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ncbi-blast+: Remove following commit
Module Name: pkgsrc-wip
Committed By: Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Sun Apr 29 08:29:25 2018 -0500
Changeset: fd77d2960f967b0d208e3c88eb99134cabd96cec
Removed Files:
ncbi-blast+/DESCR
ncbi-blast+/Makefile
ncbi-blast+/PLIST
ncbi-blast+/buildlink3.mk
ncbi-blast+/distinfo
ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
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+: Remove following commit
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=fd77d2960f967b0d208e3c88eb99134cabd96cec
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+/Makefile | 68 -
ncbi-blast+/PLIST | 4113 --------------------
ncbi-blast+/buildlink3.mk | 13 -
ncbi-blast+/distinfo | 12 -
.../patches/patch-compilers_xcode30__prj_configure | 15 -
.../patch-src_algo_blast_core_blast__kappa.c | 31 -
.../patches/patch-src_build-system_Makefile.in.top | 41 -
.../patch-src_build-system_cmake_cmake-configure | 15 -
.../patches/patch-src_build-system_configure | 15 -
...ild-system_helpers_Makefile.run__with__lock.app | 20 -
11 files changed, 4348 deletions(-)
diffs:
diff --git a/ncbi-blast+/DESCR b/ncbi-blast+/DESCR
deleted file mode 100644
index 0d7c1d401b..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+/Makefile b/ncbi-blast+/Makefile
deleted file mode 100644
index 6495f4ab9d..0000000000
--- a/ncbi-blast+/Makefile
+++ /dev/null
@@ -1,68 +0,0 @@
-# $NetBSD$
-
-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"
diff --git a/ncbi-blast+/PLIST b/ncbi-blast+/PLIST
deleted file mode 100644
index c91ed40d92..0000000000
--- a/ncbi-blast+/PLIST
+++ /dev/null
@@ -1,4113 +0,0 @@
-@comment $NetBSD$
-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
-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
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-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
deleted file mode 100644
index 929b9a9e70..0000000000
--- a/ncbi-blast+/buildlink3.mk
+++ /dev/null
@@ -1,13 +0,0 @@
-# $NetBSD$
-
-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+
diff --git a/ncbi-blast+/distinfo b/ncbi-blast+/distinfo
deleted file mode 100644
index 2823474e3f..0000000000
--- a/ncbi-blast+/distinfo
+++ /dev/null
@@ -1,12 +0,0 @@
-$NetBSD$
-
-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
diff --git a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure b/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
deleted file mode 100644
index 7697a06653..0000000000
--- a/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# 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_algo_blast_core_blast__kappa.c b/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
deleted file mode 100644
index 2565da87a3..0000000000
--- a/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
+++ /dev/null
@@ -1,31 +0,0 @@
-$NetBSD$
-
-# 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-src_build-system_Makefile.in.top b/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
deleted file mode 100644
index cfc7e09738..0000000000
--- a/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
+++ /dev/null
@@ -1,41 +0,0 @@
-$NetBSD$
-
-# 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 $(libdir)?
-
- install-gbench:
diff --git a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure b/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
deleted file mode 100644
index 9d165fba9c..0000000000
--- a/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# 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
deleted file mode 100644
index 26493f44d3..0000000000
--- a/ncbi-blast+/patches/patch-src_build-system_configure
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# 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 "$@" ; do
- | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
- | --mandir=* | --infodir=* | --docdir=* | --htmldir=* \
- | --datadir=* | --sysconfdir=* | --localstatedir=* \
-- | --with-runpath=* | --with-relative-runpath=* \
-+ | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
- | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
- | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
- | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
diff --git a/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app b/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
deleted file mode 100644
index 300aeca060..0000000000
--- a/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD$
-
-# 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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