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ncbi-blast: Remove, superseded by ncbi-blast+
Module Name: pkgsrc-wip
Committed By: Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Wed Apr 25 14:55:02 2018 -0500
Changeset: 5fbd279b7854396359369d3006e2d171578f1aef
Removed Files:
ncbi-blast/DESCR
ncbi-blast/FreeBSD-pkg-plist
ncbi-blast/Makefile
ncbi-blast/PLIST
ncbi-blast/PLIST.old
ncbi-blast/buildlink3.mk
ncbi-blast/distinfo
ncbi-blast/patches/patch-src_build-system_Makefile.in.top
ncbi-blast/patches/patch-src_build-system_configure
Log Message:
ncbi-blast: Remove, superseded by ncbi-blast+
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=5fbd279b7854396359369d3006e2d171578f1aef
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
ncbi-blast/DESCR | 5 -
ncbi-blast/FreeBSD-pkg-plist | 3894 --------------------
ncbi-blast/Makefile | 59 -
ncbi-blast/PLIST | 3789 -------------------
ncbi-blast/PLIST.old | 3789 -------------------
ncbi-blast/buildlink3.mk | 12 -
ncbi-blast/distinfo | 7 -
.../patches/patch-src_build-system_Makefile.in.top | 49 -
.../patches/patch-src_build-system_configure | 410 ---
9 files changed, 12014 deletions(-)
diffs:
diff --git a/ncbi-blast/DESCR b/ncbi-blast/DESCR
deleted file mode 100644
index 5c1ae637e5..0000000000
--- a/ncbi-blast/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-The Basic Local Alignment Search Tool (BLAST) finds regions of local
-similarity between sequences. The program compares nucleotide or protein
-sequences to sequence databases and calculates the statistical significance of
-matches. BLAST can be used to infer functional and evolutionary relationships
-between sequences as well as help identify members of gene families.
diff --git a/ncbi-blast/FreeBSD-pkg-plist b/ncbi-blast/FreeBSD-pkg-plist
deleted file mode 100644
index 9ea371cff2..0000000000
--- a/ncbi-blast/FreeBSD-pkg-plist
+++ /dev/null
@@ -1,3894 +0,0 @@
-bin/blast_formatter
-bin/blastdb_aliastool
-bin/blastdbcheck
-bin/blastdbcmd
-bin/blastdbcp
-bin/blastn
-bin/blastp
-bin/blastx
-bin/convert2blastmask
-bin/datatool
-bin/deltablast
-bin/dustmasker
-bin/gene_info_reader
-bin/legacy_blast.pl
-bin/makeblastdb
-bin/makembindex
-bin/makeprofiledb
-bin/project_tree_builder
-bin/psiblast
-bin/rpsblast
-bin/rpstblastn
-bin/seedtop
-bin/segmasker
-bin/seqdb_demo
-bin/seqdb_perf
-bin/tblastn
-bin/tblastx
-bin/update_blastdb.pl
-bin/windowmasker
-bin/windowmasker_2.2.22_adapter.py
-include/ncbi-tools++/algo/blast/api/bl2seq.hpp
-include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_aux.hpp
-include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
-include/ncbi-tools++/algo/blast/api/blast_exception.hpp
-include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
-include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
-include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
-include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_results.hpp
-include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
-include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
-include/ncbi-tools++/algo/blast/api/blast_types.hpp
-include/ncbi-tools++/algo/blast/api/blastx_options.hpp
-include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/deltablast.hpp
-include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
-include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
-include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
-include/ncbi-tools++/algo/blast/api/local_blast.hpp
-include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
-include/ncbi-tools++/algo/blast/api/local_search.hpp
-include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
-include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
-include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
-include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
-include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
-include/ncbi-tools++/algo/blast/api/psiblast.hpp
-include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
-include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
-include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
-include/ncbi-tools++/algo/blast/api/pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/query_data.hpp
-include/ncbi-tools++/algo/blast/api/remote_blast.hpp
-include/ncbi-tools++/algo/blast/api/remote_search.hpp
-include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
-include/ncbi-tools++/algo/blast/api/rps_aux.hpp
-include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
-include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
-include/ncbi-tools++/algo/blast/api/search_strategy.hpp
-include/ncbi-tools++/algo/blast/api/seedtop.hpp
-include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
-include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
-include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
-include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
-include/ncbi-tools++/algo/blast/api/setup_factory.hpp
-include/ncbi-tools++/algo/blast/api/sseqloc.hpp
-include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
-include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
-include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
-include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
-include/ncbi-tools++/algo/blast/api/uniform_search.hpp
-include/ncbi-tools++/algo/blast/api/version.hpp
-include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
-include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
-include/ncbi-tools++/algo/blast/composition_adjustment/compo_heap.h
-include/ncbi-tools++/algo/blast/composition_adjustment/compo_mode_condition.h
-include/ncbi-tools++/algo/blast/composition_adjustment/composition_adjustment.h
-include/ncbi-tools++/algo/blast/composition_adjustment/composition_constants.h
-include/ncbi-tools++/algo/blast/composition_adjustment/matrix_frequency_data.h
-include/ncbi-tools++/algo/blast/composition_adjustment/nlm_linear_algebra.h
-include/ncbi-tools++/algo/blast/composition_adjustment/optimize_target_freq.h
-include/ncbi-tools++/algo/blast/composition_adjustment/redo_alignment.h
-include/ncbi-tools++/algo/blast/composition_adjustment/smith_waterman.h
-include/ncbi-tools++/algo/blast/composition_adjustment/unified_pvalues.h
-include/ncbi-tools++/algo/blast/core/aa_ungapped.h
-include/ncbi-tools++/algo/blast/core/blast_aalookup.h
-include/ncbi-tools++/algo/blast/core/blast_aascan.h
-include/ncbi-tools++/algo/blast/core/blast_def.h
-include/ncbi-tools++/algo/blast/core/blast_diagnostics.h
-include/ncbi-tools++/algo/blast/core/blast_encoding.h
-include/ncbi-tools++/algo/blast/core/blast_engine.h
-include/ncbi-tools++/algo/blast/core/blast_export.h
-include/ncbi-tools++/algo/blast/core/blast_extend.h
-include/ncbi-tools++/algo/blast/core/blast_filter.h
-include/ncbi-tools++/algo/blast/core/blast_gapalign.h
-include/ncbi-tools++/algo/blast/core/blast_hits.h
-include/ncbi-tools++/algo/blast/core/blast_hspfilter.h
-include/ncbi-tools++/algo/blast/core/blast_hspstream.h
-include/ncbi-tools++/algo/blast/core/blast_kappa.h
-include/ncbi-tools++/algo/blast/core/blast_lookup.h
-include/ncbi-tools++/algo/blast/core/blast_message.h
-include/ncbi-tools++/algo/blast/core/blast_nalookup.h
-include/ncbi-tools++/algo/blast/core/blast_nascan.h
-include/ncbi-tools++/algo/blast/core/blast_options.h
-include/ncbi-tools++/algo/blast/core/blast_parameters.h
-include/ncbi-tools++/algo/blast/core/blast_program.h
-include/ncbi-tools++/algo/blast/core/blast_psi.h
-include/ncbi-tools++/algo/blast/core/blast_query_info.h
-include/ncbi-tools++/algo/blast/core/blast_rps.h
-include/ncbi-tools++/algo/blast/core/blast_seg.h
-include/ncbi-tools++/algo/blast/core/blast_seqsrc.h
-include/ncbi-tools++/algo/blast/core/blast_seqsrc_impl.h
-include/ncbi-tools++/algo/blast/core/blast_setup.h
-include/ncbi-tools++/algo/blast/core/blast_stat.h
-include/ncbi-tools++/algo/blast/core/blast_sw.h
-include/ncbi-tools++/algo/blast/core/blast_toolkit.h
-include/ncbi-tools++/algo/blast/core/blast_traceback.h
-include/ncbi-tools++/algo/blast/core/blast_tune.h
-include/ncbi-tools++/algo/blast/core/blast_util.h
-include/ncbi-tools++/algo/blast/core/gapinfo.h
-include/ncbi-tools++/algo/blast/core/gencode_singleton.h
-include/ncbi-tools++/algo/blast/core/greedy_align.h
-include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
-include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
-include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
-include/ncbi-tools++/algo/blast/core/link_hsps.h
-include/ncbi-tools++/algo/blast/core/lookup_util.h
-include/ncbi-tools++/algo/blast/core/lookup_wrap.h
-include/ncbi-tools++/algo/blast/core/mb_indexed_lookup.h
-include/ncbi-tools++/algo/blast/core/na_ungapped.h
-include/ncbi-tools++/algo/blast/core/ncbi_math.h
-include/ncbi-tools++/algo/blast/core/ncbi_std.h
-include/ncbi-tools++/algo/blast/core/pattern.h
-include/ncbi-tools++/algo/blast/core/phi_extend.h
-include/ncbi-tools++/algo/blast/core/phi_gapalign.h
-include/ncbi-tools++/algo/blast/core/phi_lookup.h
-include/ncbi-tools++/algo/blast/core/split_query.h
-include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
-include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
-include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
-include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
-include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
-include/ncbi-tools++/algo/blast/format/blast_format.hpp
-include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
-include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
-include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
-include/ncbi-tools++/algo/blast/format/build_archive.hpp
-include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
-include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
-include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
-include/ncbi-tools++/algo/blast/igblast/igblast.hpp
-include/ncbi-tools++/algo/dustmask/sdust.tex
-include/ncbi-tools++/algo/dustmask/symdust.hpp
-include/ncbi-tools++/algo/segmask/segmask.hpp
-include/ncbi-tools++/algo/winmask/README.API
-include/ncbi-tools++/algo/winmask/seq_masker.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_cache_boost.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_ascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_bin.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_factory.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_oascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_obinary.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_ascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_bin.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_factory.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_ascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_bin.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score_mean.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score_mean_glob.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score_min.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_uset_array.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_uset_hash.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_uset_simple.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_util.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window_ambig.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window_pattern.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window_pattern_ambig.hpp
-include/ncbi-tools++/algo/winmask/win_mask_config.hpp
-include/ncbi-tools++/algo/winmask/win_mask_counts_converter.hpp
-include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
-include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
-include/ncbi-tools++/algo/winmask/win_mask_util.hpp
-include/ncbi-tools++/cgi/caf.hpp
-include/ncbi-tools++/cgi/caf_encoded.hpp
-include/ncbi-tools++/cgi/caf_plain.hpp
-include/ncbi-tools++/cgi/cgi_exception.hpp
-include/ncbi-tools++/cgi/cgi_serial.hpp
-include/ncbi-tools++/cgi/cgi_session.hpp
-include/ncbi-tools++/cgi/cgi_util.hpp
-include/ncbi-tools++/cgi/cgiapp.hpp
-include/ncbi-tools++/cgi/cgiapp_cached.hpp
-include/ncbi-tools++/cgi/cgictx.hpp
-include/ncbi-tools++/cgi/error_codes.hpp
-include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
-include/ncbi-tools++/cgi/ncbicgi.hpp
-include/ncbi-tools++/cgi/ncbicgir.hpp
-include/ncbi-tools++/cgi/ncbires.hpp
-include/ncbi-tools++/cgi/ref_args.hpp
-include/ncbi-tools++/cgi/user_agent.hpp
-include/ncbi-tools++/common/config/ncbiconf_msvc.h
-include/ncbi-tools++/common/config/ncbiconf_msvc_site.h
-include/ncbi-tools++/common/config/ncbiconf_universal.h
-include/ncbi-tools++/common/config/ncbiconf_xcode.h
-include/ncbi-tools++/common/config/ncbiconf_xcode_site.h
-include/ncbi-tools++/common/header_template.hpp
-include/ncbi-tools++/common/metamodules_doxygen.h
-include/ncbi-tools++/common/ncbi_export.h
-include/ncbi-tools++/common/ncbi_package_ver.h
-include/ncbi-tools++/common/ncbi_pch_impl.hpp
-include/ncbi-tools++/common/ncbi_skew_guard.h
-include/ncbi-tools++/common/ncbi_source_ver.h
-include/ncbi-tools++/common/ncbiconf_impl.h
-include/ncbi-tools++/common/test_assert.h
-include/ncbi-tools++/common/test_assert_impl.h
-include/ncbi-tools++/common/test_data_path.h
-include/ncbi-tools++/connect/connect_export.h
-include/ncbi-tools++/connect/email_diag_handler.hpp
-include/ncbi-tools++/connect/error_codes.hpp
-include/ncbi-tools++/connect/ext/ncbi_crypt.h
-include/ncbi-tools++/connect/ext/ncbi_dblb.h
-include/ncbi-tools++/connect/ext/ncbi_dblb_svcmapper.hpp
-include/ncbi-tools++/connect/ext/ncbi_ifconf.h
-include/ncbi-tools++/connect/ext/ncbi_iprange.h
-include/ncbi-tools++/connect/ext/ncbi_localnet.h
-include/ncbi-tools++/connect/impl/server_connection.hpp
-include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
-include/ncbi-tools++/connect/ncbi_base64.h
-include/ncbi-tools++/connect/ncbi_buffer.h
-include/ncbi-tools++/connect/ncbi_conn_exception.hpp
-include/ncbi-tools++/connect/ncbi_conn_reader_writer.hpp
-include/ncbi-tools++/connect/ncbi_conn_stream.hpp
-include/ncbi-tools++/connect/ncbi_conn_test.hpp
-include/ncbi-tools++/connect/ncbi_connection.h
-include/ncbi-tools++/connect/ncbi_connector.h
-include/ncbi-tools++/connect/ncbi_connutil.h
-include/ncbi-tools++/connect/ncbi_core.h
-include/ncbi-tools++/connect/ncbi_core_cxx.hpp
-include/ncbi-tools++/connect/ncbi_file_connector.h
-include/ncbi-tools++/connect/ncbi_ftp_connector.h
-include/ncbi-tools++/connect/ncbi_gnutls.h
-include/ncbi-tools++/connect/ncbi_heapmgr.h
-include/ncbi-tools++/connect/ncbi_host_info.h
-include/ncbi-tools++/connect/ncbi_http_connector.h
-include/ncbi-tools++/connect/ncbi_http_session.hpp
-include/ncbi-tools++/connect/ncbi_memory_connector.h
-include/ncbi-tools++/connect/ncbi_misc.hpp
-include/ncbi-tools++/connect/ncbi_namedpipe.hpp
-include/ncbi-tools++/connect/ncbi_namedpipe_connector.hpp
-include/ncbi-tools++/connect/ncbi_pipe.hpp
-include/ncbi-tools++/connect/ncbi_pipe_connector.hpp
-include/ncbi-tools++/connect/ncbi_sendmail.h
-include/ncbi-tools++/connect/ncbi_server_info.h
-include/ncbi-tools++/connect/ncbi_service.h
-include/ncbi-tools++/connect/ncbi_service_connector.h
-include/ncbi-tools++/connect/ncbi_socket.h
-include/ncbi-tools++/connect/ncbi_socket.hpp
-include/ncbi-tools++/connect/ncbi_socket_connector.h
-include/ncbi-tools++/connect/ncbi_socket_unix.h
-include/ncbi-tools++/connect/ncbi_socket_unix.hpp
-include/ncbi-tools++/connect/ncbi_types.h
-include/ncbi-tools++/connect/ncbi_userhost.hpp
-include/ncbi-tools++/connect/ncbi_util.h
-include/ncbi-tools++/connect/server.hpp
-include/ncbi-tools++/connect/server_monitor.hpp
-include/ncbi-tools++/connect/services/blob_storage_netcache.hpp
-include/ncbi-tools++/connect/services/clparser.hpp
-include/ncbi-tools++/connect/services/compound_id.hpp
-include/ncbi-tools++/connect/services/error_codes.hpp
-include/ncbi-tools++/connect/services/grid_app_version_info.hpp
-include/ncbi-tools++/connect/services/grid_client.hpp
-include/ncbi-tools++/connect/services/grid_client_app.hpp
-include/ncbi-tools++/connect/services/grid_control_thread.hpp
-include/ncbi-tools++/connect/services/grid_globals.hpp
-include/ncbi-tools++/connect/services/grid_rw_impl.hpp
-include/ncbi-tools++/connect/services/grid_worker.hpp
-include/ncbi-tools++/connect/services/grid_worker_app.hpp
-include/ncbi-tools++/connect/services/json_over_uttp.hpp
-include/ncbi-tools++/connect/services/named_parameters.hpp
-include/ncbi-tools++/connect/services/netcache_admin.hpp
-include/ncbi-tools++/connect/services/netcache_api.hpp
-include/ncbi-tools++/connect/services/netcache_api_expt.hpp
-include/ncbi-tools++/connect/services/netcache_key.hpp
-include/ncbi-tools++/connect/services/netcomponent.hpp
-include/ncbi-tools++/connect/services/neticache_client.hpp
-include/ncbi-tools++/connect/services/netschedule_api.hpp
-include/ncbi-tools++/connect/services/netschedule_api_expt.hpp
-include/ncbi-tools++/connect/services/netschedule_key.hpp
-include/ncbi-tools++/connect/services/netservice_api.hpp
-include/ncbi-tools++/connect/services/netservice_api_expt.hpp
-include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp
-include/ncbi-tools++/connect/services/netstorage.hpp
-include/ncbi-tools++/connect/services/netstorage_admin.hpp
-include/ncbi-tools++/connect/services/netstorage_impl.hpp
-include/ncbi-tools++/connect/services/ns_client_factory.hpp
-include/ncbi-tools++/connect/services/ns_job_serializer.hpp
-include/ncbi-tools++/connect/services/ns_output_parser.hpp
-include/ncbi-tools++/connect/services/remote_app.hpp
-include/ncbi-tools++/connect/services/srv_connections.hpp
-include/ncbi-tools++/connect/services/srv_connections_expt.hpp
-include/ncbi-tools++/connect/services/timeline.hpp
-include/ncbi-tools++/connect/services/util.hpp
-include/ncbi-tools++/connect/threaded_server.hpp
-include/ncbi-tools++/corelib/blob_storage.hpp
-include/ncbi-tools++/corelib/ddumpable.hpp
-include/ncbi-tools++/corelib/env_reg.hpp
-include/ncbi-tools++/corelib/error_codes.hpp
-include/ncbi-tools++/corelib/expr.hpp
-include/ncbi-tools++/corelib/guard.hpp
-include/ncbi-tools++/corelib/hash_impl/_hash_fun.h
-include/ncbi-tools++/corelib/hash_impl/_hash_map.h
-include/ncbi-tools++/corelib/hash_impl/_hash_set.h
-include/ncbi-tools++/corelib/hash_impl/_hashtable.c
-include/ncbi-tools++/corelib/hash_impl/_hashtable.h
-include/ncbi-tools++/corelib/hash_impl/_relops_hash_cont.h
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-lib/libncbi_xreader_cache.a
-lib/libncbi_xreader_gicache-dll.so
-lib/libncbi_xreader_gicache-static.a
-lib/libncbi_xreader_gicache.a
-lib/libncbi_xreader_id1-dll.so
-lib/libncbi_xreader_id1-static.a
-lib/libncbi_xreader_id1.a
-lib/libncbi_xreader_id2-dll.so
-lib/libncbi_xreader_id2-static.a
-lib/libncbi_xreader_id2.a
-lib/libncbimime-static.a
-lib/libncbimime.a
-lib/libobjcoords-static.a
-lib/libobjcoords.a
-lib/libobjprt-static.a
-lib/libobjprt.a
-lib/libomssa-static.a
-lib/libomssa.a
-lib/libpcassay-static.a
-lib/libpcassay.a
-lib/libpcsubstance-static.a
-lib/libpcsubstance.a
-lib/libproj-static.a
-lib/libproj.a
-lib/libpub-static.a
-lib/libpub.a
-lib/libpubmed-static.a
-lib/libpubmed.a
-lib/libremap-static.a
-lib/libremap.a
-lib/libremapcli-static.a
-lib/libremapcli.a
-lib/libscoremat-static.a
-lib/libscoremat.a
-lib/libseq-static.a
-lib/libseq.a
-lib/libseqcode-static.a
-lib/libseqcode.a
-lib/libseqdb-static.a
-lib/libseqdb.a
-lib/libseqedit-static.a
-lib/libseqedit.a
-lib/libseqmasks_io-static.a
-lib/libseqmasks_io.a
-lib/libseqset-static.a
-lib/libseqset.a
-lib/libseqsplit-static.a
-lib/libseqsplit.a
-lib/libseqtest-static.a
-lib/libseqtest.a
-lib/libsequtil-static.a
-lib/libsequtil.a
-lib/libsubmit-static.a
-lib/libsubmit.a
-lib/libtables-static.a
-lib/libtables.a
-lib/libtaxon1-static.a
-lib/libtaxon1.a
-lib/libtaxon3-static.a
-lib/libtaxon3.a
-lib/libtest_mt-static.a
-lib/libtest_mt.a
-lib/libtinyseq-static.a
-lib/libtinyseq.a
-lib/libtrackmgr-static.a
-lib/libtrackmgr.a
-lib/libtrackmgrcli-static.a
-lib/libtrackmgrcli.a
-lib/libtrackmgrgridcli-static.a
-lib/libtrackmgrgridcli.a
-lib/libvalerr-static.a
-lib/libvalerr.a
-lib/libvalid-static.a
-lib/libvalid.a
-lib/libvariation-static.a
-lib/libvariation.a
-lib/libwritedb-static.a
-lib/libwritedb.a
-lib/libxalgoblastdbindex-static.a
-lib/libxalgoblastdbindex.a
-lib/libxalgodustmask-static.a
-lib/libxalgodustmask.a
-lib/libxalgosegmask-static.a
-lib/libxalgosegmask.a
-lib/libxalgowinmask-static.a
-lib/libxalgowinmask.a
-lib/libxalnmgr-static.a
-lib/libxalnmgr.a
-lib/libxblast-static.a
-lib/libxblast.a
-lib/libxblastformat-static.a
-lib/libxblastformat.a
-lib/libxcgi-static.a
-lib/libxcgi.a
-lib/libxcleanup-static.a
-lib/libxcleanup.a
-lib/libxcompress-static.a
-lib/libxcompress.a
-lib/libxconnect-static.a
-lib/libxconnect.a
-lib/libxconnext-static.a
-lib/libxconnext.a
-lib/libxconnserv-static.a
-lib/libxconnserv.a
-lib/libxcser-static.a
-lib/libxcser.a
-lib/libxfcgi-static.a
-lib/libxfcgi.a
-lib/libxformat-static.a
-lib/libxformat.a
-lib/libxhtml-static.a
-lib/libxhtml.a
-lib/libxncbi-static.a
-lib/libxncbi.a
-lib/libxnetblast-static.a
-lib/libxnetblast.a
-lib/libxnetblastcli-static.a
-lib/libxnetblastcli.a
-lib/libxobjedit-static.a
-lib/libxobjedit.a
-lib/libxobjmgr-static.a
-lib/libxobjmgr.a
-lib/libxobjread-static.a
-lib/libxobjread.a
-lib/libxobjreadex-static.a
-lib/libxobjreadex.a
-lib/libxobjsimple-static.a
-lib/libxobjsimple.a
-lib/libxobjutil-static.a
-lib/libxobjutil.a
-lib/libxregexp-static.a
-lib/libxregexp.a
-lib/libxser-static.a
-lib/libxser.a
-lib/libxthrserv-static.a
-lib/libxthrserv.a
-lib/libxutil-static.a
-lib/libxutil.a
-lib/libxxconnect-static.a
-lib/libxxconnect.a
diff --git a/ncbi-blast/Makefile b/ncbi-blast/Makefile
deleted file mode 100644
index 67911a2095..0000000000
--- a/ncbi-blast/Makefile
+++ /dev/null
@@ -1,59 +0,0 @@
-# $NetBSD: Makefile,v 1.5 2015/03/05 22:31:07 outpaddling Exp $
-
-DISTNAME= ncbi-blast-${PKGVERSION_NOREV}+-src
-PKGNAME= blast-2.2.30
-CATEGORIES= biology
-MASTER_SITES= ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= http://blast.ncbi.nlm.nih.gov/
-COMMENT= NCBI Basic Local Alignment Search Tool (Blast)
-LICENSE= public-domain
-
-USE_LANGUAGES= c c++
-USE_TOOLS+= gmake perl:run
-
-DEPENDS+= p5-List-MoreUtils>=0:../../devel/p5-List-MoreUtils
-
-GNU_CONFIGURE= yes
-
-WRKSRC= ${WRKDIR}/${DISTNAME}/c++
-
-REPLACE_PERL= src/app/blast/legacy_blast.pl \
- src/app/blast/update_blastdb.pl
-REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
-
-CHECK_PORTABILITY_SKIP= compilers/xcode30_prj/configure \
- scripts/common/check/check_make_cfg.sh \
- src/app/oligofar/tests/set1/test-oligofar.sh
-
-# The configure script forces symbol stripping
-# CONFIGURE_SCRIPT= ./configure.orig
-
-CONFIGURE_ARGS+= AR="ar cr" \
- --prefix=${PREFIX} --with-build-root=${WRKSRC}/Release \
- --with-dll --with-mt --without-caution --without-debug
-
-# amq -w hangs on BSD, not needed
-CONFIGURE_ENV+= ncbi_cv_prog_amq_w=no
-
-# statfs tends to be found on NetBSD erroneously
-CONFIGURE_ENV+= ac_cv_func_statfs=no
-
-# Default behavior patched so that all 3rd party support disable
-# by default, then enabled one by one
-CONFIGURE_ARGS+= --without-3psw \
- --with-bz2=yes --with-pcre=yes --with-z=yes
-
-# Needed for FreeBSD port on FreeBSD 10.0
-# post-patch:
-# ${REINPLACE_CMD} \
-# -e "s|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|g" \
-# ${WRKSRC}/src/build-system/configure
-
-.include "../../archivers/bzip2/buildlink3.mk"
-.include "../../devel/pcre/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/pthread.buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/ncbi-blast/PLIST b/ncbi-blast/PLIST
deleted file mode 100644
index c6aeb4e0c7..0000000000
--- a/ncbi-blast/PLIST
+++ /dev/null
@@ -1,3789 +0,0 @@
-@comment $NetBSD: PLIST,v 1.4 2015/03/05 22:31:07 outpaddling Exp $
-bin/blast_formatter
-bin/blastdb_aliastool
-bin/blastdbcheck
-bin/blastdbcmd
-bin/blastdbcp
-bin/blastn
-bin/blastp
-bin/blastx
-bin/convert2blastmask
-bin/datatool
-bin/deltablast
-bin/dustmasker
-bin/gene_info_reader
-bin/legacy_blast.pl
-bin/makeblastdb
-bin/makembindex
-bin/makeprofiledb
-bin/project_tree_builder
-bin/psiblast
-bin/rpsblast
-bin/rpstblastn
-bin/seedtop
-bin/segmasker
-bin/seqdb_demo
-bin/seqdb_perf
-bin/tblastn
-bin/tblastx
-bin/update_blastdb.pl
-bin/windowmasker
-bin/windowmasker_2.2.22_adapter.py
-include/ncbi-tools++/algo/blast/api/bl2seq.hpp
-include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_aux.hpp
-include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
-include/ncbi-tools++/algo/blast/api/blast_exception.hpp
-include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
-include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
-include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
-include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_results.hpp
-include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
-include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
-include/ncbi-tools++/algo/blast/api/blast_types.hpp
-include/ncbi-tools++/algo/blast/api/blastx_options.hpp
-include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/deltablast.hpp
-include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
-include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
-include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
-include/ncbi-tools++/algo/blast/api/local_blast.hpp
-include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
-include/ncbi-tools++/algo/blast/api/local_search.hpp
-include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
-include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
-include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
-include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
-include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
-include/ncbi-tools++/algo/blast/api/psiblast.hpp
-include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
-include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
-include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
-include/ncbi-tools++/algo/blast/api/pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/query_data.hpp
-include/ncbi-tools++/algo/blast/api/remote_blast.hpp
-include/ncbi-tools++/algo/blast/api/remote_search.hpp
-include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
-include/ncbi-tools++/algo/blast/api/rps_aux.hpp
-include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
-include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
-include/ncbi-tools++/algo/blast/api/search_strategy.hpp
-include/ncbi-tools++/algo/blast/api/seedtop.hpp
-include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
-include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
-include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
-include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
-include/ncbi-tools++/algo/blast/api/setup_factory.hpp
-include/ncbi-tools++/algo/blast/api/sseqloc.hpp
-include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
-include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
-include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
-include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
-include/ncbi-tools++/algo/blast/api/uniform_search.hpp
-include/ncbi-tools++/algo/blast/api/version.hpp
-include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
-include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
-include/ncbi-tools++/algo/blast/composition_adjustment/compo_heap.h
-include/ncbi-tools++/algo/blast/composition_adjustment/compo_mode_condition.h
-include/ncbi-tools++/algo/blast/composition_adjustment/composition_adjustment.h
-include/ncbi-tools++/algo/blast/composition_adjustment/composition_constants.h
-include/ncbi-tools++/algo/blast/composition_adjustment/matrix_frequency_data.h
-include/ncbi-tools++/algo/blast/composition_adjustment/nlm_linear_algebra.h
-include/ncbi-tools++/algo/blast/composition_adjustment/optimize_target_freq.h
-include/ncbi-tools++/algo/blast/composition_adjustment/redo_alignment.h
-include/ncbi-tools++/algo/blast/composition_adjustment/smith_waterman.h
-include/ncbi-tools++/algo/blast/composition_adjustment/unified_pvalues.h
-include/ncbi-tools++/algo/blast/core/aa_ungapped.h
-include/ncbi-tools++/algo/blast/core/blast_aalookup.h
-include/ncbi-tools++/algo/blast/core/blast_aascan.h
-include/ncbi-tools++/algo/blast/core/blast_def.h
-include/ncbi-tools++/algo/blast/core/blast_diagnostics.h
-include/ncbi-tools++/algo/blast/core/blast_encoding.h
-include/ncbi-tools++/algo/blast/core/blast_engine.h
-include/ncbi-tools++/algo/blast/core/blast_export.h
-include/ncbi-tools++/algo/blast/core/blast_extend.h
-include/ncbi-tools++/algo/blast/core/blast_filter.h
-include/ncbi-tools++/algo/blast/core/blast_gapalign.h
-include/ncbi-tools++/algo/blast/core/blast_hits.h
-include/ncbi-tools++/algo/blast/core/blast_hspfilter.h
-include/ncbi-tools++/algo/blast/core/blast_hspstream.h
-include/ncbi-tools++/algo/blast/core/blast_kappa.h
-include/ncbi-tools++/algo/blast/core/blast_lookup.h
-include/ncbi-tools++/algo/blast/core/blast_message.h
-include/ncbi-tools++/algo/blast/core/blast_nalookup.h
-include/ncbi-tools++/algo/blast/core/blast_nascan.h
-include/ncbi-tools++/algo/blast/core/blast_options.h
-include/ncbi-tools++/algo/blast/core/blast_parameters.h
-include/ncbi-tools++/algo/blast/core/blast_program.h
-include/ncbi-tools++/algo/blast/core/blast_psi.h
-include/ncbi-tools++/algo/blast/core/blast_query_info.h
-include/ncbi-tools++/algo/blast/core/blast_rps.h
-include/ncbi-tools++/algo/blast/core/blast_seg.h
-include/ncbi-tools++/algo/blast/core/blast_seqsrc.h
-include/ncbi-tools++/algo/blast/core/blast_seqsrc_impl.h
-include/ncbi-tools++/algo/blast/core/blast_setup.h
-include/ncbi-tools++/algo/blast/core/blast_stat.h
-include/ncbi-tools++/algo/blast/core/blast_sw.h
-include/ncbi-tools++/algo/blast/core/blast_toolkit.h
-include/ncbi-tools++/algo/blast/core/blast_traceback.h
-include/ncbi-tools++/algo/blast/core/blast_tune.h
-include/ncbi-tools++/algo/blast/core/blast_util.h
-include/ncbi-tools++/algo/blast/core/gapinfo.h
-include/ncbi-tools++/algo/blast/core/gencode_singleton.h
-include/ncbi-tools++/algo/blast/core/greedy_align.h
-include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
-include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
-include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
-include/ncbi-tools++/algo/blast/core/link_hsps.h
-include/ncbi-tools++/algo/blast/core/lookup_util.h
-include/ncbi-tools++/algo/blast/core/lookup_wrap.h
-include/ncbi-tools++/algo/blast/core/mb_indexed_lookup.h
-include/ncbi-tools++/algo/blast/core/na_ungapped.h
-include/ncbi-tools++/algo/blast/core/ncbi_math.h
-include/ncbi-tools++/algo/blast/core/ncbi_std.h
-include/ncbi-tools++/algo/blast/core/pattern.h
-include/ncbi-tools++/algo/blast/core/phi_extend.h
-include/ncbi-tools++/algo/blast/core/phi_gapalign.h
-include/ncbi-tools++/algo/blast/core/phi_lookup.h
-include/ncbi-tools++/algo/blast/core/split_query.h
-include/ncbi-tools++/algo/blast/dbindex/dbindex.hpp
-include/ncbi-tools++/algo/blast/dbindex/dbindex_sp.hpp
-include/ncbi-tools++/algo/blast/dbindex/sequence_istream.hpp
-include/ncbi-tools++/algo/blast/dbindex/sequence_istream_bdb.hpp
-include/ncbi-tools++/algo/blast/dbindex/sequence_istream_fasta.hpp
-include/ncbi-tools++/algo/blast/format/blast_format.hpp
-include/ncbi-tools++/algo/blast/format/blastfmtutil.hpp
-include/ncbi-tools++/algo/blast/format/blastxml2_format.hpp
-include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
-include/ncbi-tools++/algo/blast/format/build_archive.hpp
-include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
-include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
-include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
-include/ncbi-tools++/algo/blast/igblast/igblast.hpp
-include/ncbi-tools++/algo/dustmask/sdust.tex
-include/ncbi-tools++/algo/dustmask/symdust.hpp
-include/ncbi-tools++/algo/segmask/segmask.hpp
-include/ncbi-tools++/algo/winmask/README.API
-include/ncbi-tools++/algo/winmask/seq_masker.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_cache_boost.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_ascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_bin.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_factory.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_oascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_istat_obinary.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_ascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_bin.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_factory.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_ascii.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_ostat_opt_bin.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score_mean.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score_mean_glob.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_score_min.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_uset_array.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_uset_hash.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_uset_simple.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_util.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window_ambig.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window_pattern.hpp
-include/ncbi-tools++/algo/winmask/seq_masker_window_pattern_ambig.hpp
-include/ncbi-tools++/algo/winmask/win_mask_config.hpp
-include/ncbi-tools++/algo/winmask/win_mask_counts_converter.hpp
-include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
-include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
-include/ncbi-tools++/algo/winmask/win_mask_util.hpp
-include/ncbi-tools++/cgi/caf.hpp
-include/ncbi-tools++/cgi/caf_encoded.hpp
-include/ncbi-tools++/cgi/caf_plain.hpp
-include/ncbi-tools++/cgi/cgi_exception.hpp
-include/ncbi-tools++/cgi/cgi_serial.hpp
-include/ncbi-tools++/cgi/cgi_session.hpp
-include/ncbi-tools++/cgi/cgi_util.hpp
-include/ncbi-tools++/cgi/cgiapp.hpp
-include/ncbi-tools++/cgi/cgiapp_cached.hpp
-include/ncbi-tools++/cgi/cgictx.hpp
-include/ncbi-tools++/cgi/error_codes.hpp
-include/ncbi-tools++/cgi/impl/cgi_entry_reader.hpp
-include/ncbi-tools++/cgi/ncbicgi.hpp
-include/ncbi-tools++/cgi/ncbicgir.hpp
-include/ncbi-tools++/cgi/ncbires.hpp
-include/ncbi-tools++/cgi/ref_args.hpp
-include/ncbi-tools++/cgi/user_agent.hpp
-include/ncbi-tools++/common/config/ncbiconf_msvc.h
-include/ncbi-tools++/common/config/ncbiconf_msvc_site.h
-include/ncbi-tools++/common/config/ncbiconf_universal.h
-include/ncbi-tools++/common/config/ncbiconf_xcode.h
-include/ncbi-tools++/common/config/ncbiconf_xcode_site.h
-include/ncbi-tools++/common/header_template.hpp
-include/ncbi-tools++/common/metamodules_doxygen.h
-include/ncbi-tools++/common/ncbi_export.h
-include/ncbi-tools++/common/ncbi_package_ver.h
-include/ncbi-tools++/common/ncbi_pch_impl.hpp
-include/ncbi-tools++/common/ncbi_skew_guard.h
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-include/ncbi-tools++/util/sequtil/sequtil_expt.hpp
-include/ncbi-tools++/util/sequtil/sequtil_manip.hpp
-include/ncbi-tools++/util/sgml_entity.hpp
-include/ncbi-tools++/util/simple_buffer.hpp
-include/ncbi-tools++/util/smalldns.hpp
-include/ncbi-tools++/util/static_map.hpp
-include/ncbi-tools++/util/static_set.hpp
-include/ncbi-tools++/util/strbuffer.hpp
-include/ncbi-tools++/util/strbuffer.inl
-include/ncbi-tools++/util/strsearch.hpp
-include/ncbi-tools++/util/sync_queue.hpp
-include/ncbi-tools++/util/table_printer.hpp
-include/ncbi-tools++/util/tables/raw_scoremat.h
-include/ncbi-tools++/util/tables/tables_export.h
-include/ncbi-tools++/util/text_joiner.hpp
-include/ncbi-tools++/util/thread_nonstop.hpp
-include/ncbi-tools++/util/thread_pool.hpp
-include/ncbi-tools++/util/thread_pool_ctrl.hpp
-include/ncbi-tools++/util/thread_pool_old.hpp
-include/ncbi-tools++/util/time_line.hpp
-include/ncbi-tools++/util/transmissionrw.hpp
-include/ncbi-tools++/util/unicode.hpp
-include/ncbi-tools++/util/utf8.hpp
-include/ncbi-tools++/util/util_exception.hpp
-include/ncbi-tools++/util/util_misc.hpp
-include/ncbi-tools++/util/uttp.hpp
-include/ncbi-tools++/util/value_convert.hpp
-include/ncbi-tools++/util/value_convert_policy.hpp
-include/ncbi-tools++/util/weakmap.hpp
-include/ncbi-tools++/util/weakmap.inl
-include/ncbi-tools++/util/xregexp/arg_regexp.hpp
-include/ncbi-tools++/util/xregexp/mask_regexp.hpp
-include/ncbi-tools++/util/xregexp/regexp.hpp
-lib/libaccess.so
-lib/libalign_format.so
-lib/libbiblio.so
-lib/libbiotree.so
-lib/libblast.so
-lib/libblast_app_util-static.a
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-lib/libblastxml.so
-lib/libblastxml2.so
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-lib/libentrez2.so
-lib/libentrez2cli.so
-lib/libentrezgene.so
-lib/libfeatdef.so
-lib/libgbproj-static.a
-lib/libgbproj.a
-lib/libgbseq.so
-lib/libgencoll_client-static.a
-lib/libgencoll_client.a
-lib/libgene_info.so
-lib/libgeneral.so
-lib/libgenesbyloc.so
-lib/libgenome_collection.so
-lib/libhomologene.so
-lib/libid1.so
-lib/libid1cli.so
-lib/libid2.so
-lib/libid2_split.so
-lib/libid2cli.so
-lib/libigblast.so
-lib/libinsdseq.so
-lib/libmacro.so
-lib/libmedlars.so
-lib/libmedline.so
-lib/libmim.so
-lib/libmla.so
-lib/libmlacli.so
-lib/libmmdb.so
-lib/libncbi_xblobstorage_netcache.so
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-lib/libxalnmgr.so
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diff --git a/ncbi-blast/PLIST.old b/ncbi-blast/PLIST.old
deleted file mode 100644
index 532a0352b1..0000000000
--- a/ncbi-blast/PLIST.old
+++ /dev/null
@@ -1,3789 +0,0 @@
-@comment $NetBSD: PLIST.old,v 1.1 2015/03/05 22:31:07 outpaddling Exp $
-@comment Diff this against the current PLIST. A few header files are missing.
-@comment Are we missing a dependency? The FreeBSD port installs many more files.
-bin/blast_formatter
-bin/blastdb_aliastool
-bin/blastdbcheck
-bin/blastdbcmd
-bin/blastdbcp
-bin/blastn
-bin/blastp
-bin/blastx
-bin/convert2blastmask
-bin/datatool
-bin/deltablast
-bin/dustmasker
-bin/gene_info_reader
-bin/legacy_blast.pl
-bin/makeblastdb
-bin/makembindex
-bin/makeprofiledb
-bin/project_tree_builder
-bin/psiblast
-bin/rpsblast
-bin/rpstblastn
-bin/seedtop
-bin/segmasker
-bin/seqdb_demo
-bin/seqdb_perf
-bin/tblastn
-bin/tblastx
-bin/update_blastdb.pl
-bin/windowmasker
-bin/windowmasker_2.2.22_adapter.py
-include/ncbi-tools++/algo/blast/api/bl2seq.hpp
-include/ncbi-tools++/algo/blast/api/blast_advprot_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_aux.hpp
-include/ncbi-tools++/algo/blast/api/blast_dbindex.hpp
-include/ncbi-tools++/algo/blast/api/blast_exception.hpp
-include/ncbi-tools++/algo/blast/api/blast_mtlock.hpp
-include/ncbi-tools++/algo/blast/api/blast_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_options_builder.hpp
-include/ncbi-tools++/algo/blast/api/blast_options_handle.hpp
-include/ncbi-tools++/algo/blast/api/blast_prot_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_results.hpp
-include/ncbi-tools++/algo/blast/api/blast_rps_options.hpp
-include/ncbi-tools++/algo/blast/api/blast_seqinfosrc.hpp
-include/ncbi-tools++/algo/blast/api/blast_seqinfosrc_aux.hpp
-include/ncbi-tools++/algo/blast/api/blast_types.hpp
-include/ncbi-tools++/algo/blast/api/blastx_options.hpp
-include/ncbi-tools++/algo/blast/api/cdd_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/deltablast.hpp
-include/ncbi-tools++/algo/blast/api/deltablast_options.hpp
-include/ncbi-tools++/algo/blast/api/disc_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/effsearchspace_calc.hpp
-include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
-include/ncbi-tools++/algo/blast/api/local_blast.hpp
-include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
-include/ncbi-tools++/algo/blast/api/local_search.hpp
-include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
-include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
-include/ncbi-tools++/algo/blast/api/phiblast_nucl_options.hpp
-include/ncbi-tools++/algo/blast/api/phiblast_prot_options.hpp
-include/ncbi-tools++/algo/blast/api/prelim_stage.hpp
-include/ncbi-tools++/algo/blast/api/psi_pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/psibl2seq.hpp
-include/ncbi-tools++/algo/blast/api/psiblast.hpp
-include/ncbi-tools++/algo/blast/api/psiblast_iteration.hpp
-include/ncbi-tools++/algo/blast/api/psiblast_options.hpp
-include/ncbi-tools++/algo/blast/api/pssm_engine.hpp
-include/ncbi-tools++/algo/blast/api/pssm_input.hpp
-include/ncbi-tools++/algo/blast/api/query_data.hpp
-include/ncbi-tools++/algo/blast/api/remote_blast.hpp
-include/ncbi-tools++/algo/blast/api/remote_search.hpp
-include/ncbi-tools++/algo/blast/api/repeats_filter.hpp
-include/ncbi-tools++/algo/blast/api/rps_aux.hpp
-include/ncbi-tools++/algo/blast/api/rpsblast_local.hpp
-include/ncbi-tools++/algo/blast/api/rpstblastn_options.hpp
-include/ncbi-tools++/algo/blast/api/search_strategy.hpp
-include/ncbi-tools++/algo/blast/api/seedtop.hpp
-include/ncbi-tools++/algo/blast/api/seqinfosrc_seqdb.hpp
-include/ncbi-tools++/algo/blast/api/seqinfosrc_seqvec.hpp
-include/ncbi-tools++/algo/blast/api/seqsrc_multiseq.hpp
-include/ncbi-tools++/algo/blast/api/seqsrc_seqdb.hpp
-include/ncbi-tools++/algo/blast/api/setup_factory.hpp
-include/ncbi-tools++/algo/blast/api/sseqloc.hpp
-include/ncbi-tools++/algo/blast/api/subj_ranges_set.hpp
-include/ncbi-tools++/algo/blast/api/tblastn_options.hpp
-include/ncbi-tools++/algo/blast/api/tblastx_options.hpp
-include/ncbi-tools++/algo/blast/api/traceback_stage.hpp
-include/ncbi-tools++/algo/blast/api/uniform_search.hpp
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-include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
-include/ncbi-tools++/algo/blast/blastinput/blast_scope_src.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastp_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/blastx_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
-include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/rpstblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/tblastn_args.hpp
-include/ncbi-tools++/algo/blast/blastinput/tblastx_args.hpp
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-include/ncbi-tools++/util/table_printer.hpp
-include/ncbi-tools++/util/tables/raw_scoremat.h
-include/ncbi-tools++/util/tables/tables_export.h
-include/ncbi-tools++/util/text_joiner.hpp
-include/ncbi-tools++/util/thread_nonstop.hpp
-include/ncbi-tools++/util/thread_pool.hpp
-include/ncbi-tools++/util/thread_pool_ctrl.hpp
-include/ncbi-tools++/util/thread_pool_old.hpp
-include/ncbi-tools++/util/time_line.hpp
-include/ncbi-tools++/util/transmissionrw.hpp
-include/ncbi-tools++/util/unicode.hpp
-include/ncbi-tools++/util/utf8.hpp
-include/ncbi-tools++/util/util_exception.hpp
-include/ncbi-tools++/util/util_misc.hpp
-include/ncbi-tools++/util/uttp.hpp
-include/ncbi-tools++/util/value_convert.hpp
-include/ncbi-tools++/util/value_convert_policy.hpp
-include/ncbi-tools++/util/weakmap.hpp
-include/ncbi-tools++/util/weakmap.inl
-include/ncbi-tools++/util/xregexp/arg_regexp.hpp
-include/ncbi-tools++/util/xregexp/mask_regexp.hpp
-include/ncbi-tools++/util/xregexp/regexp.hpp
-lib/libaccess.so
-lib/libalign_format.so
-lib/libbiblio.so
-lib/libbiotree.so
-lib/libblast.so
-lib/libblast_app_util-static.a
-lib/libblast_app_util.a
-lib/libblast_services.so
-lib/libblastdb.so
-lib/libblastdb_format.so
-lib/libblastinput.so
-lib/libblastxml.so
-lib/libblastxml2.so
-lib/libcdd.so
-lib/libcn3d.so
-lib/libcomposition_adjustment.so
-lib/libconnect.so
-lib/libconnext.so
-lib/libconnssl.so
-lib/libcreaders.so
-lib/libdbapi.so
-lib/libdbapi_driver-static.a
-lib/libdbapi_driver.a
-lib/libdbapi_driver.so
-lib/libdocsum.so
-lib/libentrez2.so
-lib/libentrez2cli.so
-lib/libentrezgene.so
-lib/libfeatdef.so
-lib/libgbproj-static.a
-lib/libgbproj.a
-lib/libgbseq.so
-lib/libgencoll_client-static.a
-lib/libgencoll_client.a
-lib/libgene_info.so
-lib/libgeneral.so
-lib/libgenesbyloc.so
-lib/libgenome_collection.so
-lib/libhomologene.so
-lib/libid1.so
-lib/libid1cli.so
-lib/libid2.so
-lib/libid2_split.so
-lib/libid2cli.so
-lib/libigblast.so
-lib/libinsdseq.so
-lib/libmacro.so
-lib/libmedlars.so
-lib/libmedline.so
-lib/libmim.so
-lib/libmla.so
-lib/libmlacli.so
-lib/libmmdb.so
-lib/libncbi_xblobstorage_netcache.so
-lib/libncbi_xcache_dbapi-static.a
-lib/libncbi_xcache_dbapi.a
-lib/libncbi_xcache_dbapi.so
-lib/libncbi_xcache_netcache-static.a
-lib/libncbi_xcache_netcache.a
-lib/libncbi_xcache_netcache.so
-lib/libncbi_xloader_blastdb.so
-lib/libncbi_xloader_blastdb_rmt.so
-lib/libncbi_xloader_genbank-static.a
-lib/libncbi_xloader_genbank.a
-lib/libncbi_xloader_genbank.so
-lib/libncbi_xreader-static.a
-lib/libncbi_xreader.a
-lib/libncbi_xreader.so
-lib/libncbi_xreader_cache-static.a
-lib/libncbi_xreader_cache.a
-lib/libncbi_xreader_cache.so
-lib/libncbi_xreader_gicache-static.a
-lib/libncbi_xreader_gicache.a
-lib/libncbi_xreader_gicache.so
-lib/libncbi_xreader_id1-static.a
-lib/libncbi_xreader_id1.a
-lib/libncbi_xreader_id1.so
-lib/libncbi_xreader_id2-static.a
-lib/libncbi_xreader_id2.a
-lib/libncbi_xreader_id2.so
-lib/libncbimime.so
-lib/libobjcoords.so
-lib/libobjprt.so
-lib/libomssa.so
-lib/libpcassay.so
-lib/libpcsubstance.so
-lib/libproj.so
-lib/libpub.so
-lib/libpubmed.so
-lib/libremap.so
-lib/libremapcli.so
-lib/libscoremat.so
-lib/libseq.so
-lib/libseqcode.so
-lib/libseqdb.so
-lib/libseqedit.so
-lib/libseqmasks_io.so
-lib/libseqset.so
-lib/libseqsplit.so
-lib/libseqtest.so
-lib/libsequtil.so
-lib/libsubmit.so
-lib/libtables.so
-lib/libtaxon1.so
-lib/libtaxon3.so
-lib/libtest_mt.so
-lib/libtinyseq.so
-lib/libtrackmgr-static.a
-lib/libtrackmgr.a
-lib/libtrackmgrcli-static.a
-lib/libtrackmgrcli.a
-lib/libtrackmgrgridcli-static.a
-lib/libtrackmgrgridcli.a
-lib/libvalerr.so
-lib/libvalid.so
-lib/libvariation.so
-lib/libwritedb.so
-lib/libxalgoblastdbindex.so
-lib/libxalgodustmask.so
-lib/libxalgosegmask.so
-lib/libxalgowinmask.so
-lib/libxalnmgr.so
-lib/libxblast.so
-lib/libxblastformat.so
-lib/libxcgi.so
-lib/libxcleanup.so
-lib/libxcompress.so
-lib/libxconnect.so
-lib/libxconnext.so
-lib/libxconnserv.so
-lib/libxcser.so
-lib/libxfcgi.so
-lib/libxformat.so
-lib/libxhtml.so
-lib/libxncbi.so
-lib/libxnetblast.so
-lib/libxnetblastcli.so
-lib/libxobjedit.so
-lib/libxobjmgr.so
-lib/libxobjread.so
-lib/libxobjreadex.so
-lib/libxobjsimple.so
-lib/libxobjutil.so
-lib/libxregexp.so
-lib/libxser.so
-lib/libxthrserv.so
-lib/libxutil.so
-lib/libxxconnect.so
diff --git a/ncbi-blast/buildlink3.mk b/ncbi-blast/buildlink3.mk
deleted file mode 100644
index 3acd06c4d3..0000000000
--- a/ncbi-blast/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.2 2014/10/08 12:44:35 fhajny Exp $
-
-BUILDLINK_TREE+= blast
-
-.if !defined(BLAST_BUILDLINK3_MK)
-BLAST_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.blast+= blast>=2.2.29
-BUILDLINK_PKGSRCDIR.blast?= ../../wip/ncbi-blast
-.endif # BLAST_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -blast
diff --git a/ncbi-blast/distinfo b/ncbi-blast/distinfo
deleted file mode 100644
index 3be227930f..0000000000
--- a/ncbi-blast/distinfo
+++ /dev/null
@@ -1,7 +0,0 @@
-$NetBSD: distinfo,v 1.6 2015/03/05 22:31:07 outpaddling Exp $
-
-SHA1 (ncbi-blast-2.2.30+-src.tar.gz) = 2b4a36559dc06ef0321f81d2615f429f2ab5fb21
-RMD160 (ncbi-blast-2.2.30+-src.tar.gz) = af8b04f0bb6ae6c58195aa9d2ae8d467483450eb
-Size (ncbi-blast-2.2.30+-src.tar.gz) = 18985378 bytes
-SHA1 (patch-src_build-system_Makefile.in.top) = 1948585a8609045bafb7c6e2e4a6444836e10c83
-SHA1 (patch-src_build-system_configure) = be7784de4737194aff2bda483ffc266ed9d40cb1
diff --git a/ncbi-blast/patches/patch-src_build-system_Makefile.in.top b/ncbi-blast/patches/patch-src_build-system_Makefile.in.top
deleted file mode 100644
index 6501c0f462..0000000000
--- a/ncbi-blast/patches/patch-src_build-system_Makefile.in.top
+++ /dev/null
@@ -1,49 +0,0 @@
-$NetBSD: patch-src_build-system_Makefile.in.top,v 1.2 2014/10/09 16:51:53 outpaddling Exp $
-
-Add DESTDIR support.
---- src/build-system/Makefile.in.top.orig 2014-08-01 18:43:59.000000000 +0000
-+++ src/build-system/Makefile.in.top
-@@ -36,30 +36,30 @@ check: $(PROJECTS)
- fi
-
- install-toolkit:
-- -$(RMDIR) $(pincludedir)
-- $(INSTALL) -d $(bindir) $(libdir) $(pincludedir)
-- $(INSTALL) $(lbindir)/* $(bindir)
-- $(INSTALL) -m 644 $(llibdir)/*.* $(libdir)
-+ -$(RMDIR) $(DESTDIR)$(pincludedir)
-+ $(INSTALL) -d $(DESTDIR)$(bindir) $(DESTDIR)$(libdir) $(DESTDIR)$(pincludedir)
-+ $(INSTALL) $(lbindir)/* $(DESTDIR)$(bindir)
-+ $(INSTALL) -m 644 $(llibdir)/*.* $(DESTDIR)$(libdir)
- if test -d $(llibdir)/ncbi; then \
-- cp -pPR $(llibdir)/ncbi $(libdir)/; \
-+ cp -pPR $(llibdir)/ncbi $(DESTDIR)$(libdir)/; \
- fi
-- -rm -f $(libdir)/lib*-static.a
-- cd $(libdir) && \
-+ -rm -f $(DESTDIR)$(libdir)/lib*-static.a
-+ cd $(DESTDIR)$(libdir) && \
- for x in *.a; do \
-- $(LN_S) "$$x" "`/usr/bin/basename \"$$x\" .a`-static.a"; \
-+ $(LN_S) "$$x" "`basename \"$$x\" .a`-static.a"; \
- done
- cd $(includedir0) && find * -name CVS -prune -o -print |\
-- cpio -pd $(pincludedir)
-- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
-+ cpio -pd $(DESTDIR)$(pincludedir)
-+ $(INSTALL) -m 644 $(incdir)/* $(DESTDIR)$(pincludedir)
- ## set up appropriate build and status directories somewhere under $(libdir)?
-
- install-gbench:
- cd $(builddir)/app/gbench/gbench_install && \
-- $(MAKE) $(MFLAGS) install_dir=$(exec_prefix)
-+ $(MAKE) $(MFLAGS) install_dir=$(DESTDIR)$(exec_prefix)
-
- install:
- if test -d $(lbindir)/gbench; then \
-- $(MAKE) $(MFLAGS) install-gbench; \
-+ $(MAKE) $(MFLAGS) $(DESTDIR) install-gbench; \
- else \
-- $(MAKE) $(MFLAGS) install-toolkit; \
-+ $(MAKE) $(MFLAGS) $(DESTDIR) install-toolkit; \
- fi
diff --git a/ncbi-blast/patches/patch-src_build-system_configure b/ncbi-blast/patches/patch-src_build-system_configure
deleted file mode 100644
index ce589ea9b8..0000000000
--- a/ncbi-blast/patches/patch-src_build-system_configure
+++ /dev/null
@@ -1,410 +0,0 @@
-$NetBSD: patch-src_build-system_configure,v 1.3 2014/10/13 17:11:52 fhajny Exp $
-
-Fix --infodir/--mandir support. Add fake --with-libiconv-prefix and
---with-libintl-prefix options.
-Change logic to disable all 3rd party support and enable one by one.
---- src/build-system/configure.orig 2014-09-08 15:04:15.000000000 +0000
-+++ src/build-system/configure
-@@ -1588,6 +1588,7 @@ for x_arg in "$@" ; do
- | --with-universal=* | --with-tcheck=* \
- | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \
- | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \
-+ | --infodir=* | --mandir=* | --with-libiconv-prefix=* | --with-libintl-prefix=* \
- | [A-Z]*=* \
- | --with-z=* | --with-bz2=* | --with-lzo=* \
- | --with-pcre=* | --with-ncbi-c=* | --with-sss=* \
-@@ -2038,338 +2039,282 @@ case "$with_3psw" in
- ;;
- no )
- if test "${with_ncbi_c-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-ncbi-c but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_ncbi_c=no
- fi
- if test "${with_sss-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sss but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sss=no
- fi
- if test "${with_sssutils-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sssutils but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sssutils=no
- fi
- if test "${with_sssdb-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sssdb but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sssdb=no
- fi
- if test "${with_z-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-z but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_z=no
- fi
- if test "${with_bz2-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-bz2 but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_bz2=no
- fi
- if test "${with_lzo-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-lzo but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_lzo=no
- fi
- if test "${with_pcre-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-pcre but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_pcre=no
- fi
- if test "${with_gcrypt-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-gcrypt but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_gcrypt=no
- fi
- if test "${with_gnutls-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-gnutls but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_gnutls=no
- fi
- if test "${with_openssl-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-openssl but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_openssl=no
- fi
- if test "${with_krb5-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-krb5 but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_krb5=no
- fi
- if test "${with_boost-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-boost but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_boost=no
- fi
- if test "${with_sybase-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sybase but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sybase=no
- fi
- if test "${with_ftds-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-ftds but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_ftds=no
- fi
- if test "${with_mysql-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-mysql but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_mysql=no
- fi
- if test "${with_opengl-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-opengl but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_opengl=no
- fi
- if test "${with_mesa-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-mesa but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_mesa=no
- fi
- if test "${with_glut-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-glut but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_glut=no
- fi
- if test "${with_glew-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-glew but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_glew=no
- fi
- if test "${with_wxwidgets-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-wxwidgets but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_wxwidgets=no
- fi
- if test "${with_freetype-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-freetype but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_freetype=no
- fi
- if test "${with_ftgl-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-ftgl but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_ftgl=no
- fi
- if test "${with_fastcgi-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-fastcgi but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_fastcgi=no
- fi
- if test "${with_bdb-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-bdb but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_bdb=no
- fi
- if test "${with_orbacus-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-orbacus but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_orbacus=no
- fi
- if test "${with_odbc-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-odbc but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_odbc=no
- fi
- if test "${with_python-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-python but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_python=no
- fi
- if test "${with_perl-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-perl but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_perl=no
- fi
- if test "${with_jni-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-jni but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_jni=no
- fi
- if test "${with_sqlite3-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sqlite3 but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sqlite3=no
- fi
- if test "${with_mimetic-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-mimetic but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_mimetic=no
- fi
- if test "${with_sge-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sge but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sge=no
- fi
- if test "${with_icu-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-icu but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_icu=no
- fi
- if test "${with_sp-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sp but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sp=no
- fi
- if test "${with_expat-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-expat but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_expat=no
- fi
- if test "${with_sablot-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-sablot but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_sablot=no
- fi
- if test "${with_libxml-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-libxml but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_libxml=no
- fi
- if test "${with_libxslt-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-libxslt but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_libxslt=no
- fi
- if test "${with_libexslt-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-libexslt but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_libexslt=no
- fi
- if test "${with_xerces-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-xerces but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_xerces=no
- fi
- if test "${with_xalan-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-xalan but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_xalan=no
- fi
- if test "${with_zorba-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-zorba but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_zorba=no
- fi
- if test "${with_oechem-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-oechem but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_oechem=no
- fi
- if test "${with_muparser-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-muparser but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_muparser=no
- fi
- if test "${with_hdf5-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-hdf5 but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_hdf5=no
- fi
- if test "${with_gif-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-gif but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_gif=no
- fi
- if test "${with_jpeg-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-jpeg but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_jpeg=no
- fi
- if test "${with_png-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-png but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_png=no
- fi
- if test "${with_tiff-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-tiff but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_tiff=no
- fi
- if test "${with_xpm-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-xpm but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_xpm=no
- fi
- if test "${with_magic-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-magic but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_magic=no
- fi
- if test "${with_curl-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-curl but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_curl=no
- fi
- if test "${with_gsoap-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-gsoap but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_gsoap=no
- fi
- if test "${with_avro-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-avro but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_avro=no
- fi
- if test "${with_mongodb-no}" != "no"; then
-- { echo "$as_me: error: incompatible options: --with-mongodb but --without-3psw" >&2
-- { (exit 1); exit 1; }; }
-+ true
- else
- with_mongodb=no
- fi
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