=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for hmmer-3.0.tar.gz => Checksum SHA512 OK for hmmer-3.0.tar.gz ===> Installing dependencies for hmmer-3.0 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency cwrappers>=20150314: found cwrappers-20180325 ===> 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'. ===> Overriding tools for hmmer-3.0 ===> Extracting for hmmer-3.0 ===> Patching for hmmer-3.0 => Applying pkgsrc patches for hmmer-3.0 => Verifying /usr/pkgsrc/biology/hmmer/patches/patch-aa => Applying pkgsrc patch /usr/pkgsrc/biology/hmmer/patches/patch-aa Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-aa,v 1.5 2013/07/21 15:58:51 wen Exp $ |replace "mkdir -p" with ${MKDIR} |--- Makefile.in.orig 2013-07-21 23:25:33.000000000 +0000 |+++ Makefile.in -------------------------- Patching file Makefile.in using Plan A... Hunk #1 succeeded at 51. Hunk #2 succeeded at 176. done ===> Creating toolchain wrappers for hmmer-3.0 ===> Configuring for hmmer-3.0 => 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 => Checking for portability problems in extracted files configure: Configuring HMMER for your system. checking build system type... powerpc--netbsd checking host system type... powerpc--netbsd configure: Full HMMER source distribution - using full configuration checking for powerpc--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 for C compiler vendor... gnu checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for powerpc--netbsd-gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking how to run the C preprocessor... gcc -E checking for C compiler vendor... (cached) gnu checking for gcc option to accept ISO C99... none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking for powerpc--netbsd-ranlib... no checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether your make is GNU make... nope, assuming sysv make. checking whether C compiler accepts -faltivec... no checking whether C compiler accepts -maltivec -mabi=altivec... yes checking whether Altivec/VMX is supported... yes configure: Activating Altivec/VMX optimized DP implementation checking compiler support --start-group... yes 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 checking for stdint.h... yes checking for unistd.h... yes checking for sys/types.h... (cached) yes checking sys/sysctl.h usability... yes checking sys/sysctl.h presence... yes checking for sys/sysctl.h... yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking altivec.h usability... yes checking altivec.h presence... yes checking for altivec.h... yes checking whether byte ordering is bigendian... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... yes checking for mkstemp... yes checking for popen... yes checking for strcasecmp... yes checking for times... yes checking for getpid... yes checking for sysctl... yes checking for sysconf... yes checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_vmx/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating Makefile config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: linking src/impl_vmx to src/impl HMMER configuration: compiler: gcc -O2 -D_FORTIFY_SOURCE=2 -maltivec -mabi=altivec -pthread linker: -Wl,-zrelro -Wl,-R/usr/pkg/lib libraries: DP implementation: vmx