=> Bootstrap dependency digest>=20010302: found digest-20190127
===> Skipping vulnerability checks.
WARNING: No /var/db/pkg/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /var/db/pkg fetch-pkg-vulnerabilities'.
=> 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+-2.8.1nb7
==========================================================================
The following variables will affect the build process of this package,
ncbi-blast+-2.8.1nb7. 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-5.0.17
=> Tool dependency gmake>=3.81: found gmake-4.2.1nb1
=> Tool dependency perl>=5.0: found perl-5.30.2
=> 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-0.9.25
=> Full dependency gnutls>=3.6.12nb1: found gnutls-3.6.13nb1
=> Full dependency libtasn1>=0.3.0: found libtasn1-4.16.0
=> Full dependency nettle>=3.5.1: found nettle-3.5.1
=> Full dependency gmp>=6.0: found gmp-6.2.0
=> Full dependency p11-kit>=0.23.15nb1: found p11-kit-0.23.15nb1
=> 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-1.37
=> Full dependency python37>=3.7.0: found python37-3.7.7
===> Overriding tools for ncbi-blast+-2.8.1nb7
===> Extracting for ncbi-blast+-2.8.1nb7
===> Patching for ncbi-blast+-2.8.1nb7
=> Applying pkgsrc patches for ncbi-blast+-2.8.1nb7
=> Verifying /data/pkgsrc/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-unix.sh
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-configure
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_configure
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
=> Applying pkgsrc patch /data/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 /data/pkgsrc/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
=> Applying pkgsrc patch /data/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+-2.8.1nb7
===> Configuring for ncbi-blast+-2.8.1nb7
=> Substituting "configure" in /data/scratch/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.
=> 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-pbulkXXX@/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 pbulkXXX -g users
checking for x86_64--netbsd-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 10.0.0
*** Error code 1
Stop.
make[1]: stopped in /data/pkgsrc/biology/ncbi-blast+
*** Error code 1
Stop.
make: stopped in /data/pkgsrc/biology/ncbi-blast+