[med-svn] [Git][med-team/libgenome][master] 11 commits: routine-update: Standards-Version: 4.5.0
Andreas Tille
gitlab at salsa.debian.org
Thu Jul 23 14:07:10 BST 2020
Andreas Tille pushed to branch master at Debian Med / libgenome
Commits:
d569bafb by Andreas Tille at 2020-07-23T14:46:19+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
aea8a1cf by Andreas Tille at 2020-07-23T14:46:19+02:00
routine-update: debhelper-compat 13
- - - - -
0bfcd02b by Andreas Tille at 2020-07-23T14:47:44+02:00
routine-update: Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
e8b84d76 by Andreas Tille at 2020-07-23T14:47:44+02:00
routine-update: Remove trailing whitespace in debian/control
- - - - -
4931af77 by Andreas Tille at 2020-07-23T14:47:45+02:00
routine-update: Add salsa-ci file
- - - - -
6887d1cb by Andreas Tille at 2020-07-23T14:47:45+02:00
routine-update: Rules-Requires-Root: no
- - - - -
744add82 by Andreas Tille at 2020-07-23T14:47:47+02:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
6053e22b by Andreas Tille at 2020-07-23T14:47:47+02:00
debian/copyright: use spaces rather than tabs to start continuation lines..
Changes-By: lintian-brush
Fixes: lintian: tab-in-license-text
See-also: https://lintian.debian.org/tags/tab-in-license-text.html
- - - - -
4b61d6b6 by Andreas Tille at 2020-07-23T14:52:45+02:00
Remove libGenome.la from build to make dh_missing happy
- - - - -
c948a653 by Andreas Tille at 2020-07-23T14:59:08+02:00
Update symbols for gcc-10
- - - - -
3c10ca2e by Andreas Tille at 2020-07-23T15:00:57+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/libgenome0.symbols.amd64
- debian/rules
- + debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+libgenome (1.3.11+svn20110227.4616-3) unstable; urgency=medium
+
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
+ update)
+ * Remove trailing whitespace in debian/control (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Trim trailing whitespace.
+ * debian/copyright: use spaces rather than tabs to start continuation lines.
+ * Remove libGenome.la from build to make dh_missing happy
+ * Update symbols for gcc-10
+ Closes: #957442
+
+ -- Andreas Tille <tille at debian.org> Thu, 23 Jul 2020 14:59:20 +0200
+
libgenome (1.3.11+svn20110227.4616-2) unstable; urgency=medium
* Update symbols for GCC 8 and make them amd64-only (Closes: #905566)
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,12 +3,13 @@ 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 (= 13),
d-shlibs (>= 0.61)
-Standards-Version: 4.1.5
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/libgenome
Vcs-Git: https://salsa.debian.org/med-team/libgenome.git
Homepage: https://sourceforge.net/projects/libgenome/
+Rules-Requires-Root: no
Package: libgenome-dev
Architecture: any
@@ -22,9 +23,9 @@ Description: toolkit for developing bioinformatic related software (devel)
libGenome is a freely available toolkit for developing bioinformatic related
software in C++. It is intended to take the hassle out of performing common
tasks on genetic sequence and annotation data.
- .
+ .
Among other things, libGenome can help you:
- .
+ .
* Read and write Multi-FastA format files
* Read and write GenBank flat file database entries
* Append, chop, truncate, reverse, complement, translate, and otherwise
@@ -48,9 +49,9 @@ Description: toolkit for developing bioinformatic related software
libGenome is a freely available toolkit for developing bioinformatic related
software in C++. It is intended to take the hassle out of performing common
tasks on genetic sequence and annotation data.
- .
+ .
Among other things, libGenome can help you:
- .
+ .
* Read and write Multi-FastA format files
* Read and write GenBank flat file database entries
* Append, chop, truncate, reverse, complement, translate, and otherwise
=====================================
debian/copyright
=====================================
@@ -5,9 +5,9 @@ Source: http://libgenome.cvs.sourceforge.net/viewvc/libgenome/
Files: *
Copyright: © 2003-2013 Aaron Darling <darling at cs.wisc.edu>,
- Robert Mau <mau at genome.wisc.edu>,
- Nicole T. Perna <perna at ahabs.wisc.edu>,
- Frederick R. Blattner <fred at genome.wisc.edu>
+ Robert Mau <mau at genome.wisc.edu>,
+ Nicole T. Perna <perna at ahabs.wisc.edu>,
+ Frederick R. Blattner <fred at genome.wisc.edu>
License: GPL-2+
Files: debian/*
=====================================
debian/libgenome0.symbols.amd64
=====================================
@@ -620,7 +620,14 @@ libGenome.so.0 libgenome0 #MINVER#
_ZNK6genome9gnFeature5CloneEv at Base 1.3.11+svn20110227.4616
_ZNKSt5ctypeIcE8do_widenEc at Base 1.3.11+svn20110227.4616
_ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 1.3.11+svn20110227.4616
+ _ZNSt12_Vector_baseIPN6genome12gnFileContigESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+ _ZNSt12_Vector_baseIPN6genome12gnFileContigESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
+ _ZNSt12_Vector_baseIPN6genome13gnBaseFeatureESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+ _ZNSt12_Vector_baseIPN6genome13gnBaseFeatureESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
+ _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+ _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIN6genome10gnLocationESaIS1_EE17_M_realloc_insertIJRKS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIN6genome10gnLocationESaIS1_EED1Ev at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIN6genome10gnLocationESaIS1_EED2Ev at Base 1.3.11+svn20110227.4616
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
@@ -630,20 +637,18 @@ libGenome.so.0 libgenome0 #MINVER#
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS5_S7_EE at Base 1.3.11+svn20110227.4616
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 1.3.11+svn20110227.4616
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 1.3.11+svn20110227.4616
(optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
(optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS2_S4_EERS7_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE13_M_insert_auxIS2_EEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
(optional)_ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE13_M_insert_auxIS2_EEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
@@ -653,19 +658,13 @@ libGenome.so.0 libgenome0 #MINVER#
_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt6vectorIySaIyEE17_M_realloc_insertIJyEEEvN9__gnu_cxx17__normal_iteratorIPyS1_EEDpOT_ at Base 1.3.11+svn20110227.4616
_ZNSt7__cxx1110_List_baseINS_12basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
+ _ZNSt7__cxx1110_List_baseIPKN6genome12gnBaseFilterESaIS4_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
(optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
- _ZNSt7__cxx114listIPKN6genome12gnBaseFilterESaIS4_EE18_M_assign_dispatchISt20_List_const_iteratorIS4_EEEvT_SA_St12__false_type at Base 1.3.11+svn20110227.4616
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE16_M_insert_uniqueISB_EES6_ISt17_Rb_tree_iteratorISB_EbEOT_ at Base 1.3.11+svn20110227.4616
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE20_Reuse_or_alloc_nodeclIRKS8_EEPSt13_Rb_tree_nodeIS8_EOT_ at Base 1.3.11+svn20110227.4616
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 1.3.11+svn20110227.4616
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE7_M_copyINSE_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS8_EPKSI_PSt18_Rb_tree_node_baseRT_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EEaSERKSE_ at Base 1.3.11+svn20110227.4616
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_ at Base 1.3.11+svn20110227.4616
_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EES5_RKS8_ at Base 1.3.11+svn20110227.4616
_ZTIN6genome10gnBaseSpecE at Base 1.3.11+svn20110227.4616
_ZTIN6genome10gnLocationE at Base 1.3.11+svn20110227.4616
=====================================
debian/rules
=====================================
@@ -16,10 +16,12 @@ override_dh_install:
--movedev debian/tmp/usr/include/* usr/include \
--movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
debian/tmp/usr/lib/*/*.so
+ find debian -name libGenome.la -delete
override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo 'Disable test since some header (gnDNXSource.h) seems to be missing.'
+endif
get-orig-source:
. debian/get-orig-source
-
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
View it on GitLab: https://salsa.debian.org/med-team/libgenome/-/compare/1834fedd8e18e3cabebd156c80fcbd406bb5c3da...3c10ca2e18d1221150181a59de6bc622a41b04fd
--
View it on GitLab: https://salsa.debian.org/med-team/libgenome/-/compare/1834fedd8e18e3cabebd156c80fcbd406bb5c3da...3c10ca2e18d1221150181a59de6bc622a41b04fd
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