=> 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+-2.8.1nb12 ========================================================================== The following variables will affect the build process of this package, ncbi-blast+-2.8.1nb12. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 38 Based on these variables, the following variables have been set: * PYPACKAGE = python38 You may want to abort the process now with CTRL-C and change their value before continuing. Be sure to run `/opt/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency gmake>=3.81: found gmake-4.2.1nb1 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency perl>=5.8.0: found perl-5.32.0nb1 => 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-8.44 => Full dependency lmdb>=0.9.14: found lmdb-0.9.27nb1 => Full dependency gnutls>=3.6.13nb2: found gnutls-3.7.0 => Full dependency libtasn1>=0.3.0: found libtasn1-4.16.0 => Full dependency nettle>=3.6: found nettle-3.6 => Full dependency gmp>=6.0: found gmp-6.2.1 => Full dependency p11-kit>=0.23.15nb1: found p11-kit-0.23.22nb1 => Full dependency libidn2>=2.0.0: found libidn2-2.3.0 => Full dependency libgcrypt>=1.6.0: found libgcrypt-1.8.7 => Full dependency libgpg-error>=1.10nb1: found libgpg-error-1.39 => Full dependency sqlite3>=3.33.0nb1: found sqlite3-3.34.0 => Full dependency python38>=3.8.0: found python38-3.8.7 ===> Skipping vulnerability checks. WARNING: No /opt/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/opt/pkg/sbin/pkg_admin -K /opt/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Overriding tools for ncbi-blast+-2.8.1nb12 ===> Extracting for ncbi-blast+-2.8.1nb12 ===> Patching for ncbi-blast+-2.8.1nb12 => Applying pkgsrc patches for ncbi-blast+-2.8.1nb12 => Verifying /opt/pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure => Applying pkgsrc patch /opt/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 /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c => Applying pkgsrc patch /opt/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 3413. done => Verifying /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top => Applying pkgsrc patch /opt/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 /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh => Applying pkgsrc patch /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_build-system_cmake_cmake-cfg-unix.sh,v 1.1 2019/01/07 15:00:10 bacon Exp $ | |# Portability | |--- src/build-system/cmake/cmake-cfg-unix.sh.orig 2019-01-02 01:22:44.549100012 +0000 |+++ src/build-system/cmake/cmake-cfg-unix.sh -------------------------- Patching file src/build-system/cmake/cmake-cfg-unix.sh using Plan A... Hunk #1 succeeded at 166. done => Verifying /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure => Applying pkgsrc patch /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$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 -------------------------- Patching file src/build-system/cmake/cmake-configure using Plan A... Hunk #1 succeeded at 478 (offset 10 lines). done => Verifying /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure => Applying pkgsrc patch /opt/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 1.1 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 -------------------------- Patching file src/build-system/configure using Plan A... Hunk #1 succeeded at 1784 (offset 29 lines). done => Verifying /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app => Applying pkgsrc patch /opt/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 /opt/pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h => Applying pkgsrc patch /opt/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+-2.8.1nb12 ===> Configuring for ncbi-blast+-2.8.1nb12 => Substituting "configure" in /opt/work/biology/ncbi-blast+/work/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. 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. => Checking for portability problems in extracted files touch: configure.lock/for-sjmulder@/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... aarch64-apple-darwin20 checking host system type... aarch64-apple-darwin20 checking for a BSD-compatible install... /usr/bin/install -c -o sjmulder -g staff checking for aarch64-apple-darwin20-gcc... clang 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 clang accepts -g... yes checking for clang option to accept ISO C89... none needed checking how to run the C preprocessor... clang -E checking for gcc... gcc checking whether we are using the GNU C compiler... (cached) 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 whether we are using the GNU C++ compiler... yes checking whether clang++ accepts -g... yes configure: error: Do not know how to parse GCC version number 12.0.0 *** Error code 1 Stop. bmake[1]: stopped in /opt/pkgsrc/biology/ncbi-blast+ *** Error code 1 Stop. bmake: stopped in /opt/pkgsrc/biology/ncbi-blast+