=> Checksum BLAKE2s OK for MACS2-2.2.9.1.tar.gz => Checksum SHA512 OK for MACS2-2.2.9.1.tar.gz ===> Installing dependencies for py313-macs2-2.2.9.1nb1 ========================================================================== The following variables will affect the build process of this package, py313-macs2-2.2.9.1nb1. Their current value is shown below: * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp * PYTHON_VERSION_DEFAULT = 312 Based on these variables, the following variables have been set: * BLAS_INCLUDES = -I/opt/pkg/include/netlib * BLAS_LIBS = -lblas * BLAS_PC = blas * BLAS_TYPE = netlib * CBLAS_LIBS = -lcblas -lblas * CBLAS_PC = cblas * LAPACKE_LIBS = -llapacke -llapack -lblas * LAPACKE_PC = lapacke * LAPACK_LIBS = -llapack -lblas * LAPACK_PC = lapack * PYPACKAGE = python313 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/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency py313-cython-[0-9]*: found py313-cython-3.0.12nb1 => Tool dependency py313-setuptools>=75.8.2: found py313-setuptools-78.1.0 => Tool dependency py313-build>=0: found py313-build-1.2.2.post1nb1 => Tool dependency py313-installer>=0.7.0nb1: found py313-installer-0.7.0nb3 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency py313-numpy>=1.20.3nb1: found py313-numpy-2.2.3 => Full dependency python313>=3.13: found python313-3.13.3 => Full dependency blas>=3.9.0: found blas-3.12.0 => Full dependency cblas>=3.9.0: found cblas-3.12.0 => Full dependency gettext-lib>=0.22: found gettext-lib-0.22.5 => Full dependency libiconv>=1.9.1: found libiconv-1.17 => Full dependency lapack>=3.9.0: found lapack-3.12.0 => Full dependency lapacke>=3.9.0: found lapacke-3.12.0 ===> Overriding tools for py313-macs2-2.2.9.1nb1 ===> Extracting for py313-macs2-2.2.9.1nb1 ===> Patching for py313-macs2-2.2.9.1nb1 => Applying pkgsrc patches for py313-macs2-2.2.9.1nb1 => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-MACS2_IO_CallPeakUnit.pyx,v 1.1 2023/12/23 16:15:02 bacon Exp $ | |# Fix cython 3 error | |--- MACS2/IO/CallPeakUnit.pyx.orig 2023-12-23 15:31:06.614325825 +0000 |+++ MACS2/IO/CallPeakUnit.pyx -------------------------- Patching file MACS2/IO/CallPeakUnit.pyx using Plan A... Hunk #1 succeeded at 197. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-upstream-arm64/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-MACS2_IO_FixWidthTrack.pyx,v 1.1 2023/12/23 16:15:02 bacon Exp $ | |# Fix cython 3 error | |--- MACS2/IO/FixWidthTrack.pyx.orig 2023-07-21 14:25:59.000000000 +0000 |+++ MACS2/IO/FixWidthTrack.pyx -------------------------- Patching file MACS2/IO/FixWidthTrack.pyx using Plan A... Hunk #1 succeeded at 946. done ===> Creating toolchain wrappers for py313-macs2-2.2.9.1nb1 ===> Configuring for py313-macs2-2.2.9.1nb1 /bin/mv /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/cPosValCalculation.c /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1 /bin/rm -f /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*.c /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*/*.c cd /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1 && /opt/pkg/bin/cythonize-3.13 /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakDetect.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakModel.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Pileup.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Prob.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Signal.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Statistics.pyx cd /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1 && /opt/pkg/bin/cythonize-3.13 /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*/*.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraph.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraphIO.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/FixWidthTrack.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/FixWidthTrack.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PairedEndTrack.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PairedEndTrack.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/Parser.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/Parser.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PeakIO.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PeakIO.pyx Compiling /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/ScoreTrack.pyx because it changed. [1/1] Cythonizing /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/ScoreTrack.pyx /bin/mv /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/cPosValCalculation.c /Users/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2