.2+dfsg
_ZNK6SeqLib9BamRecord15AsGenomicRegionEv at Base 1.1.1+dfsg
_ZNK6SeqLib9BamRecord15PairOrientationEv at Base 1.1.2+dfsg
_ZNK6SeqLib9BamRecord15PositionEndMateEv at Base 1.1.2+dfsg
@@ -243,20 +244,18 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZNKSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE5countERS7_ at Base 1.1.1+dfsg
_ZNKSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEE19_M_find_before_nodeEmRS7_m at Base 1.1.1+dfsg
_ZNKSt5ctypeIcE8do_widenEc at Base 1.1.1+dfsg
- _ZNKSt6vectorIN6SeqLib13GenomicRegionESaIS1_EE12_M_check_lenEmPKc at Base 1.1.2+dfsg
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE10_M_emplaceIJS6_IS5_S9_EEEES6_INSC_14_Node_iteratorISA_Lb0ELb1EEEbESt17integral_constantIbLb1EEDpOT_ at Base 1.1.1+dfsg
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSC_10_Hash_nodeISA_Lb1EEEm at Base 1.1.2+dfsg
+ _ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE9_M_rehashEmRKm at Base 1.1.2+dfsg
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEE10_M_emplaceIJS6_IS5_iEEEES6_INSA_14_Node_iteratorIS8_Lb0ELb1EEEbESt17integral_constantIbLb1EEDpOT_ at Base 1.1.1+dfsg
- _ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSA_10_Hash_nodeIS8_Lb1EEEm at Base 1.1.2+dfsg
+ _ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEE9_M_rehashEmRKm at Base 1.1.2+dfsg
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEED1Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEED2Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE10_M_emplaceIJS0_IiS4_EEEES0_INS7_14_Node_iteratorIS5_Lb0ELb0EEEbESt17integral_constantIbLb1EEDpOT_ at Base 1.1.2+dfsg
- _ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNS7_10_Hash_nodeIS5_Lb0EEEm at Base 1.1.2+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE5clearEv at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE9_M_rehashEmRKm at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEED1Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEED2Ev at Base 1.1.1+dfsg
- _ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSA_10_Hash_nodeIS8_Lb0EEEm at Base 1.1.2+dfsg
_ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEE9_M_rehashEmRKm at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEED1Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEED2Ev at Base 1.1.1+dfsg
@@ -325,6 +324,7 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED2Ev at Base 1.1.1+dfsg
_ZNSt5dequeIPN12aho_corasick5stateIcEESaIS3_EE16_M_push_back_auxIJRKS3_EEEvDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.1+dfsg
+ _ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.2+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.1.1+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE9push_backERKS2_ at Base 1.1.1+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EEC1ERKS4_ at Base 1.1.1+dfsg
@@ -354,6 +354,7 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZNSt6vectorIPN6SeqLib11PlottedReadESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIPcSaIS0_EE12emplace_backIJS0_EEEvDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIPcSaIS0_EE17_M_realloc_insertIJS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_ at Base 1.1.1+dfsg
+ _ZNSt6vectorIcSaIcEE17_M_realloc_insertIJRKcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_ at Base 1.1.2+dfsg
_ZNSt6vectorIdSaIdEE12emplace_backIJdEEEvDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIdSaIdEE17_M_realloc_insertIJdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIiSaIiEE12emplace_backIJiEEEvDpOT_ at Base 1.1.1+dfsg
@@ -374,8 +375,6 @@ libseqlib.so.1 libseqlib1 #MINVER#
_ZNSt8_Rb_treeIcSt4pairIKcSt10unique_ptrIN12aho_corasick5stateIcEESt14default_deleteIS5_EEESt10_Select1stIS9_ESt4lessIcESaIS9_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS9_ERS1_ at Base 1.1.1+dfsg
_ZNSt8_Rb_treeIcSt4pairIKcSt10unique_ptrIN12aho_corasick5stateIcEESt14default_deleteIS5_EEESt10_Select1stIS9_ESt4lessIcESaIS9_EE8_M_eraseEPSt13_Rb_tree_nodeIS9_E at Base 1.1.1+dfsg
_ZNSt8__detail9_Map_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS6_N6SeqLib4_BamEESaISB_ENS_10_Select1stESt8equal_toIS6_ESt4hashIS6_ENS_18_Mod_range_hashingENS_20_Default_ranged_hashENS_20_Prime_rehash_policyENS_17_Hashtable_traitsILb1ELb0ELb1EEELb1EEixERS8_ at Base 1.1.1+dfsg
- _ZSt10__pop_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_SK_RT0_ at Base 1.1.2+dfsg
- _ZSt10__pop_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_SK_RT0_ at Base 1.1.2+dfsg
_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_RT0_ at Base 1.1.1+dfsg
_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_RT0_ at Base 1.1.1+dfsg
_ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN6SeqLib11PlottedReadESt6vectorIS3_SaIS3_EEEENS0_5__ops15_Iter_less_iterEEvT_SB_RT0_ at Base 1.1.1+dfsg
View it on GitLab: https://salsa.debian.org/med-team/libseqlib/compare/e7f4c66447a3c22a08dce101f64ece0c9145cbb5...0309b8af0f1f49cf0d847cfc40ed564f1c60b92d
--
View it on GitLab: https://salsa.debian.org/med-team/libseqlib/compare/e7f4c66447a3c22a08dce101f64ece0c9145cbb5...0309b8af0f1f49cf0d847cfc40ed564f1c60b92d
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