=> Bootstrap dependency digest>=20010302: found digest-20190127 => Checksum SHA1 OK for ncbi-blast-2.8.1+-src.tar.gz => Checksum RMD160 OK for ncbi-blast-2.8.1+-src.tar.gz => Checksum SHA512 OK for ncbi-blast-2.8.1+-src.tar.gz ===> Installing dependencies for ncbi-blast+-2.8.1nb5 ========================================================================== The following variables will affect the build process of this package, ncbi-blast+-2.8.1nb5. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 37 Based on these variables, the following variables have been set: * PYPACKAGE = python37 You may want to abort the process now with CTRL-C and change their value before continuing. Be sure to run `/usr/bin/make clean' after the changes. ========================================================================== => Tool dependency bash-[0-9]*: found bash-5.0.11nb1 => Tool dependency gmake>=3.81: found gmake-4.2.1nb1 => Tool dependency perl>=5.0: found perl-5.30.1 => Build dependency cwrappers>=20150314: found cwrappers-20180325 => Full dependency lzo>=2.01: found lzo-2.10 => Full dependency pcre>=8.30nb1: found pcre-8.43 => Full dependency lmdb>=0.9.14: found lmdb-0.9.24 => Full dependency gnutls>=3.6.8nb1: found gnutls-3.6.11.1 => Full dependency libtasn1>=0.3.0: found libtasn1-4.14nb1 => Full dependency nettle>=3.5.1: found nettle-3.5.1 => Full dependency gmp>=6.0: found gmp-6.1.2 => Full dependency p11-kit>=0.23: found p11-kit-0.23.15 => Full dependency libidn2>=2.0.0: found libidn2-2.3.0 => Full dependency libgcrypt>=1.6.0: found libgcrypt-1.8.5 => Full dependency libgpg-error>=1.10nb1: found libgpg-error-1.36nb1 => Full dependency python37>=3.7.0: found python37-3.7.5 ===> Overriding tools for ncbi-blast+-2.8.1nb5 ===> Extracting for ncbi-blast+-2.8.1nb5 ===> Patching for ncbi-blast+-2.8.1nb5 => Applying pkgsrc patches for ncbi-blast+-2.8.1nb5 ===> Creating toolchain wrappers for ncbi-blast+-2.8.1nb5 ===> Configuring for ncbi-blast+-2.8.1nb5 => Substituting "configure" in /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/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. => 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. 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... alpha--netbsd checking host system type... alpha--netbsd checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g users checking for alpha--netbsd-gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 gcc... gcc checking whether we are using the GNU C compiler... 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/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/app/dustmasker/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/app/segmasker/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/app/winmasker/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/app/blastdb/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/app/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/app/blast/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/cgi/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/serial/datatool/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/serial/Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/./Makefile config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/inc/common/ncbi_build_ver.h config.status: creating /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/inc/ncbiconf_unix.h config.status: executing default commands /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/corelib/ncbicfg.c is updated /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/inc/common/ncbi_build_ver.h is updated /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/.tools/bin/make -f /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-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/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/build-system/helpers' Updating dependency information for /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/src/build-system/helpers/run_with_lock.c. gcc -c -g -O2 -Wall -Wno-format-y2k -pthread -fopenmp -O2 -mieee -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.7 -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.7 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/inc -I/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/include /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-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 -O run_with_lock.o -Wl,-rpath-link,/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/lib -L/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/lib -lm -lpthread -o run_with_lock strip run_with_lock /bin/sh /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/scripts/common/impl/if_diff.sh /bin/ln -f run_with_lock /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/bin /bin/ln -f run_with_lock /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/bin/run_with_lock make[1]: Leaving directory '/tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/build-system/helpers' Platform not defined for NetBSD alpha -- 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 -mieee -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.7 -fPIC CXXFLAGS = -Wall -Wno-format-y2k -pthread -fopenmp -O2 -mieee -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.7 -fPIC CPPFLAGS = -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/python3.7 -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 -O LIBRARIES: build as static by default FEATURES: 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 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.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 OECHEM SGE MUPARSER HDF5 JPEG PNG TIFF GIF UNGIF XPM FreeType FTGL MIMETIC GSOAP AVRO Cereal SASL2 MONGODB MONGODB3 GMOCK LAPACK LocalLMDB LIBUV LIBSSH2 CASSANDRA NGHTTP2 H2O LIBXLSXWRITER PROTOBUF GRPC MSGSL AWS_SDK PROJECTS: enabled: cgi serial objects dbapi app algo disabled: local_lbsm connext ncbi_crypt bdb ctools gui gbench Tools / flags / paths: /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build/Makefile.mk Configuration header: /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/inc/ncbiconf_unix.h To build everything: cd /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/ncbi-blast-2.8.1+-src/c++/ReleaseMT/build && /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/.tools/bin/make all_r or simply run /tmp/pkgbuild/biology/ncbi-blast+/work.alpha/.tools/bin/make in the current directory ******* CONFIGURATION SUCCESSFUL *******