=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for MACS2-2.2.7.1.tar.gz => Checksum SHA512 OK for MACS2-2.2.7.1.tar.gz ===> Installing dependencies for py38-macs2-2.2.7.1 ========================================================================== The following variables will affect the build process of this package, py38-macs2-2.2.7.1. Their current value is shown below: * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp * PYTHON_VERSION_DEFAULT = 310 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 = python38 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 py38-cython-[0-9]*: found py38-cython-0.29.33 => Tool dependency py38-setuptools-[0-9]*: found py38-setuptools-67.2.0 => 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 python38>=3.8.0: found python38-3.8.16 => Full dependency py38-numpy>=1.20.3nb1: found py38-numpy-1.23.5 ===> 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 py38-macs2-2.2.7.1 ===> Extracting for py38-macs2-2.2.7.1 mv -f /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/cPosValCalculation.c /tmp/biology/py-macs2/work/MACS-2.2.7.1 /bin/rm /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*.c /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*/*.c cd /tmp/biology/py-macs2/work/MACS-2.2.7.1 && /usr/pkg/bin/cythonize-3.8 /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakDetect.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakModel.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Pileup.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Prob.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Signal.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Statistics.pyx cd /tmp/biology/py-macs2/work/MACS-2.2.7.1 && /usr/pkg/bin/cythonize-3.8 /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/BedGraph.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/BedGraphIO.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/CallPeakUnit.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/FixWidthTrack.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/FixWidthTrack.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/PairedEndTrack.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/PairedEndTrack.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/Parser.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/Parser.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/PeakIO.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/PeakIO.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/ScoreTrack.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/IO/ScoreTrack.pyx mv -f /tmp/biology/py-macs2/work/MACS-2.2.7.1/cPosValCalculation.c /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2 ===> Patching for py38-macs2-2.2.7.1 => Applying pkgsrc patches for py38-macs2-2.2.7.1 => 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 1.1 2023/01/22 23:30:11 bacon Exp $ | |# Remove lexical version check and pip requirement | |--- setup.py.orig 2020-04-12 00:00:15.000000000 +0000 |+++ setup.py -------------------------- Patching file setup.py using Plan A... Hunk #1 succeeded at 20. done ===> Creating toolchain wrappers for py38-macs2-2.2.7.1 ===> Configuring for py38-macs2-2.2.7.1 => Checking for portability problems in extracted files