=> "/opt/local/bin/bmake" ["-C", "/data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink", "configure", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] => Checksum BLAKE2s OK for plink-1.07-src.zip => Checksum SHA512 OK for plink-1.07-src.zip ===> Installing dependencies for plink-1.07nb1 ========================================================================== The following variables will affect the build process of this package, plink-1.07nb1. Their current value is shown below: * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp Based on these variables, the following variables have been set: * BLAS_INCLUDES (not defined) * BLAS_LIBS = -lblas * BLAS_PC = blas * BLAS_TYPE = netlib * CBLAS_LIBS (not defined) * CBLAS_PC (not defined) * LAPACKE_LIBS (not defined) * LAPACKE_PC (not defined) * LAPACK_LIBS = -llapack -lblas * LAPACK_PC = lapack 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 `/opt/local/bin/bmake clean' after the changes. ========================================================================== => Tool dependency gmake>=3.81: found gmake-4.4.1 => Tool dependency unzip-[0-9]*: found unzip-6.0nb11 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency gcc13>=13.4.0: found gcc13-13.4.0 => Full dependency gcc13-libs>=13.4.0: found gcc13-libs-13.4.0 => Full dependency lapack>=3.9.0nb1: found lapack-3.12.1 => Full dependency libf2c>=20090201nb3: found libf2c-20090201nb3 => Full dependency zlib>=1.2.3: found zlib-1.3.1 => Full dependency blas>=3.9.0: found blas-3.12.1 ===> Overriding tools for plink-1.07nb1 ===> Extracting for plink-1.07nb1 ===> Patching for plink-1.07nb1 => Applying pkgsrc patches for plink-1.07nb1 => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-Makefile => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-Makefile Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-Makefile,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $ | |--- Makefile.orig 2009-10-10 16:00:20.000000000 +0000 |+++ Makefile -------------------------- Patching file Makefile using Plan A... Hunk #1 succeeded at 19. Hunk #2 succeeded at 59. Hunk #3 succeeded at 125. Hunk #4 succeeded at 151. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-elf.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-elf.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-elf.cpp,v 1.1 2012/11/16 00:32:07 joerg Exp $ | |--- elf.cpp.orig 2012-11-15 12:41:01.000000000 +0000 |+++ elf.cpp -------------------------- Patching file elf.cpp using Plan A... Hunk #1 succeeded at 1175. Hunk #2 succeeded at 1189. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-genogroup.h => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-genogroup.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-genogroup.h,v 1.1 2026/01/03 11:45:59 wiz Exp $ | |Fix |error: static assertion failed: comparison object must be invocable as const | |--- genogroup.h.orig 2026-01-03 11:44:09.583290253 +0000 |+++ genogroup.h -------------------------- Patching file genogroup.h using Plan A... Hunk #1 succeeded at 42. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-homozyg.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-homozyg.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-homozyg.cpp,v 1.1 2026/01/03 11:45:59 wiz Exp $ | |Fix |error: static assertion failed: comparison object must be invocable as const | |--- homozyg.cpp.orig 2009-10-10 16:00:21.000000000 +0000 |+++ homozyg.cpp -------------------------- Patching file homozyg.cpp using Plan A... Hunk #1 succeeded at 33. Hunk #2 succeeded at 70. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-idhelp.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-idhelp.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-idhelp.cpp,v 1.1 2012/11/16 00:32:07 joerg Exp $ | |--- idhelp.cpp.orig 2012-11-15 12:44:01.000000000 +0000 |+++ idhelp.cpp -------------------------- Patching file idhelp.cpp using Plan A... Hunk #1 succeeded at 772. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-plink.h => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-plink.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-plink.h,v 1.1 2026/01/03 11:45:59 wiz Exp $ | |Fix |error: static assertion failed: comparison object must be invocable as const | |--- plink.h.orig 2026-01-03 11:39:25.306972822 +0000 |+++ plink.h -------------------------- Patching file plink.h using Plan A... Hunk #1 succeeded at 387. done => Verifying /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-sets.cpp => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-trunk-x86_64/biology/plink/patches/patch-sets.cpp Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-sets.cpp,v 1.1 2012/11/16 00:32:07 joerg Exp $ | |--- sets.cpp.orig 2012-11-15 12:39:15.000000000 +0000 |+++ sets.cpp -------------------------- Patching file sets.cpp using Plan A... Hunk #1 succeeded at 768. done ===> Creating toolchain wrappers for plink-1.07nb1 /usr/bin/sed -e '/^#/d' -e 's,@LINK_ARCH_DEFAULT@,link_arch64,g' -e 's,@LINK_LIBGCC_DEFAULT@,link_libgcc_arch64,g' -e 's,@LIBGCC_PREFIX@,/opt/local/gcc13/x86_64-sun-solaris2.11,g' < ../../extra/gcc13-libs/files/specs.pkgsrc > /tmp/work/biology/plink/work/.cwrapper/specs.pkgsrc ===> Configuring for plink-1.07nb1