=> Checksum BLAKE2s OK for ncbi-blast-2.16.0+-src.tar.gz
=> Checksum SHA512 OK for ncbi-blast-2.16.0+-src.tar.gz
===> Installing dependencies for ncbi-blast+-2.16.0nb1
==========================================================================
The following variables will affect the build process of this package,
ncbi-blast+-2.16.0nb1.  Their current value is shown below:

        * PYTHON_VERSION_DEFAULT = 312

Based on these variables, the following variables have been set:

        * PYPACKAGE = python312

You may want to abort the process now with CTRL-C and change the value
of variables in the first group before continuing.  Be sure to run
`/opt/pkg/bin/bmake clean' after the changes.
==========================================================================
=> Tool dependency gmake>=3.81: found gmake-4.4.1
=> Tool dependency nbpatch-[0-9]*: found nbpatch-20151107
=> Tool dependency perl>=5.0: found perl-5.40.2
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Full dependency bzip2>=1.0.3: found bzip2-1.0.8
=> Full dependency gmp>=6.0: found gmp-6.3.0
=> Full dependency gnutls>=3.8.9nb1: found gnutls-3.8.9nb1
=> Full dependency libgcrypt>=1.6.0: found libgcrypt-1.11.0nb2
=> Full dependency libgpg-error>=1.10nb1: found libgpg-error-1.53
=> Full dependency libidn2>=2.3.3nb1: found libidn2-2.3.7
=> Full dependency libtasn1>=0.3.0: found libtasn1-4.20.0
=> Full dependency lmdb>=0.9.14: found lmdb-0.9.33
=> Full dependency lzo>=2.01: found lzo-2.10
=> Full dependency nettle>=3.6: found nettle-3.10.1
=> Full dependency p11-kit>=0.24.0nb3: found p11-kit-0.25.5
=> Full dependency pcre>=8.30nb1: found pcre-8.45
=> Full dependency python312>=3.12.0: found python312-3.12.10nb1
=> Full dependency sqlite3>=3.49.1nb3: found sqlite3-3.49.1nb3
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
=> Full dependency zstd>=1.3.6: found zstd-1.5.7
=> Full dependency gettext-lib>=0.22: found gettext-lib-0.22.5
=> Full dependency libiconv>=1.9.1: found libiconv-1.17
=> Full dependency libffi>=1.20: found libffi-3.4.8
=> Full dependency libunistring>=0.9.3: found libunistring-1.2
===> Overriding tools for ncbi-blast+-2.16.0nb1
===> Extracting for ncbi-blast+-2.16.0nb1
===> Patching for ncbi-blast+-2.16.0nb1
=> Applying pkgsrc patches for ncbi-blast+-2.16.0nb1
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-compilers_xcode30__prj_configure,v 1.3 2025/01/16 01:06:31 bacon Exp $
|
|# Nonportable extension
|
|--- compilers/xcode30_prj/configure.orig	2023-08-26 13:06:39.313163201 +0000
|+++ compilers/xcode30_prj/configure
--------------------------
Patching file compilers/xcode30_prj/configure using Plan A...
Hunk #1 succeeded at 284.
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.2 2019/01/07 15:00:10 bacon Exp $
|
|# Work around NetBSD stderr def choking macro
|
|--- src/algo/blast/core/blast_kappa.c.orig	2019-01-02 04:00:17.000000000 +0000
|+++ src/algo/blast/core/blast_kappa.c
--------------------------
Patching file src/algo/blast/core/blast_kappa.c using Plan A...
Hunk #1 succeeded at 32.
Hunk #2 succeeded at 58.
Hunk #3 succeeded at 3427 (offset 14 lines).
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$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
--------------------------
Patching file src/build-system/Makefile.in.top using Plan A...
Hunk #1 succeeded at 37.
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_build-system_configure
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_build-system_configure
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_build-system_configure,v 1.4 2023/05/28 22:48:27 bacon Exp $
|
|# Avert missing --with-libiconv-prefix option
|
|--- src/build-system/configure.orig	2021-06-10 19:44:11.069762486 +0000
|+++ src/build-system/configure
--------------------------
Patching file src/build-system/configure using Plan A...
Hunk #1 succeeded at 2057 (offset 42 lines).
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$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
--------------------------
Patching file src/build-system/helpers/Makefile.run_with_lock.app using Plan A...
Hunk #1 succeeded at 7 (offset 1 line).
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_util_checksum_cityhash_city.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $
|
|Ensure bswap_32() and bswap_64() is defined on NetBSD.
|
|--- src/util/checksum/cityhash/city.cc.orig	2018-09-28 20:34:39.000000000 +0000
|+++ src/util/checksum/cityhash/city.cc
--------------------------
Patching file src/util/checksum/cityhash/city.cc using Plan A...
Hunk #1 succeeded at 82.
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_util_checksum_farmhash_farmhash.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $
|
|Ensure bswap_32() and bswap_64() gets defined on NetBSD.
|
|--- src/util/checksum/farmhash/farmhash.cc.orig	2018-09-26 12:38:06.000000000 +0000
|+++ src/util/checksum/farmhash/farmhash.cc
--------------------------
Patching file src/util/checksum/farmhash/farmhash.cc using Plan A...
Hunk #1 succeeded at 158.
done
=> Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
=> Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_util_checksum_farmhash_farmhash.h,v 1.1 2019/01/07 15:00:11 bacon Exp $
|
|# __GNUC__ does not imply location of endian.h.  Check for BSD first.
|
|--- src/util/checksum/farmhash/farmhash.h.orig	2018-09-26 12:38:06.000000000 +0000
|+++ src/util/checksum/farmhash/farmhash.h
--------------------------
Patching file src/util/checksum/farmhash/farmhash.h using Plan A...
Hunk #1 succeeded at 305.
done
===> Creating toolchain wrappers for ncbi-blast+-2.16.0nb1
===> Configuring for ncbi-blast+-2.16.0nb1
=> Substituting "configure" in src/build-system/configure
=> Modifying GNU configure scripts to avoid --recheck
=> Replacing config-guess with pkgsrc versions
=> Replacing config-sub with pkgsrc versions
=> Replacing install-sh with pkgsrc version
=> Replacing python interpreter in src/app/winmasker/windowmasker_2.2.22_adapter.py src/app/blast/cleanup-blastdb-volumes.py.
=> Replacing bash interpreter in scripts/common/impl/define_random_macros.sh src/app/blast/get_species_taxids.sh.
INFO: [replace-interpreter] Nothing changed in src/app/blast/get_species_taxids.sh.
=> Replacing Perl interpreter in src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl.
configure: WARNING: unrecognized options: --with-libiconv-prefix
touch: configure.lock/for-pbulk@/bin/hostname: No such file or directory
configure: loading site script ./src/build-system/config.site

configure: creating cache config.cache
checking TeamCity build number... none
checking VCS revision... unknown
checking NCBI stable components' version... unknown
checking build system type... aarch64-apple-darwin23
checking host system type... aarch64-apple-darwin23
checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g staff
checking for aarch64-apple-darwin23-gcc... clang
checking whether the C compiler works... yes
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checking for suffix of executables... 
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checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
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checking how to run the C preprocessor... gcc -E
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ accepts -g... yes
adjusted C   compiler: /Users/pbulk/build-disk/biology/ncbi-blast+/work/.cwrapper/bin/clang 
adjusted C++ compiler: /Users/pbulk/build-disk/biology/ncbi-blast+/work/.cwrapper/bin/clang++ 
configure: WARNING: No dlfcn.h in /usr/include or /sw/include.
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
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checking how to enable modern C++ features in /Users/pbulk/build-disk/biology/ncbi-blast+/work/.cwrapper/bin/clang++  -stdlib=libc++... -std=gnu++17
checking how to enable modern C features in /Users/pbulk/build-disk/biology/ncbi-blast+/work/.cwrapper/bin/clang ... -std=gnu18 -fgnu89-inline
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configure: WARNING: x86intrin.h: present but cannot be compiled
configure: WARNING: x86intrin.h:     check for missing prerequisite headers?
configure: WARNING: x86intrin.h: see the Autoconf documentation
configure: WARNING: x86intrin.h:     section "Present But Cannot Be Compiled"
configure: WARNING: x86intrin.h: proceeding with the compiler's result
configure: WARNING:     ## ---------------------------------------- ##
configure: WARNING:     ## Report this to cpp-core@ncbi.nlm.nih.gov ##
configure: WARNING:     ## ---------------------------------------- ##
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Build session ID: 013D501A-B8D4-4FEE-B27D-7DA67FC8D22A
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make[1]: Entering directory '/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/build/build-system/helpers'
Updating dependency information for /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/src/build-system/helpers/run_with_lock.c.
gcc -c  -g -O2 -Wall -Wno-format-y2k -m64 -fpascal-strings  -pipe -Os -I/opt/pkg/include -I/opt/pkg/include/python3.12 -Wno-deprecated-register -fno-common    -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -m64 -I/opt/pkg/include -I/opt/pkg/include/python3.12 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/inc -I/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/include  -DNCBI_APP_BUILT_AS=run_with_lock -DNCBI_BUILD_SESSION_ID=013D501A-B8D4-4FEE-B27D-7DA67FC8D22A /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/src/build-system/helpers/run_with_lock.c -o run_with_lock.o 
gcc -Wl,-rpath,/opt/pkg/lib/ncbi-tools++ -m64 -flat_namespace -headerpad_max_install_names -L/opt/pkg/lib -dylib_file /opt/pkg/lib/ncbi-tools++/libdbapi_driver.dylib:/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib/libdbapi_driver.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libgui_utils.dylib:/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib/libgui_utils.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xloader_genbank.dylib:/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib/libncbi_xloader_genbank.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xreader.dylib:/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib/libncbi_xreader.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xreader_id1.dylib:/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib/libncbi_xreader_id1.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xreader_pubseqos.dylib:/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib/libncbi_xreader_pubseqos.dylib -O run_with_lock.o -L/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/lib -lm -Wl,-framework,ApplicationServices -lpthread -o run_with_lock
strip run_with_lock
/opt/pkg/bin/mksh /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f run_with_lock /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/bin
/bin/ln -f run_with_lock /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/bin/run_with_lock
make[1]: Leaving directory '/Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/build/build-system/helpers'
Prebuilt project_tree_builder not found
===============================================================================
NCBI C++ Toolkit documentation:
  Online:   https://www.ncbi.nlm.nih.gov/toolkit/doc/book/
  Local:    ./doc/public/index.html
For the available configuration flags run:  ./configure --help

CFLAGS   =  -Wall -Wno-format-y2k -m64 -fpascal-strings  -pipe -Os -I/opt/pkg/include -I/opt/pkg/include/python3.12 -Wno-deprecated-register -fno-common 
CXXFLAGS =  -Wall -Wno-format-y2k -m64 -fpascal-strings  -pipe -Os -I/opt/pkg/include -I/opt/pkg/include/python3.12 -Wno-deprecated-register -fno-common 
CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -m64 -I/opt/pkg/include -I/opt/pkg/include/python3.12 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL
LDFLAGS  =  -m64 -flat_namespace -headerpad_max_install_names  -L/opt/pkg/lib -dylib_file /opt/pkg/lib/ncbi-tools++/libdbapi_driver.dylib:$(libdir)/libdbapi_driver.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libgui_utils.dylib:$(libdir)/libgui_utils.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xloader_genbank.dylib:$(libdir)/libncbi_xloader_genbank.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xreader.dylib:$(libdir)/libncbi_xreader.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xreader_id1.dylib:$(libdir)/libncbi_xreader_id1.dylib -dylib_file /opt/pkg/lib/ncbi-tools++/libncbi_xreader_pubseqos.dylib:$(libdir)/libncbi_xreader_pubseqos.dylib  -O

LIBRARIES:  build as static by default
FEATURES:   Int8GI AppleClang Clang MT LFS DLL unix WinMain Darwin
PACKAGES:
  enabled:  UUID Iconv Z BZ2 LZO ZSTD PCRE MBEDTLS GMP GMP NETTLE NETTLE KRB5 CURL OpenGL EXPAT LIBXML LIBXSLT LIBEXSLT SQLITE3 SASL2 LAPACK LMDB
  disabled: FUSE LIBUNWIND LIBDW BACKWARD_CPP LocalZ LocalBZ2 LocalPCRE GCRYPT GNUTLS OPENSSL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON PYTHON25 PYTHON26 PYTHON27 PYTHON3 PERL Boost.Chrono Boost.Filesystem Boost.Iostreams Boost.Program-Options Boost.Regex Boost.Serialization Boost.Spirit Boost.System Boost.Test Boost.Test.Included Boost.Thread C-Toolkit NCBICRYPT MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI FASTCGIPP LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU SABLOT Xerces Xalan Zorba SQLITE3ASYNC VDB NGS OECHEM SGE DRMAA2 MUPARSER HDF5 JPEG PNG TIFF GIF UNGIF XPM GL2PS FreeType FTGL MAGIC MIMETIC GSOAP AVRO Cereal MONGODB MONGODB3 LEVELDB LIBURING ROCKSDB GMOCK LocalLMDB LIBUV LIBSSH2 CASSANDRA NGHTTP2 H2O INFLUXDB LIBXLSXWRITER PROTOBUF GRPC MSGSL AWS_SDK CRC32C GOOGLE_CLOUD HIREDIS APACHE_ARROW LIBRDKAFKA CPPKAFKA THRIFT NLohmann_JSON YAML_CPP OPENTRACING JAEGER
PROJECTS:
  enabled:  cgi serial objects dbapi app algo 
  disabled: bdb ctools gui gbench

Tools / flags / paths:  /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/build/Makefile.mk
Configuration  header:  /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/inc/ncbiconf_unix.h

To build everything:  cd /Users/pbulk/build-disk/biology/ncbi-blast+/work/ncbi-blast-2.16.0+-src/c++/ReleaseMT/build && /Users/pbulk/build-disk/biology/ncbi-blast+/work/.tools/bin/make all_r
or simply run /Users/pbulk/build-disk/biology/ncbi-blast+/work/.tools/bin/make in the current directory


******* CONFIGURATION SUCCESSFUL *******
configure: WARNING: unrecognized options: --with-libiconv-prefix