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CVS commit: pkgsrc/biology/ncbi-blast+
Module Name: pkgsrc
Committed By: bacon
Date: Fri Apr 27 20:28:28 UTC 2018
Added Files:
pkgsrc/biology/ncbi-blast+: DESCR Makefile PLIST buildlink3.mk distinfo
pkgsrc/biology/ncbi-blast+/patches:
patch-compilers_xcode30__prj_configure
patch-src_algo_blast_core_blast__kappa.c
patch-src_build-system_Makefile.in.top
patch-src_build-system_cmake_cmake-configure
patch-src_build-system_configure
patch-src_build-system_helpers_Makefile.run__with__lock.app
Log Message:
biology/ncbi-blast+: import ncbi-blast+-2.7.1
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.
OK wiz@
To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/ncbi-blast+/DESCR \
pkgsrc/biology/ncbi-blast+/Makefile pkgsrc/biology/ncbi-blast+/PLIST \
pkgsrc/biology/ncbi-blast+/buildlink3.mk \
pkgsrc/biology/ncbi-blast+/distinfo
cvs rdiff -u -r0 -r1.1 \
pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure \
pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure \
pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Added files:
Index: pkgsrc/biology/ncbi-blast+/DESCR
diff -u /dev/null pkgsrc/biology/ncbi-blast+/DESCR:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/DESCR Fri Apr 27 20:28:28 2018
@@ -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.
Index: pkgsrc/biology/ncbi-blast+/Makefile
diff -u /dev/null pkgsrc/biology/ncbi-blast+/Makefile:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/Makefile Fri Apr 27 20:28:28 2018
@@ -0,0 +1,68 @@
+# $NetBSD: Makefile,v 1.1 2018/04/27 20:28:28 bacon 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= post-patch
+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= 2.7.1
+
+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"
Index: pkgsrc/biology/ncbi-blast+/PLIST
diff -u /dev/null pkgsrc/biology/ncbi-blast+/PLIST:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/PLIST Fri Apr 27 20:28:28 2018
@@ -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
+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/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
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+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
Index: pkgsrc/biology/ncbi-blast+/buildlink3.mk
diff -u /dev/null pkgsrc/biology/ncbi-blast+/buildlink3.mk:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/buildlink3.mk Fri Apr 27 20:28:28 2018
@@ -0,0 +1,13 @@
+# $NetBSD: buildlink3.mk,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+BUILDLINK_TREE+= ncbi-blast+
+
+.if !defined(NCBI_BLAST+_BUILDLINK3_MK)
+NCBI_BLAST+_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.ncbi-blast++= ncbi-blast+>=2.7.1
+BUILDLINK_PKGSRCDIR.ncbi-blast+?= ../../wip/ncbi-blast+
+
+.endif # NCBI_BLAST+_BUILDLINK3_MK
+
+BUILDLINK_TREE+= -ncbi-blast+
Index: pkgsrc/biology/ncbi-blast+/distinfo
diff -u /dev/null pkgsrc/biology/ncbi-blast+/distinfo:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/distinfo Fri Apr 27 20:28:28 2018
@@ -0,0 +1,12 @@
+$NetBSD: distinfo,v 1.1 2018/04/27 20:28:28 bacon Exp $
+
+SHA1 (ncbi-blast-2.7.1+-src.tar.gz) = d04a25f01c386abd8515957a2ce1dabf376743f8
+RMD160 (ncbi-blast-2.7.1+-src.tar.gz) = 7277419e16fb215aae4136a16e13bec963b70cbd
+SHA512 (ncbi-blast-2.7.1+-src.tar.gz) = e4b3914f51165ae4c82051068ed9d3470687a4e0f1df6274018c0ba14b241666a570d72265c7d167b8ce2a9075652744244a00e3e95c00c4252da0fbd80d17c6
+Size (ncbi-blast-2.7.1+-src.tar.gz) = 23254824 bytes
+SHA1 (patch-compilers_xcode30__prj_configure) = b89b3be8671c6c692ba474476879ee67a76fdbe5
+SHA1 (patch-src_algo_blast_core_blast__kappa.c) = a580a5fb2d5a3af04c27dd63a7edd349b7ae1be7
+SHA1 (patch-src_build-system_Makefile.in.top) = 71d5246867a8c985c1175c338fb0af664094ca01
+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) = 0fb99ac4e582938fd47e66c146da71695f009b98
Index: pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure Fri Apr 27 20:28:28 2018
@@ -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"
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c Fri Apr 27 20:28:28 2018
@@ -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, \
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top Fri Apr 27 20:28:28 2018
@@ -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 $(libdir)?
+
+ install-gbench:
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure Fri Apr 27 20:28:28 2018
@@ -0,0 +1,15 @@
+$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
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure Fri Apr 27 20:28:28 2018
@@ -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 "$@" ; do
+ | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+ | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
+ | --datadir=* | --sysconfdir=* | --localstatedir=* \
+- | --with-runpath=* | --with-relative-runpath=* \
++ | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
+ | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
+ | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
+ | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
Index: pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
diff -u /dev/null pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app:1.1
--- /dev/null Fri Apr 27 20:28:28 2018
+++ pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app Fri Apr 27 20:28:28 2018
@@ -0,0 +1,20 @@
+$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.1 2018/04/27 20:28:28 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 2018-04-27 16:21:07.000000000 +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) -Wl,-z,relro,-z,now
++CPPFLAGS = $(CPPFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now
++LDFLAGS = $(LDFLAGS_FOR_BUILD) -Wl,-z,relro,-z,now
+ LIBS = $(C_LIBS)
+ LINK = $(CC)
+ LINK_WRAPPER =
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