+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/py310-macs2-2.2.9.1/work.log + su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=310 WRKLOG=/tmp/bulklog/py310-macs2-2.2.9.1/work.log => Bootstrap dependency digest>=20211023: found digest-20220214 => 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 py310-macs2-2.2.9.1 ========================================================================== The following variables will affect the build process of this package, py310-macs2-2.2.9.1. 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_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 = python310 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/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency py310-cython-[0-9]*: found py310-cython-3.0.6 => Tool dependency py310-build>=0: found py310-build-1.0.3nb1 => Tool dependency py310-installer>=0.7.0nb1: found py310-installer-0.7.0nb1 => Tool dependency mktools-[0-9]*: found mktools-20220614 => 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 python310>=3.10.0: found python310-3.10.13nb4 => Full dependency py310-numpy>=1.20.3nb1: found py310-numpy-1.26.2nb1 ===> Overriding tools for py310-macs2-2.2.9.1 ===> Extracting for py310-macs2-2.2.9.1 ===> Patching for py310-macs2-2.2.9.1 => Applying pkgsrc patches for py310-macs2-2.2.9.1 => Verifying /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/py-macs2/patches/patch-MACS2_IO_CallPeakUnit.pyx => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/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 /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/biology/py-macs2/patches/patch-MACS2_IO_FixWidthTrack.pyx => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-el9-trunk-x86_64/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 py310-macs2-2.2.9.1 ===> Configuring for py310-macs2-2.2.9.1 /bin/mv /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/cPosValCalculation.c /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1 /bin/rm -f /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*.c /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*/*.c cd /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1 && /usr/pkg/bin/cythonize-3.10 /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakDetect.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakModel.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Pileup.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Prob.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Signal.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Statistics.pyx cd /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1 && /usr/pkg/bin/cythonize-3.10 /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*/*.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraph.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraphIO.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/FixWidthTrack.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/FixWidthTrack.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PairedEndTrack.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PairedEndTrack.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/Parser.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/Parser.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PeakIO.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/PeakIO.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/ScoreTrack.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/ScoreTrack.pyx /bin/mv /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/cPosValCalculation.c /home/pbulk/build/biology/py-macs2/work/MACS-2.2.9.1/MACS2 => Checking for portability problems in extracted files