=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for MACS2-2.2.8.tar.gz => Checksum SHA512 OK for MACS2-2.2.8.tar.gz ===> Installing dependencies for py312-macs2-2.2.8 ========================================================================== The following variables will affect the build process of this package, py312-macs2-2.2.8. Their current value is shown below: * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp * PYTHON_VERSION_DEFAULT = 311 Based on these variables, the following variables have been set: * BLAS_INCLUDES = -I/usr/pkg/include/netlib * BLAS_LIBS = -lblas * BLAS_TYPE = netlib * CBLAS_LIBS = -lcblas -lblas * LAPACKE_LIBS = -llapacke -llapack -lblas * LAPACK_LIBS = -llapack -lblas * PYPACKAGE = python312 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/bin/make clean' after the changes. ========================================================================== => Tool dependency py312-cython-[0-9]*: found py312-cython-0.29.36 => Tool dependency py312-setuptools-[0-9]*: found py312-setuptools-68.2.2nb1 => Tool dependency mktools-[0-9]*: found mktools-20220614 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency python312>=3.12.0: found python312-3.12.0nb3 => Full dependency py312-numpy>=1.20.3nb1: found py312-numpy-1.25.2nb1 ===> 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 py312-macs2-2.2.8 ===> Extracting for py312-macs2-2.2.8 mv -f /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/cPosValCalculation.c /tmp/biology/py-macs2/work/MACS-2.2.8 /bin/rm -f /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*.c /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*/*.c cd /tmp/biology/py-macs2/work/MACS-2.2.8 && /usr/pkg/bin/cythonize-3.12 /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakDetect.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakModel.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Pileup.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Prob.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Signal.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Statistics.pyx cd /tmp/biology/py-macs2/work/MACS-2.2.8 && /usr/pkg/bin/cythonize-3.12 /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraph.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraphIO.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/FixWidthTrack.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/FixWidthTrack.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/PairedEndTrack.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/PairedEndTrack.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/Parser.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/Parser.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/PeakIO.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/PeakIO.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/ScoreTrack.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/ScoreTrack.pyx mv -f /tmp/biology/py-macs2/work/MACS-2.2.8/cPosValCalculation.c /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2 ===> Patching for py312-macs2-2.2.8 => Applying pkgsrc patches for py312-macs2-2.2.8 => Verifying /amd/pkgsrc/CHROOT/P/pkgsrc/biology/py-macs2/patches/patch-setup.py => Applying pkgsrc patch /amd/pkgsrc/CHROOT/P/pkgsrc/biology/py-macs2/patches/patch-setup.py Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-setup.py,v 1.3 2023/05/18 14:01:58 bacon Exp $ | |# Unbundle numpy | |--- setup.py.orig 2023-05-18 12:06:38.965674517 +0000 |+++ setup.py -------------------------- Patching file setup.py using Plan A... Hunk #1 succeeded at 25. done ===> Creating toolchain wrappers for py312-macs2-2.2.8 ===> Configuring for py312-macs2-2.2.8 => Checking for portability problems in extracted files