+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/ncbi-blast+-2.13.0nb5/work.log + su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/ncbi-blast+-2.13.0nb5/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for ncbi-blast-2.13.0+-src.tar.gz => Checksum SHA512 OK for ncbi-blast-2.13.0+-src.tar.gz ===> Installing dependencies for ncbi-blast+-2.13.0nb5 ========================================================================== The following variables will affect the build process of this package, ncbi-blast+-2.13.0nb5. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 310 Based on these variables, the following variables have been set: * PYPACKAGE = python310 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/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency mktools-[0-9]*: found mktools-20220614 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency perl>=5.0: found perl-5.36.0 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency zlib>=1.2.3: found zlib-1.2.13 => Full dependency lzo>=2.01: found lzo-2.10 => Full dependency bzip2>=1.0.3: found bzip2-1.0.8 => Full dependency pcre>=8.30nb1: found pcre-8.45 => Full dependency lmdb>=0.9.14: found lmdb-0.9.29 => Full dependency gnutls>=3.7.8nb1: found gnutls-3.7.8nb1 => Full dependency libtasn1>=0.3.0: found libtasn1-4.19.0 => Full dependency nettle>=3.6: found nettle-3.8.1 => Full dependency gmp>=6.0: found gmp-6.2.1nb3 => Full dependency p11-kit>=0.24.0nb3: found p11-kit-0.24.1 => Full dependency libidn2>=2.3.3nb1: found libidn2-2.3.4 => Full dependency libgcrypt>=1.6.0: found libgcrypt-1.10.1 => Full dependency libgpg-error>=1.10nb1: found libgpg-error-1.46 => Full dependency sqlite3>=3.40.0nb1: found sqlite3-3.40.0nb1 => Full dependency python310>=3.10.0: found python310-3.10.9 ===> Overriding tools for ncbi-blast+-2.13.0nb5 ===> Extracting for ncbi-blast+-2.13.0nb5 ===> Patching for ncbi-blast+-2.13.0nb5 => Applying pkgsrc patches for ncbi-blast+-2.13.0nb5 => Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 1.2 2022/04/10 20:54:51 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 240 (offset 22 lines). done => Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-src_build-system_configure => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 1.3 2022/04/10 20:54:51 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 2039 (offset 24 lines). done => Verifying /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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 /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/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+-2.13.0nb5 ===> Configuring for ncbi-blast+-2.13.0nb5 => 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. => Checking for portability problems in extracted files touch: cannot 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-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking for a BSD-compatible install... /bin/install -c -o pbulk -g pbulk checking for x86_64-redhat-linux-gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cc -E checking for x86_64-redhat-linux-gnu-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: /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/cc adjusted C++ compiler: /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/c++ checking for grep that handles long lines and -e... (cached) /bin/grep checking for egrep... (cached) /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 checking for stdint.h... yes 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 /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/cc has an option to export all symbols... -Wl,-export-dynamic checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/cc supports -Wl,--{en,dis}able-new-dtags... yes checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/cc has an option to discard unneeded shared libraries... -Wl,--as-needed checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/cc has an option to link in whole static archives... -Wl,--whole-archive checking whether _LIBCPP_VERSION is declared... no checking how to enable modern C++ features in /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/c++ ... no configure: error: Please upgrade to a compiler supporting C++ '17, such as GCC 7.1 or newer. *** Error code 1 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+ *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/ncbi-blast+