=> Bootstrap dependency digest>=20211023: found digest-20211023
=> Checksum BLAKE2s OK for ncbi-blast-2.11.0+-src.tar.gz
=> Checksum SHA512 OK for ncbi-blast-2.11.0+-src.tar.gz
===> Installing dependencies for ncbi-blast+-2.11.0nb2
==========================================================================
The following variables will affect the build process of this package,
ncbi-blast+-2.11.0nb2.  Their current value is shown below:

        * PYTHON_VERSION_DEFAULT = 39

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

        * PYPACKAGE = python39

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
`/usr/bin/make clean' after the changes.
==========================================================================
=> Tool dependency bash-[0-9]*: found bash-5.1.16
=> Tool dependency gmake>=3.81: found gmake-4.3nb3
=> Tool dependency perl>=5.0: found perl-5.34.0nb3
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency cwrappers>=20150314: found cwrappers-20180325
=> Full dependency lzo>=2.01: found lzo-2.10
=> Full dependency pcre>=8.30nb1: found pcre-8.45
=> Full dependency lmdb>=0.9.14: found lmdb-0.9.29
=> Full dependency gnutls>=3.7.2nb1: found gnutls-3.7.3
=> Full dependency libtasn1>=0.3.0: found libtasn1-4.18.0
=> Full dependency nettle>=3.6: found nettle-3.7.3
=> Full dependency gmp>=6.0: found gmp-6.2.1nb2
=> Full dependency p11-kit>=0.24.0nb3: found p11-kit-0.24.1
=> Full dependency libidn2>=2.0.0: found libidn2-2.3.2
=> Full dependency libgcrypt>=1.6.0: found libgcrypt-1.9.4
=> Full dependency libgpg-error>=1.10nb1: found libgpg-error-1.44
=> Full dependency python39>=3.9.0: found python39-3.9.10
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Overriding tools for ncbi-blast+-2.11.0nb2
===> Extracting for ncbi-blast+-2.11.0nb2
===> Patching for ncbi-blast+-2.11.0nb2
=> Applying pkgsrc patches for ncbi-blast+-2.11.0nb2
=> Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 1.1 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
--------------------------
Patching file compilers/xcode30_prj/configure using Plan A...
Hunk #1 succeeded at 280.
done
=> Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 3411 (offset -2 lines).
done
=> Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.1 2021/06/11 13:47:40 bacon Exp $
|
|# Portability
|
|--- src/build-system/cmake/cmake-cfg-xcode.sh.orig	2021-06-10 11:54:05.800996703 +0000
|+++ src/build-system/cmake/cmake-cfg-xcode.sh
--------------------------
Patching file src/build-system/cmake/cmake-cfg-xcode.sh using Plan A...
Hunk #1 succeeded at 218.
done
=> Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 1.2 2021/06/11 13:47:40 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 2015.
done
=> Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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 6.
done
=> Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
=> Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/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+-2.11.0nb2
===> Configuring for ncbi-blast+-2.11.0nb2
=> 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.
=> Replacing Perl interpreter in src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl.
=> Checking for portability problems in extracted files
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 Subversion revision... unknown
checking NCBI stable components' version... unknown
checking build system type... x86_64--netbsd
checking host system type... x86_64--netbsd
checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g wheel
checking for x86_64--netbsd-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for x86_64--netbsd-gcc... no
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking how to run the C preprocessor... gcc -E
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
adjusted C   compiler: /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc 
adjusted C++ compiler: /tmp/biology/ncbi-blast+/work/.cwrapper/bin/c++ 
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... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
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checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  has an option to export all symbols... -Wl,-export-dynamic
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  supports -Wl,--{en,dis}able-new-dtags... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  has an option to discard unneeded shared libraries... -Wl,--as-needed
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  has an option to link in whole static archives... -Wl,--whole-archive
checking whether _LIBCPP_VERSION is declared... no
checking how to enable C++ '14 features in /tmp/biology/ncbi-blast+/work/.cwrapper/bin/c++ ... -std=gnu++14
checking how to enable C '11 or at least '99 features in /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc ... -std=gnu11 -fgnu89-inline
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  supports -msse4.2... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/c++  -std=gnu++14 supports -msse4.2... yes
checking for dpkg-architecture... no
checking for gawk... /usr/bin/awk
checking for GNU make... make
checking for /usr/bin/awk... /usr/bin/awk
checking for make... /tmp/biology/ncbi-blast+/work/.tools/bin/make
checking whether ln -s works... yes
checking for x86_64--netbsd-ranlib... no
checking for ranlib... ranlib
checking for ar... ar cr
checking ranlib's effectiveness... neutral
checking for strip... strip
checking whether strip loses runtime type information... no
checking for ccache... no
checking for tail... /tmp/biology/ncbi-blast+/work/.tools/bin/tail
checking whether /tmp/biology/ncbi-blast+/work/.tools/bin/tail accepts modern syntax (-n N)... yes
checking for basename... /tmp/biology/ncbi-blast+/work/.tools/bin/basename
checking for sed... /usr/bin/sed
checking for touch... /usr/bin/touch
checking for egrep... (cached) /usr/bin/egrep
checking how to run /usr/bin/egrep quietly... /usr/bin/egrep -q
checking for valgrind... no
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checking whether /usr/bin/ldd accepts -r... no
checking for uuidgen... /usr/pkg/bin/uuidgen
checking for cd_reporter... no
checking for size_t... yes
checking size of size_t... 8
checking for amq... /usr/sbin/amq
checking whether /usr/sbin/amq -w works... (cached) no
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports -Wl,--no-allow-shlib-undefined... yes
checking how to run the C preprocessor... gcc -E
checking whether cross-directory hard links work... yes
checking how to run the C++ preprocessor... /tmp/biology/ncbi-blast+/work/.cwrapper/bin/c++  -std=gnu++14 -msse4.2 -E
checking iostream usability... yes
checking iostream presence... yes
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checking iostream.h usability... no
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checking fstream.h usability... no
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checking strstrea.h usability... no
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checking for inttypes.h... (cached) yes
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checking limits.h usability... yes
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checking for unistd.h... (cached) yes
checking windows.h usability... no
checking windows.h presence... no
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checking for wstring... yes
checking for socklen_t... yes
checking atomic.h usability... yes
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checking cpuid.h usability... yes
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checking dlfcn.h usability... yes
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checking sys/sysinfo.h usability... no
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checking alloca.h usability... no
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checking arpa/inet.h usability... yes
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checking dirent.h usability... yes
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checking errno.h usability... yes
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checking fcntl.h usability... yes
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checking getopt.h usability... yes
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checking netdb.h usability... yes
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checking cxxabi.h usability... yes
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checking for getpwuid_r... 5
checking for getlogin_r... yes
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checking return type of localtime_r... struct
checking whether pthread mutexes are available... yes
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checking for statfs... (cached) no
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checking return type of signal handlers... void
checking whether select updates the timeout when interrupted... no
checking whether strcasecmp treats letters as lowercase... yes
checking for Linux-like sysinfo with 1 arg... no
checking for getloadavg... yes
checking for readdir_r... 3
checking whether stdio supports locking... yes
checking for an ANSI C-conforming const... yes
checking whether byte ordering is bigendian... no
checking whether char is unsigned... no
checking size of char... 1
checking size of double... 8
checking size of float... 4
checking size of int... 4
checking size of long... 8
checking size of long double... 16
checking size of long long... 8
checking size of short... 2
checking size of void*... 8
checking size of wchar_t... 4
checking size of __int64... 0
checking for intptr_t... yes
checking for uintptr_t... yes
checking for struct sockaddr_in.sin_len... yes
checking for struct tm.tm_zone... yes
checking for struct tm.__tm_zone... no
checking whether function prototypes can use throw(...)... yes
checking for ios(_base)::register_callback... yes
checking for SysV semaphores... yes
checking for union semun... no
checking which way the stack grows... down
checking whether the preprocessor supports C99-style variadic macros... yes
checking whether the preprocessor supports GNU-style variadic macros... yes
checking how to force inlining... inline __attribute__((always_inline))
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports __attribute__((visibility("default")))... (cached) unnecessary
checking whether the C compiler supports C99 restrict... __restrict__
checking whether the C++ compiler supports C99 restrict... __restrict__
checking syntax for declaring thread-local variables... __thread
checking whether FIONBIO requires BSD_COMP to be defined... no
checking whether INADDR_NONE is defined... yes
checking whether unaligned reads are permissible... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports SIMD vector arithmetic... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports -funsafe-math-optimizations... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports -msse4.1... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports -maes... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/gcc  -msse4.2 -std=gnu11 -fgnu89-inline supports -fdiagnostics-color=always... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/c++  -std=gnu++14 -msse4.2 supports __builtin_bswap32... yes
checking whether /tmp/biology/ncbi-blast+/work/.cwrapper/bin/c++  -std=gnu++14 -msse4.2 supports __builtin_expect... yes
checking whether in-house NCBI resources are available... no
checking for library containing gethostbyname... none required
checking for library containing connect... none required
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checking for inet_ntoa_r... no
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checking for library containing setkey... -lcrypt
checking for library containing dlopen... none required
checking for library containing uuid_generate... no
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checking for library containing clock_gettime... none required
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checking for sched_yield... yes
checking whether CLOCK_MONOTONIC is declared... yes
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checking whether CLOCK_REALTIME is declared... yes
checking for library containing iconv... none required
checking for iconv declaration... 
       extern size_t iconv (iconv_t cd, const char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for libdw... no
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checking for libbz2... yes
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checking for libpcre in /usr/pkg... yes
configure: using local mbedTLS copy in connect/mbedtls
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config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/blastdb_format/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/blastdb_format/unit_test/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/gene_info_reader/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/gene_info_reader/demo/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/gene_info_reader/unit_test/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/seqdb_reader/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/seqdb_reader/demo/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/seqdb_reader/test/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/seqdb_writer/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/seqdb_writer/unit_test/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/services/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/blast/services/unit_test/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/cleanup/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/blastdb/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/genbank/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/genbank/cache/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/genbank/gicache/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/genbank/id1/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/data_loaders/genbank/id2/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/edit/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/format/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/logging/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/pubseq_gateway/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/pubseq_gateway/client/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/pubseq_gateway/client/test/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/readers/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/seqmasks_io/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/objtools/simple/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/serial/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/serial/datatool/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/serial/grpc_integration/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/bitset/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/compress/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/compress/api/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/compress/bzip2/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/compress/zlib/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/creaders/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/lmdb/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/lmdbxx/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/regexp/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/sequtil/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/tables/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/util/xregexp/Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/./Makefile
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/inc/common/ncbi_build_ver.h
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/include/common/ncbi_revision.h
config.status: creating /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/inc/ncbiconf_unix.h
config.status: executing default commands
/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/corelib/ncbicfg.c is updated
/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/inc/common/ncbi_build_ver.h is updated
Build session ID: 34d4a27d-d9ed-4f44-91fa-e0f0c746a473
/tmp/biology/ncbi-blast+/work/.tools/bin/make -f /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/src/build-system/helpers TMPL=run_with_lock -k all
touch: make_run_with_lock.lock/for-pbulk@/bin/hostname: No such file or directory
make[1]: Entering directory '/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/build-system/helpers'
Updating dependency information for /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/src/build-system/helpers/run_with_lock.c.
gcc -c  -g -O2 -Wall -Wno-format-y2k  -pthread -fopenmp -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.9 -fPIC    -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.9 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/inc -I/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/include  -DNCBI_APP_BUILT_AS=run_with_lock -DNCBI_BUILD_SESSION_ID=34d4a27d-d9ed-4f44-91fa-e0f0c746a473 /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/src/build-system/helpers/run_with_lock.c -o run_with_lock.o 
gcc -Wl,-rpath,/usr/pkg/lib/ncbi-tools++ -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fopenmp -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 run_with_lock.o -Wl,-rpath-link,/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/lib -L/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/lib -lm -lpthread -o run_with_lock
strip run_with_lock
/bin/sh /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f run_with_lock /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/bin
/bin/ln -f run_with_lock /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/bin/run_with_lock
make[1]: Leaving directory '/tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/build-system/helpers'
Platform not defined for NetBSD amd64 -- please fix me
Prebuilt project_tree_builder not found
===============================================================================
NCBI C++ Toolkit documentation:
  Online:   http://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  -pthread -fopenmp -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.9 -fPIC 
CXXFLAGS =  -Wall -Wno-format-y2k  -pthread -fopenmp -O2 -fPIC -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.9 -fPIC 
CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.9 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL
LDFLAGS  =  -Wl,--enable-new-dtags -Wl,-export-dynamic  -pthread -fopenmp -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib  -O2

LIBRARIES:  build as static by default
FEATURES:   PSGLoader GCC MT LFS DLL unix WinMain BSD
PACKAGES:
  enabled:  Iconv Z BZ2 LZO PCRE MBEDTLS GMP GMP NETTLE NETTLE OPENSSL PYTHON EXPAT SQLITE3 MAGIC LMDB
  disabled: UUID FUSE LIBUNWIND LIBDW BACKWARD_CPP LocalZ LocalBZ2 ZSTD LocalPCRE GCRYPT GNUTLS KRB5 CURL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC 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 OpenGL MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU SABLOT LIBXML LIBXSLT LIBEXSLT Xerces Xalan Zorba SQLITE3ASYNC VDB NGS OECHEM SGE MUPARSER HDF5 JPEG PNG TIFF GIF UNGIF XPM GL2PS FreeType FTGL MIMETIC GSOAP AVRO Cereal SASL2 MONGODB MONGODB3 LEVELDB GMOCK LAPACK LocalLMDB LIBUV LIBSSH2 CASSANDRA NGHTTP2 H2O INFLUXDB LIBXLSXWRITER PROTOBUF GRPC MSGSL AWS_SDK HIREDIS APACHE_ARROW LIBRDKAFKA CPPKAFKA
PROJECTS:
  enabled:  cgi serial objects dbapi app algo 
  disabled: local_lbsm connext ncbi_crypt bdb ctools gui gbench

Tools / flags / paths:  /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build/Makefile.mk
Configuration  header:  /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/inc/ncbiconf_unix.h

To build everything:  cd /tmp/biology/ncbi-blast+/work/ncbi-blast-2.11.0+-src/c++/ReleaseMT/build && /tmp/biology/ncbi-blast+/work/.tools/bin/make all_r
or simply run /tmp/biology/ncbi-blast+/work/.tools/bin/make in the current directory


******* CONFIGURATION SUCCESSFUL *******