[med-svn] [seqan2] 01/03: Merge branch 'debian-experimental'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Jan 14 17:54:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository seqan2.
commit 7b71c29c583d23da2e52430f8940041713910d5f
Merge: 0ea7aaa aa1ade6
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Sat Jan 14 03:53:50 2017 -0800
Merge branch 'debian-experimental'
CHANGELOG.rst | 99 ++
CMakeLists.txt | 7 +
CONTRIBUTING.rst | 7 +-
README.rst | 5 +-
apps/alf/CMakeLists.txt | 6 +-
apps/bs_tools/CMakeLists.txt | 10 +-
apps/bs_tools/casbar.cpp | 1 +
apps/bs_tools/casbar.h | 14 +-
apps/bs_tools/casbar_score.h | 2 +
apps/bs_tools/tests/run_tests.py | 6 +-
apps/dfi/CMakeLists.txt | 6 +-
apps/dfi/dfi.cpp | 2 +
apps/fiona/CMakeLists.txt | 12 +-
apps/fiona/compute_gain.cpp | 4 +-
apps/fiona/error_rate_from_sam.cpp | 4 +-
apps/fiona/fiona.cpp | 10 +-
apps/fiona/index_qgram_parallel.h | 44 +-
apps/fx_tools/CMakeLists.txt | 6 +-
apps/gustaf/CMakeLists.txt | 6 +-
apps/gustaf/msplazer.h | 6 +-
apps/gustaf/msplazer_algorithms.h | 2 +-
apps/gustaf/msplazer_main.h | 2 +-
apps/gustaf/msplazer_out.h | 6 +-
apps/gustaf/tests/pairedEnd_st1_l30.stdout | 2 +-
apps/gustaf/tests/reference2_st1_l30.stdout | 2 +-
apps/gustaf/tests/st1_l30.stdout | 2 +-
apps/gustaf/tests/st1_l30_gth3.stdout | 2 +-
apps/gustaf/tests/st1_l30_ith5.stdout | 2 +-
apps/gustaf/tests/st1_l30_m.stdout | 2 +-
apps/gustaf/tests/st2_l100.stdout | 2 +-
apps/insegt/CMakeLists.txt | 6 +-
apps/mason2/CMakeLists.txt | 10 +-
apps/mason2/README.mason_splicing | 2 +-
apps/mason2/mason_options.cpp | 8 +-
apps/micro_razers/CMakeLists.txt | 6 +-
apps/ngs_roi/CMakeLists.txt | 8 +-
apps/ngs_roi/project_spliced.h | 2 +-
apps/pair_align/CMakeLists.txt | 6 +-
apps/pair_align/pair_align.cpp | 2 +-
apps/param_chooser/CMakeLists.txt | 6 +-
apps/rabema/CMakeLists.txt | 8 +-
apps/rabema/README | 4 +-
apps/rabema/rabema_build_gold_standard.cpp | 2 +-
apps/rabema/rabema_evaluate.cpp | 10 +-
apps/rabema/ref_id_mapping.h | 2 +-
apps/razers/CMakeLists.txt | 6 +-
apps/razers/razers.h | 2 +-
apps/razers/razers_matepairs.h | 2 +-
apps/razers/readSimulator.h | 2 +
apps/razers3/CMakeLists.txt | 12 +-
apps/razers3/razers.cpp | 2 +-
apps/razers3/razers.h | 2 +-
apps/razers3/razers_match_filter.h | 8 +-
apps/razers3/razers_matepairs.h | 2 +-
apps/razers3/razers_matepairs_parallel.h | 2 +-
apps/razers3/razers_parallel.h | 2 +-
apps/razers3/readSimulator.h | 2 +
apps/rep_sep/CMakeLists.txt | 6 +-
apps/rep_sep/rep_sep.cpp | 2 +-
apps/sak/CMakeLists.txt | 6 +-
apps/sak/README | 2 +-
apps/sam2matrix/CMakeLists.txt | 6 +-
apps/samcat/CMakeLists.txt | 10 +-
apps/samcat/README | 2 +-
apps/samcat/README.md | 2 +-
apps/samcat/samcat.cpp | 2 +-
apps/searchjoin/CMakeLists.txt | 8 +-
apps/seqan_tcoffee/CMakeLists.txt | 6 +-
apps/seqcons2/CMakeLists.txt | 8 +-
apps/seqcons2/seqcons.cpp | 2 +-
apps/seqcons2/seqcons_options.cpp | 4 +-
apps/seqcons2/seqcons_options.h | 2 +-
.../tests/alns1.contig_consensus.sam.stderr | 2 +-
.../tests/alns1.contig_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.nop.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.nop.txt.stderr | 2 +-
.../tests/alns1.overlap_consensus.sam.stderr | 2 +-
.../tests/alns1.overlap_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.pos_consensus.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.pos_consensus.txt.stderr | 2 +-
apps/seqcons2/tests/alns1.realign.sam.stderr | 2 +-
apps/seqcons2/tests/alns1.realign.txt.stderr | 2 +-
apps/seqcons2/tests/seqs1.align_consensus.stderr | 2 +-
apps/seqcons2/tests/seqs1.nop.stderr | 2 +-
apps/seqcons2/tests/seqs1.overlap_consensus.stderr | 2 +-
.../tests/seqs2.align_consensus.sam.stderr | 2 +-
.../tests/seqs2.align_consensus.txt.stderr | 2 +-
apps/sgip/CMakeLists.txt | 6 +-
apps/sgip/sgip.cpp | 24 +-
apps/snp_store/CMakeLists.txt | 10 +-
apps/splazers/CMakeLists.txt | 6 +-
apps/splazers/readSimulator.h | 2 +
apps/stellar/CMakeLists.txt | 6 +-
apps/stellar/README | 2 +-
apps/stellar/stellar.cpp | 2 +-
apps/tree_recon/CMakeLists.txt | 6 +-
apps/yara/CMakeLists.txt | 12 +-
debian/changelog | 52 +
debian/control | 6 +-
debian/libseqan2-dev.install | 6 +-
debian/patches/pthread-linking | 34 -
debian/patches/series | 5 +-
debian/patches/skip-seqan-revision | 26 +
debian/patches/spelling.patch | 1155 --------------------
debian/rules | 32 +-
demos/tutorial/basics/strings.cpp | 4 +-
demos/tutorial/blast_io/write_assignment.cpp | 2 +-
.../index_iterators/UNUSED_index_assignment3.cpp | 26 -
.../UNUSED_index_assignment3.cpp.stdout | 16 -
.../index_iterators/index_assignment4.cpp.stdout | 14 -
.../index_iterators/index_bidirectional_search.cpp | 36 +
.../index_bidirectional_search.cpp.stdout | 4 +
.../index_iterators/iterator_assignment2.cpp | 2 +-
.../index_iterators/iterator_solution2.cpp | 2 +-
.../index_iterators/iterator_solution2.cpp.stdout | 31 +-
...ndex_assignment4.cpp => iterator_solution3.cpp} | 2 +-
.../index_iterators/iterator_solution3.cpp.stdout | 17 +
demos/tutorial/indices/fm_index.cpp | 29 +
demos/tutorial/indices/fm_index.stdout | 0
.../tutorial_file_io/solution3.cpp | 4 +-
dox/CMakeLists.txt | 47 +-
dox/dox_only.sh | 4 +-
dox/images/docs2/position_vs_id.png | Bin 0 -> 175321 bytes
dox/pages/index.dox | 2 +-
dox/pages/language_entities.dox | 2 +-
dox/pages/suffix_array.dox | 2 +-
dox/run.sh | 4 +-
include/seqan/align.h | 2 +-
include/seqan/align/align_interface_wrapper.h | 2 +-
include/seqan/align/dp_align_simd_helper.h | 2 +-
include/seqan/align/gaps_base.h | 2 +-
include/seqan/align/gaps_iterator_array.h | 4 +-
include/seqan/align/gaps_iterator_base.h | 2 +-
.../align/global_alignment_myers_hirschberg_impl.h | 1 -
include/seqan/align/global_alignment_unbanded.h | 4 +-
include/seqan/align/local_alignment_unbanded.h | 2 +-
include/seqan/arg_parse.h | 5 +
include/seqan/arg_parse/arg_parse_argument.h | 189 +++-
include/seqan/arg_parse/arg_parse_ctd_support.h | 34 +-
include/seqan/arg_parse/arg_parse_doc.h | 229 +++-
include/seqan/arg_parse/arg_parse_option.h | 14 +-
include/seqan/arg_parse/arg_parse_parse.h | 25 +-
include/seqan/arg_parse/arg_parse_type_support.h | 62 +-
include/seqan/arg_parse/arg_parse_version_check.h | 474 ++++++++
include/seqan/arg_parse/argument_parser.h | 41 +-
include/seqan/arg_parse/tool_doc.h | 61 +-
include/seqan/bam_io/bam_alignment_record_util.h | 2 +-
include/seqan/bam_io/bam_file.h | 7 +-
include/seqan/bam_io/bam_header_record.h | 4 +-
include/seqan/bam_io/cigar.h | 19 +-
include/seqan/bam_io/write_bam.h | 51 +-
include/seqan/bam_io/write_sam.h | 14 +-
include/seqan/basic/aggregate_concept.h | 5 +-
include/seqan/basic/basic_allocator.h | 1 -
include/seqan/basic/basic_simd_vector.h | 48 +-
include/seqan/basic/fundamental_tags.h | 56 +
include/seqan/basic/iterator_zip.h | 2 +-
include/seqan/basic/metaprogramming_enable_if.h | 8 +-
include/seqan/basic/metaprogramming_type.h | 2 +-
include/seqan/basic/tuple_bit_compressed.h | 38 +-
include/seqan/blast/blast_record.h | 99 +-
include/seqan/blast/blast_report_out.h | 18 +-
include/seqan/blast/blast_tabular.h | 144 +--
include/seqan/blast/blast_tabular_in.h | 74 +-
include/seqan/blast/blast_tabular_out.h | 145 ++-
include/seqan/file/file_page.h | 42 +-
include/seqan/file/string_external.h | 200 ++--
include/seqan/find/find_base.h | 4 +-
include/seqan/find/find_begin.h | 2 +-
include/seqan/gff_io/gff_io_base.h | 3 +
include/seqan/graph_algorithms.h | 2 +
.../seqan/graph_algorithms/depth_first_search.h | 101 +-
.../strongly_connected_compnents.h | 29 +
include/seqan/graph_align/graph_impl_align.h | 12 +
include/seqan/graph_msa/graph_align_tcoffee_io.h | 2 +-
.../seqan/graph_msa/graph_align_tcoffee_library.h | 71 +-
include/seqan/graph_types/graph_impl_automaton.h | 55 +
include/seqan/graph_types/graph_impl_directed.h | 64 +-
include/seqan/graph_types/graph_impl_hmm.h | 12 +
include/seqan/graph_types/graph_impl_tree.h | 12 +
include/seqan/graph_types/graph_impl_undirected.h | 50 +
include/seqan/graph_types/graph_interface.h | 14 +
include/seqan/index/find_index.h | 1 +
include/seqan/index/index_bidirectional.h | 41 +-
include/seqan/index/index_bidirectional_stree.h | 153 ++-
include/seqan/index/index_bifm.h | 2 +
include/seqan/index/index_bifm_stree.h | 4 +-
include/seqan/index/index_esa_algs_multi.h | 22 +-
include/seqan/index/index_esa_base.h | 5 +-
include/seqan/index/index_esa_stree.h | 2 +-
include/seqan/index/index_fm.h | 64 +-
include/seqan/index/index_fm_dox.h | 2 +-
include/seqan/index/index_fm_lf_table.h | 36 +-
.../seqan/index/index_fm_rank_dictionary_base.h | 10 +-
.../seqan/index/index_fm_rank_dictionary_levels.h | 727 ++++++++----
include/seqan/index/index_fm_rank_dictionary_wt.h | 21 +-
include/seqan/index/index_sa_qsort.h | 5 +-
include/seqan/index/index_sa_stree.h | 4 +-
include/seqan/index/index_wotd.h | 2 +-
include/seqan/index/pump_extender7.h | 24 +-
include/seqan/index/shape_threshold.h | 2 +
include/seqan/journaled_set/score_biaffine.h | 31 +-
include/seqan/misc/bit_twiddling.h | 4 +-
include/seqan/modifier/modifier_padding.h | 12 +
include/seqan/parallel/parallel_lock.h | 22 +-
include/seqan/parallel/parallel_splitting.h | 2 +-
include/seqan/pipe/pipe_edit_environment.h | 4 +-
include/seqan/platform.h | 17 +-
include/seqan/{arg_parse.h => rna_io.h} | 51 +-
include/seqan/rna_io/bpseq_read_write.h | 240 ++++
include/seqan/rna_io/connect_read_write.h | 302 +++++
include/seqan/rna_io/dot_bracket_read_write.h | 409 +++++++
include/seqan/rna_io/ebpseq_read_write.h | 672 ++++++++++++
.../seqan/rna_io/rna_header.h | 144 +--
.../rna_io_context.h} | 151 ++-
include/seqan/rna_io/rna_record.h | 279 +++++
include/seqan/rna_io/rna_struct_file.h | 347 ++++++
include/seqan/rna_io/stockholm_read_write.h | 339 ++++++
include/seqan/rna_io/vienna_read_write.h | 280 +++++
include/seqan/score.h | 2 +-
include/seqan/seeds/banded_chain_alignment.h | 2 +-
include/seqan/seeds/banded_chain_alignment_impl.h | 19 +-
include/seqan/seq_io.h | 1 +
include/seqan/seq_io/bam_sam.h | 554 ++++++++++
include/seqan/seq_io/fai_index.h | 2 +-
include/seqan/seq_io/fasta_fastq.h | 123 +--
include/seqan/seq_io/read_embl.h | 8 +-
include/seqan/seq_io/read_genbank.h | 8 +-
include/seqan/seq_io/sequence_file.h | 246 ++++-
include/seqan/sequence/sequence_interface.h | 2 +-
include/seqan/sequence/string_cstyle.h | 12 +-
include/seqan/sequence/string_set_base.h | 15 +-
.../seqan/sequence/string_set_dependent_generous.h | 29 +
.../seqan/sequence/string_set_dependent_tight.h | 55 +-
include/seqan/statistics/statistics_base.h | 8 +-
include/seqan/store/store_io_gff.h | 6 +-
include/seqan/stream/file_stream.h | 28 +-
include/seqan/stream/formatted_file.h | 20 +
include/seqan/stream/stream_base.h | 11 +-
include/seqan/stream/tokenization.h | 45 +-
include/seqan/tabix_io/tabix_index_tbi.h | 5 +-
include/seqan/vcf_io/read_vcf.h | 48 +-
include/seqan/version.h | 4 +-
manual/attic/Tutorial/IndicesOld.rst | 2 +-
.../Infrastructure/Contribute/GitWorkflow.rst | 70 +-
.../Infrastructure/Use/CustomBuildSystem.rst | 36 +
.../source/Infrastructure/Use/FindSeqAnCMake.rst | 29 +-
manual/source/Infrastructure/Use/Install.rst | 44 +-
manual/source/Intel-Logo-300x198.jpg | Bin 0 -> 41926 bytes
.../Alignment/PairwiseSequenceAlignment.rst | 2 +-
.../Tutorial/DataStructures/Indices/FMIndex.rst | 93 ++
.../DataStructures/Indices/IndexIterators.rst | 52 +-
.../DataStructures/Indices/StringIndices.rst | 6 +-
.../Tutorial/DataStructures/Indices/index.rst | 1 +
.../Tutorial/DataStructures/Indices/preOrder.png | Bin 0 -> 35567 bytes
.../GettingStarted/BackgroundAndMotivation.rst | 6 +-
.../Tutorial/Workflows/GenerateKnimeNodes.rst | 12 +-
.../Tutorial/Workflows/KnimeReadySeqAnApp.rst | 4 +-
.../Tutorial/Workflows/UseSeqAnNodesInKnime.rst | 10 +-
manual/source/deNBI_Logo_rgb.jpg | Bin 0 -> 110243 bytes
manual/source/index.rst | 20 +-
tests/align/CMakeLists.txt | 4 +-
tests/align_extend/CMakeLists.txt | 4 +-
tests/align_profile/CMakeLists.txt | 4 +-
tests/align_split/CMakeLists.txt | 4 +-
tests/alignment_free/CMakeLists.txt | 4 +-
tests/arg_parse/CMakeLists.txt | 24 +-
tests/arg_parse/test_app.ctd | 14 +-
tests/arg_parse/test_arg_parse.cpp | 17 +-
tests/arg_parse/test_arg_parse.h | 51 +
tests/arg_parse/test_arg_parse_argument.h | 94 +-
.../test_arg_parse_version_check.cpp} | 53 +-
tests/arg_parse/test_arg_parse_version_check.h | 278 +++++
tests/bam_io/CMakeLists.txt | 6 +-
tests/bam_io/test_bam_file.h | 42 +
tests/bam_io/test_bam_io.cpp | 4 +
tests/basic/CMakeLists.txt | 4 +-
tests/basic/test_basic_allocator.h | 2 +-
tests/basic/test_basic_simd_vector.cpp | 6 +-
tests/basic/test_basic_simd_vector.h | 7 +-
tests/bed_io/CMakeLists.txt | 4 +-
tests/bed_io/test_bed_io.cpp | 42 +
tests/blast/CMakeLists.txt | 4 +-
tests/consensus/CMakeLists.txt | 4 +-
tests/consensus/test_consensus_realign.h | 2 +-
tests/consensus_v2/CMakeLists.txt | 4 +-
tests/find/CMakeLists.txt | 4 +-
tests/gff_io/CMakeLists.txt | 4 +-
tests/gff_io/test_gff_io.cpp | 4 +
tests/gff_io/test_gff_io.h | 38 +
tests/graph_algorithms/CMakeLists.txt | 4 +-
tests/graph_align/CMakeLists.txt | 4 +-
tests/graph_align/test_graph_impl_align.h | 10 +
tests/graph_msa/CMakeLists.txt | 4 +-
tests/graph_msa/test_graph_tcoffee.h | 2 +-
tests/graph_types/CMakeLists.txt | 4 +-
tests/graph_types/test_graph_types_types.cpp | 58 +-
tests/index/CMakeLists.txt | 6 +-
tests/index/test_index_bifm.cpp | 58 +-
tests/index/test_index_finder.cpp | 2 +-
tests/index/test_index_fm_rank_dictionary.cpp | 14 +-
tests/journaled_set/CMakeLists.txt | 4 +-
tests/journaled_string_tree/CMakeLists.txt | 6 +-
tests/journaled_string_tree/test_delta_store.h | 8 +-
tests/map/CMakeLists.txt | 4 +-
tests/misc/CMakeLists.txt | 4 +-
tests/modifier/CMakeLists.txt | 4 +-
tests/modifier/test_modifier_view.h | 2 +-
tests/modifier_cyclic_shape/CMakeLists.txt | 4 +-
tests/multiple_translation_units/CMakeLists.txt | 4 +-
tests/parallel/CMakeLists.txt | 6 +-
tests/parse_lm/CMakeLists.txt | 4 +-
tests/pipe/CMakeLists.txt | 4 +-
tests/platform/CMakeLists.txt | 4 +-
tests/random/CMakeLists.txt | 4 +-
tests/realign/CMakeLists.txt | 4 +-
tests/realign/test_realign.cpp | 2 +-
tests/reduced_aminoacid/CMakeLists.txt | 4 +-
tests/{roi_io => rna_io}/CMakeLists.txt | 17 +-
tests/rna_io/example.bpseq | 52 +
tests/rna_io/example.ct | 74 ++
tests/rna_io/example.dbn | 3 +
tests/rna_io/example.dbv | 9 +
tests/rna_io/example.ebpseq | 39 +
tests/rna_io/example.sth | 20 +
.../test_vcf_io.cpp => rna_io/test_rna_io.cpp} | 27 +-
tests/rna_io/test_rna_io.h | 472 ++++++++
tests/roi_io/CMakeLists.txt | 4 +-
tests/roi_io/test_roi_io.cpp | 42 +
tests/score/CMakeLists.txt | 4 +-
tests/seeds/CMakeLists.txt | 4 +-
tests/seeds/test_align_banded_chain_impl.cpp | 18 +
tests/seq_io/CMakeLists.txt | 13 +-
tests/seq_io/small_sequences.bam | Bin 0 -> 214 bytes
tests/seq_io/small_sequences.sam | 5 +
tests/seq_io/test_genbank.gbk | 90 ++
tests/seq_io/test_read_bam.h | 135 +++
tests/seq_io/test_seq_io.cpp | 25 +
tests/seq_io/test_sequence_file.h | 42 +
tests/seq_io/test_tag_select_intersect.h | 108 ++
tests/seq_io/test_write_bam.h | 144 +++
tests/sequence/CMakeLists.txt | 4 +-
tests/sequence_journaled/CMakeLists.txt | 4 +-
tests/simple_intervals_io/CMakeLists.txt | 4 +-
tests/statistics/CMakeLists.txt | 4 +-
tests/store/CMakeLists.txt | 6 +-
tests/stream/CMakeLists.txt | 8 +-
tests/swift_local/CMakeLists.txt | 4 +-
tests/tabix_io/CMakeLists.txt | 6 +-
tests/translation/CMakeLists.txt | 6 +-
tests/ucsc_io/CMakeLists.txt | 4 +-
tests/vcf_io/CMakeLists.txt | 4 +-
tests/vcf_io/test_vcf_io.cpp | 3 +
tests/vcf_io/test_vcf_io.h | 38 +
util/cmake/SeqAnBuildSystem.cmake | 115 +-
util/cmake/SetCPackSystemName.cmake | 2 +
util/cmake/package.cmake | 8 +-
util/cmake/{FindSeqAn.cmake => seqan-config.cmake} | 30 +-
util/pkgconfig/seqan.pc.in | 3 +-
util/raw_cmake_project/CMakeLists.txt | 2 +-
360 files changed, 10187 insertions(+), 3172 deletions(-)
diff --cc debian/changelog
index 93077d8,b7f6356..30c553e
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,26 -1,55 +1,78 @@@
+ seqan2 (2.3.1+dfsg-2) experimental; urgency=medium
+
+ * Remove archs with failing builds: armhf mips mipsel
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 14 Jan 2017 00:23:26 -0800
+
+ seqan2 (2.3.1+dfsg-1) experimental; urgency=medium
+
+ * Try to save more memory on kfreebsd-*
+ * Fix parallel build disabling to not produce warnings
+ * New upstream release, three incorporated patched removed
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 13 Jan 2017 05:36:28 -0800
+
+ seqan2 (2.3.0~1.20161019~af07bc1+dfsg-4) experimental; urgency=medium
+
+ * Try out -O3 for many architectures as that is upstream's default.
+ * Skip unneeded build for -indep.
+ * Fix architecture detection logic.
+ * Fix from upstream for another sparc64 related typo.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 26 Oct 2016 03:31:54 -0700
+
+ seqan2 (2.3.0~1.20161019~af07bc1+dfsg-3) experimental; urgency=medium
+
+ * Fix recursive variable expansion error.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 24 Oct 2016 07:54:44 -0700
+
+ seqan2 (2.3.0~1.20161019~af07bc1+dfsg-2) experimental; urgency=medium
+
+ * Fix typo from upstream's patch.
+ * Work around GNU Hurd TANDEM problem
+ * Skip armel
+ * Test -O1 for mips[el]
+ * Test turning off parallel builds for armhf, mips, kfreebsd-*
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 20 Oct 2016 04:48:11 -0700
+
+ seqan2 (2.3.0~0.201610100~af07bc1+dfsg+1) experimental; urgency=medium
+
+ * Second experimental build to test fix for #840030. Source from
+ https://github.com/seqan/seqan/pull/1887/commits/af07bc19087e662117b70d733e963a1611aa9b9a
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 20 Oct 2016 02:06:15 -0700
+
+ seqan2 (2.3.0~0.20161011~73a5aaf+dfsg-1) experimental; urgency=low
+
+ * Experimental build to test fix for #840030
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 11 Oct 2016 07:08:05 -0700
+
+seqan2 (2.2.0+dfsg-6) UNRELEASED; urgency=medium
+
+ * Drop Soeren Sonnenburg from Uploaders
+
+ -- Andreas Tille <tille at debian.org> Sat, 03 Dec 2016 08:08:51 +0100
+
+seqan2 (2.2.0+dfsg-5) unstable; urgency=medium
+
+ * Fix build issue with boost 1.62 (Thanks for the patch to Graham Inggs
+ <ginggs at debian.org>)
+ Closes: #846617
+ * debhelper 10
+ * d/watch: version=4
+
+ -- Andreas Tille <tille at debian.org> Fri, 02 Dec 2016 19:01:10 +0100
+
+seqan2 (2.2.0+dfsg-4) unstable; urgency=medium
+
+ * Restrict to known working archs for now. Closes: #840025
+ * Use upstream's patch. Closes: #840030, #840026
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 11 Oct 2016 12:20:59 -0700
+
seqan2 (2.2.0+dfsg-3) unstable; urgency=medium
* Fix arch specific build. Closes: #840023
diff --cc debian/patches/series
index 52f6cc2,a1ed085..18e2946
--- a/debian/patches/series
+++ b/debian/patches/series
@@@ -1,5 -1,3 +1,2 @@@
- pthread-linking
- spelling.patch
short-description
--
- boost1.62.patch
+ skip-seqan-revision
--
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