=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for plinkseq-0.08.tar.gz => Checksum SHA512 OK for plinkseq-0.08.tar.gz ===> Installing dependencies for plinkseq-0.08nb17 => Tool dependency libtool-base>=2.4.2nb9: found libtool-base-2.4.7nb1 => Tool dependency mktools-[0-9]*: found mktools-20250213 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency gcc10>=10.3.0nb2: found gcc10-10.5.0nb4 => Full dependency bash-[0-9]*: found bash-5.3.9 => Full dependency gcc10-libs>=10.2.0: found gcc10-libs-10.5.0nb5 => Full dependency protobuf>=33.3nb1: found protobuf-34.1 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Overriding tools for plinkseq-0.08nb17 ===> Extracting for plinkseq-0.08nb17 /bin/cp /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/files/pp.proto /tmp/biology/plinkseq/work/plinkseq-0.08/lib/ /bin/cp /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/files/variant.proto /tmp/biology/plinkseq/work/plinkseq-0.08/lib/ ===> Patching for plinkseq-0.08nb17 => Applying pkgsrc patches for plinkseq-0.08nb17 => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-browser_main.c => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-browser_main.c Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-browser_main.c,v 1.2 2023/11/23 09:04:24 wiz Exp $ | |not needed on sunos | |--- browser/main.c.orig 2011-11-17 17:17:36.000000000 +0000 |+++ browser/main.c -------------------------- Patching file browser/main.c using Plan A... Hunk #1 succeeded at 21. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-browser_mongoose.c => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-browser_mongoose.c Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-browser_mongoose.c,v 1.3 2016/12/17 12:55:29 rillig Exp $ | |__BSD_VISIBLE is needed on FreeBSD. |_XOPEN_SOURCE is not needed on sunos. | |--- browser/mongoose.c.orig 2011-11-17 17:17:36.000000000 +0000 |+++ browser/mongoose.c -------------------------- Patching file browser/mongoose.c using Plan A... Hunk #1 succeeded at 21. Hunk #2 succeeded at 216. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-lib_annot.cpp => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-lib_annot.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-lib_annot.cpp,v 1.2 2023/11/23 09:04:24 wiz Exp $ | |rename to avoid collision on sunos | |--- lib/annot.cpp.orig 2012-03-19 20:00:45.000000000 +0000 |+++ lib/annot.cpp -------------------------- Patching file lib/annot.cpp using Plan A... Hunk #1 succeeded at 34. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-lib_annot.h => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-lib_annot.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-lib_annot.h,v 1.2 2023/11/23 09:04:24 wiz Exp $ | |rename to avoid collision on sunos | |--- lib/annot.h.orig 2012-03-19 11:35:59.000000000 +0000 |+++ lib/annot.h -------------------------- Patching file lib/annot.h using Plan A... Hunk #1 succeeded at 35. done => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-lib_token.cpp => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq/patches/patch-lib_token.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-lib_token.cpp,v 1.2 2023/11/23 09:04:24 wiz Exp $ | |fix math ambiguity on sunos | |--- lib/token.cpp.orig 2012-03-17 17:06:01.000000000 +0000 |+++ lib/token.cpp -------------------------- Patching file lib/token.cpp using Plan A... Hunk #1 succeeded at 1232. Hunk #2 succeeded at 1249. Hunk #3 succeeded at 2141. Hunk #4 succeeded at 2154. Hunk #5 succeeded at 2168. Hunk #6 succeeded at 2181. Hunk #7 succeeded at 2202. done ===> Creating toolchain wrappers for plinkseq-0.08nb17 ===> Configuring for plinkseq-0.08nb17 => 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 bash interpreter in browser/pbrowse.in index/index.in. => Checking for portability problems in extracted files checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g wheel checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... /usr/bin/awk checking whether make sets $(MAKE)... yes checking build system type... x86_64--netbsd checking host system type... x86_64--netbsd checking for style of include used by make... GNU checking for x86_64--netbsd-gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /usr/bin/ld option to reload object files... -r checking how to recognize dependent libraries... match_pattern /lib[^/]+(\.so|_pic\.a)$ checking for x86_64--netbsd-ar... no checking for ar... ar checking for x86_64--netbsd-strip... no checking for strip... strip checking for x86_64--netbsd-ranlib... no checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E 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 dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... rm: conftest*: No such file or directory yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... rm: conftest*: No such file or directory no checking dynamic linker characteristics... NetBSD ld.elf_so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for main in -lprotobuf... no configure: error: Cannot find protobuf, which is required to build PLINK/SEQ. Please install protobuf (2.4.1) on your system. If you do not have root access, you can install protobuf to a local directory and link to it with: ./configure --with-protobuf=/path/to/protobuf/prefix *** Error code 1 Stop. make[1]: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq *** Error code 1 Stop. make: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/plinkseq