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ncbi-blast+: Testing upgrade to 2.8.1

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Jan 1 19:47:28 2019 -0600
Changeset:	08235aab321203b034019ec0103b8081d579d714

Modified Files:
	Makefile
Added Files:
	ncbi-blast+/DESCR
	ncbi-blast+/Makefile
	ncbi-blast+/PLIST
	ncbi-blast+/buildlink3.mk
	ncbi-blast+/distinfo
	ncbi-blast+/patch-src_algo_blast_core_blast__kappa.c
	ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
	ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
	ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
	ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
	ncbi-blast+/patches/patch-src_build-system_configure
	ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app

Log Message:
ncbi-blast+: Testing upgrade to 2.8.1

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=08235aab321203b034019ec0103b8081d579d714

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                           |    1 +
 ncbi-blast+/DESCR                                  |    5 +
 ncbi-blast+/Makefile                               |   68 +
 ncbi-blast+/PLIST                                  | 4113 ++++++++++++++++++++
 ncbi-blast+/buildlink3.mk                          |   13 +
 ncbi-blast+/distinfo                               |   12 +
 .../patch-src_algo_blast_core_blast__kappa.c       |   31 +
 .../patches/patch-compilers_xcode30__prj_configure |   15 +
 .../patches/patch-src_build-system_Makefile.in.top |   41 +
 .../patch-src_build-system_cmake_cmake-cfg-unix.sh |   15 +
 .../patch-src_build-system_cmake_cmake-configure   |   15 +
 .../patches/patch-src_build-system_configure       |   15 +
 ...ild-system_helpers_Makefile.run__with__lock.app |   20 +
 13 files changed, 4364 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 46f55f147b..cf68dbef80 100644
--- a/Makefile
+++ b/Makefile
@@ -2241,6 +2241,7 @@ SUBDIR+=	navit-git
 SUBDIR+=	nbfc
 SUBDIR+=	ncbi
 SUBDIR+=	ncbi-bin
+SUBDIR+=	ncbi-blast+
 SUBDIR+=	ncbi-c++-lib
 SUBDIR+=	ncbi-lib
 SUBDIR+=	ncp
diff --git a/ncbi-blast+/DESCR b/ncbi-blast+/DESCR
new file mode 100644
index 0000000000..0d7c1d401b
--- /dev/null
+++ b/ncbi-blast+/DESCR
@@ -0,0 +1,5 @@
+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+/Makefile b/ncbi-blast+/Makefile
new file mode 100644
index 0000000000..b05668d6d4
--- /dev/null
+++ b/ncbi-blast+/Makefile
@@ -0,0 +1,68 @@
+# $NetBSD: Makefile,v 1.4 2018/07/20 03:34:03 ryoon Exp $
+
+DISTNAME=	ncbi-blast-${PV}+-src
+PKGNAME=	ncbi-blast+-${PV}
+CATEGORIES=	biology
+MASTER_SITES=	https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
+		https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PV}/
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://blast.ncbi.nlm.nih.gov/
+COMMENT=	NCBI implementation of Basic Local Alignment Search Tool
+LICENSE=	public-domain
+
+# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
+# Fix "unknown options" in configure
+SUBST_CLASSES+=		configure
+SUBST_STAGE.configure=	pre-configure
+SUBST_SED.configure+=	-e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
+SUBST_SED.configure+=	-e '/--infodir=DIR/d'
+SUBST_SED.configure+=	-e '/--mandir=DIR/d'
+SUBST_FILES.configure+=	${WRKSRC}/src/build-system/configure
+
+USE_TOOLS+=	gmake
+USE_LANGUAGES=	c c++
+GNU_CONFIGURE=	yes
+# REPLACE_BASH=	compilers/xcode30_prj/configure
+REPLACE_PERL=	src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
+REPLACE_PYTHON=	src/app/winmasker/windowmasker_2.2.22_adapter.py
+
+# The test for amq can hang, but amq is not needed so just avoid the test
+# configure chooses /usr/local/bin/ar with no flags
+# Resolve a conflict with libproj by moving libs to a subdir
+CONFIGURE_ENV=		ncbi_cv_prog_amq_w=no
+CONFIGURE_ARGS+=	AR="ar cr" --without-boost
+CONFIGURE_ARGS+=	--libdir=${PREFIX}/lib/ncbi-tools++
+# MAKE_JOBS_SAFE=		no	# Intermittent issues
+WRKSRC=			${WRKDIR}/${DISTNAME}/c++
+
+.include "../../mk/bsd.prefs.mk"
+
+.if ${OPSYS} == NetBSD
+# statfs is deprecated on NetBSD, but still exists in libc
+# configure checks only for undefined reference, not for usability
+CONFIGURE_ENV+=		ac_cv_func_statfs=no
+.endif
+
+PV=	2.8.1
+
+post-install:
+	${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
+	${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/lzo/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../devel/pcre/buildlink3.mk"
+.include "../../databases/lmdb/buildlink3.mk"
+.include "../../security/gnutls/buildlink3.mk"
+.include "../../devel/gmp/buildlink3.mk"
+.include "../../devel/libidn2/buildlink3.mk"
+.include "../../security/nettle/buildlink3.mk"
+.include "../../security/libtasn1/buildlink3.mk"
+.include "../../security/p11-kit/buildlink3.mk"
+.include "../../security/libgcrypt/buildlink3.mk"
+.include "../../databases/sqlite3/buildlink3.mk"
+.include "../../security/libgpg-error/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
new file mode 100644
index 0000000000..3d4dd3c282
--- /dev/null
+++ b/ncbi-blast+/PLIST
@@ -0,0 +1,4113 @@
+@comment $NetBSD: PLIST,v 1.1 2018/04/27 20:28:28 bacon 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/gc_cli
+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/run_with_lock
+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/blastp_kmer_options.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/magicblast.hpp
+include/ncbi-tools++/algo/blast/api/magicblast_options.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_asn1_input.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/kblastp_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/magicblast_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/hspfilter_mapper.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/spliced_hits.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_async_format.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/sam.hpp
+include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
+include/ncbi-tools++/algo/blast/igblast/igblast.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmer.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerindex.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmeroptions.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerresults.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/blastkmerutils.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/kblastapi.hpp
+include/ncbi-tools++/algo/blast/proteinkmer/mhfile.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_version.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/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/boost_skew_guard.hpp
+include/ncbi-tools++/common/config/ncbiconf_msvc.h
+include/ncbi-tools++/common/config/ncbiconf_universal.h
+include/ncbi-tools++/common/config/ncbiconf_xcode.h
+include/ncbi-tools++/common/header_template.hpp
+include/ncbi-tools++/common/metamodules_doxygen.h
+include/ncbi-tools++/common/ncbi_build_ver.h
+include/ncbi-tools++/common/ncbi_build_ver.h.in
+include/ncbi-tools++/common/ncbi_build_ver.h.last
+include/ncbi-tools++/common/ncbi_export.h
+include/ncbi-tools++/common/ncbi_package_ver.h
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+lib/ncbi-tools++/libxconnserv.a
+lib/ncbi-tools++/libxcser-static.a
+lib/ncbi-tools++/libxcser.a
+lib/ncbi-tools++/libxfcgi-static.a
+lib/ncbi-tools++/libxfcgi.a
+lib/ncbi-tools++/libxformat-static.a
+lib/ncbi-tools++/libxformat.a
+lib/ncbi-tools++/libxhtml-static.a
+lib/ncbi-tools++/libxhtml.a
+lib/ncbi-tools++/libxncbi-static.a
+lib/ncbi-tools++/libxncbi.a
+lib/ncbi-tools++/libxnetblast-static.a
+lib/ncbi-tools++/libxnetblast.a
+lib/ncbi-tools++/libxnetblastcli-static.a
+lib/ncbi-tools++/libxnetblastcli.a
+lib/ncbi-tools++/libxobjedit-static.a
+lib/ncbi-tools++/libxobjedit.a
+lib/ncbi-tools++/libxobjmgr-static.a
+lib/ncbi-tools++/libxobjmgr.a
+lib/ncbi-tools++/libxobjread-static.a
+lib/ncbi-tools++/libxobjread.a
+lib/ncbi-tools++/libxobjreadex-static.a
+lib/ncbi-tools++/libxobjreadex.a
+lib/ncbi-tools++/libxobjsimple-static.a
+lib/ncbi-tools++/libxobjsimple.a
+lib/ncbi-tools++/libxobjutil-static.a
+lib/ncbi-tools++/libxobjutil.a
+lib/ncbi-tools++/libxregexp-static.a
+lib/ncbi-tools++/libxregexp.a
+lib/ncbi-tools++/libxregexp_template_tester-static.a
+lib/ncbi-tools++/libxregexp_template_tester.a
+lib/ncbi-tools++/libxser-static.a
+lib/ncbi-tools++/libxser.a
+lib/ncbi-tools++/libxthrserv-static.a
+lib/ncbi-tools++/libxthrserv.a
+lib/ncbi-tools++/libxutil-static.a
+lib/ncbi-tools++/libxutil.a
+lib/ncbi-tools++/libxxconnect-static.a
+lib/ncbi-tools++/libxxconnect.a
diff --git a/ncbi-blast+/buildlink3.mk b/ncbi-blast+/buildlink3.mk
new file mode 100644
index 0000000000..056086d48e
--- /dev/null
+++ b/ncbi-blast+/buildlink3.mk
@@ -0,0 +1,13 @@
+# $NetBSD: buildlink3.mk,v 1.2 2018/04/29 21:00:04 adam Exp $
+
+BUILDLINK_TREE+=	ncbi-blast+
+
+.if !defined(NCBI_BLAST+_BUILDLINK3_MK)
+NCBI_BLAST+_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.ncbi-blast++=	ncbi-blast+>=2.8.1
+BUILDLINK_PKGSRCDIR.ncbi-blast+?=	../../biology/ncbi-blast+
+
+.endif	# NCBI_BLAST+_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-ncbi-blast+
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
new file mode 100644
index 0000000000..50453dddda
--- /dev/null
+++ b/ncbi-blast+/distinfo
@@ -0,0 +1,12 @@
+$NetBSD$
+
+SHA1 (ncbi-blast-2.8.1+-src.tar.gz) = 16573b642d7861d0bed67f3eb1174fc646819eec
+RMD160 (ncbi-blast-2.8.1+-src.tar.gz) = ef8df6c4b3cae18b2ab4509af15554ee8d8f9bfd
+SHA512 (ncbi-blast-2.8.1+-src.tar.gz) = 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f
+Size (ncbi-blast-2.8.1+-src.tar.gz) = 24973554 bytes
+SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
+SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
+SHA1 (patch-src_build-system_cmake_cmake-cfg-unix.sh) = 90468f3109800e01fc7351926adb331919a12fb2
+SHA1 (patch-src_build-system_cmake_cmake-configure) = 7b9a10447b1dd665200ee73a2180b3210f586b97
+SHA1 (patch-src_build-system_configure) = 90becd948f8aca87fd68081e689bdc8c49b419c6
+SHA1 (patch-src_build-system_helpers_Makefile.run__with__lock.app) = d69b9e349646c970c3b296707f917defbe39cccd
diff --git a/ncbi-blast+/patch-src_algo_blast_core_blast__kappa.c b/ncbi-blast+/patch-src_algo_blast_core_blast__kappa.c
new file mode 100644
index 0000000000..328c1f2a82
--- /dev/null
+++ b/ncbi-blast+/patch-src_algo_blast_core_blast__kappa.c
@@ -0,0 +1,31 @@
+$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+# Work around NetBSD stderr def choking macro
+
+--- src/algo/blast/core/blast_kappa.c.orig	2018-03-26 21:55:44.000000000 +0000
++++ src/algo/blast/core/blast_kappa.c
+@@ -32,6 +32,7 @@
+  * system for each match in blastpgp
+  */
+ 
++#include <stdio.h>
+ #include <float.h>
+ #include <algo/blast/core/ncbi_math.h>
+ #include <algo/blast/core/blast_hits.h>
+@@ -3404,13 +3405,15 @@ Blast_RedoAlignmentCore_MT(EBlastProgram
+     }
+ 
+     Boolean interrupt = FALSE;
++    /* NetBSD defines stderr as (&__sF[2]), which the macro below chokes on */
++    FILE *my_stderr = stderr;
+ #pragma omp parallel \
+     default(none) num_threads(actual_num_threads) \
+     if(actual_num_threads>1) \
+     shared(interrupt, seqsrc_tld, score_params_tld, hit_params_tld, \
+     gap_align_tld, results_tld, \
+     redoneMatches_tld, \
+-    stderr, \
++    my_stderr, \
+     numQueries, numMatches, theseMatches, \
+     numFrames, program_number, subjectBlk_tld, positionBased, \
+     default_db_genetic_code, localScalingFactor, queryInfo, \
diff --git a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
new file mode 100644
index 0000000000..7cc26bd745
--- /dev/null
+++ b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
@@ -0,0 +1,15 @@
+$NetBSD: patch-compilers_xcode30__prj_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+# Nonportable extension
+
+--- compilers/xcode30_prj/configure.orig	2018-04-27 14:19:43.000000000 +0000
++++ compilers/xcode30_prj/configure
+@@ -280,7 +280,7 @@ arch=`arch`
+ platform=`xcodebuild -version 2>/dev/null | grep 'Xcode [0-9][0-9]*' | sed -e 's/[ .]//g'`
+ 
+ # ------- target architecture
+-if test "$use_64" == "yes"; then
++if test "$use_64" = "yes"; then
+   use_arch="x86_64"
+ else
+   use_arch="i386"
diff --git a/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top b/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
new file mode 100644
index 0000000000..b45adbd2d5
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
@@ -0,0 +1,41 @@
+$NetBSD: patch-src_build-system_Makefile.in.top,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+# Add destdir suppot and fix perms on installed files
+
+--- src/build-system/Makefile.in.top.orig	2017-02-01 16:52:02.000000000 +0000
++++ src/build-system/Makefile.in.top
+@@ -37,22 +37,26 @@ 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) -m 755 $(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) "$$x" "`$(BASENAME) \"$$x\" .a`-static.a"; \
+ 	    done
++	find $(DESTDIR)$(libdir) -name '*.a' -exec chmod 644 '{}' \;
++	find $(DESTDIR)$(libdir) -name '*.so*' -exec chmod 755 '{}' \;
+ 	for d in $(includedir0) $(incdir); do \
+ 	    cd $$d && find * -name .svn -prune -o -print | \
+-                cpio -pd $(pincludedir) ; \
++                cpio -pd $(DESTDIR)$(pincludedir) ; \
+ 	done
++	find $(DESTDIR)$(pincludedir) -type f -exec chmod 644 '{}' \;
++	find $(DESTDIR)$(pincludedir) -type d -exec chmod 755 '{}' \;
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+ 
+ install-gbench:
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
new file mode 100644
index 0000000000..c51cfed7ca
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- src/build-system/cmake/cmake-cfg-unix.sh.orig	2019-01-02 01:22:44.549100012 +0000
++++ src/build-system/cmake/cmake-cfg-unix.sh
+@@ -166,7 +166,7 @@ CMAKE_ARGS="$CMAKE_ARGS -DBUILD_SHARED_L
+ CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_CCACHE=$USE_CCACHE"
+ CMAKE_ARGS="$CMAKE_ARGS -DCMAKE_USE_DISTCC=$USE_DISTCC"
+ build_root=CMake-${CC_NAME}${CC_VERSION}-${BUILD_TYPE}
+-if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
++if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
+   build_root="$build_root"DLL
+ fi
+ #build_root="$build_root"64
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
new file mode 100644
index 0000000000..afa61932c7
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_build-system_cmake_cmake-configure,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+# Fix portability issue
+
+--- src/build-system/cmake/cmake-configure.orig	2018-03-26 14:13:44.229849356 +0000
++++ src/build-system/cmake/cmake-configure
+@@ -468,7 +468,7 @@ fi
+ if [ -z "$ROOT" ]; then
+     if [ -z "$GPIPEROOT" ]; then
+         ROOT="CMake-$BUILD_TYPE"
+-        if [ "$BUILD_SHARED_LIBS" == "ON" ]; then
++        if [ "$BUILD_SHARED_LIBS" = "ON" ]; then
+             ROOT="$ROOT"DLL
+         fi
+     else
diff --git a/ncbi-blast+/patches/patch-src_build-system_configure b/ncbi-blast+/patches/patch-src_build-system_configure
new file mode 100644
index 0000000000..466f7b69c5
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_configure
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_build-system_configure,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+# Fix support for localstatedir
+
+--- src/build-system/configure.orig	2018-02-19 01:32:40 UTC
++++ src/build-system/configure
+@@ -1755,7 +1755,7 @@ for x_arg in "$@" ; do
+       | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+       | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
+       | --datadir=* | --sysconfdir=* | --localstatedir=* \
+-      | --with-runpath=* | --with-relative-runpath=* \
++      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
+       | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
+       | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
+       | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
diff --git a/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app b/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
new file mode 100644
index 0000000000..036b153d87
--- /dev/null
+++ b/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
@@ -0,0 +1,20 @@
+$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.2 2018/05/22 21:37:29 bacon Exp $
+
+# Missing RELRO for this one binary
+# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820959
+
+--- src/build-system/helpers/Makefile.run_with_lock.app.orig	2016-02-23 17:06:47.000000000 +0000
++++ src/build-system/helpers/Makefile.run_with_lock.app
+@@ -6,9 +6,9 @@ CC          = $(CC_FOR_BUILD)
+ CC_WRAPPER  =
+ CXX_WRAPPER =
+ CPP         = $(CPP_FOR_BUILD)
+-CFLAGS      = $(CFLAGS_FOR_BUILD)
+-CPPFLAGS    = $(CPPFLAGS_FOR_BUILD)
+-LDFLAGS     = $(LDFLAGS_FOR_BUILD)
++CFLAGS      := $(CFLAGS_FOR_BUILD) $(CFLAGS)
++CPPFLAGS    := $(CPPFLAGS_FOR_BUILD) $(CPPFLAGS)
++LDFLAGS     := $(LDFLAGS_FOR_BUILD) $(LDFLAGS)
+ LIBS        = $(C_LIBS)
+ LINK        = $(CC)
+ LINK_WRAPPER =
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