+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/py311-macs3-3.0.2nb2/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/py311-macs3-3.0.2nb2/work.log
=> Checksum BLAKE2s OK for macs-3.0.2.tar.gz
=> Checksum SHA512 OK for macs-3.0.2.tar.gz
===> Installing dependencies for py311-macs3-3.0.2nb2
==========================================================================
The following variables will affect the build process of this package,
py311-macs3-3.0.2nb2.  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 = python311

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 py311-setuptools>=78: found py311-setuptools-80.9.0
=> Tool dependency py311-build>=0: found py311-build-1.2.2.post1nb1
=> Tool dependency py311-installer>=0.7.0nb1: found py311-installer-0.7.0nb3
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency simde>=0.7.2: found simde-0.8.2
=> Full dependency py311-scipy>=1.11.1: found py311-scipy-1.15.3
=> Full dependency py311-cykhash>=2.0: found py311-cykhash-2.0.1nb2
=> Full dependency py311-scikit-learn>=1.3: found py311-scikit-learn-1.6.1
=> Full dependency py311-hmmlearn>=0.3.2: found py311-hmmlearn-0.3.3nb1
=> Full dependency py311-cython>=0.12.1: found py311-cython-3.1.2
=> Full dependency py311-numpy>=1.20.3nb1: found py311-numpy-2.3.1
=> Full dependency python311>=3.11.0: found python311-3.11.13
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
=> 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-1.17nb1
=> 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 py311-macs3-3.0.2nb2
===> Extracting for py311-macs3-3.0.2nb2
===> Patching for py311-macs3-3.0.2nb2
=> Applying pkgsrc patches for py311-macs3-3.0.2nb2
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/py-macs3/patches/patch-MACS3_fermi-lite_ksw.c
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-MACS3_fermi-lite_ksw.c,v 1.3 2024/10/14 22:21:16 bacon Exp $
|
|# Use SIMDE sse2.h
|
|--- MACS3/fermi-lite/ksw.c.orig	2023-12-21 22:20:16.716124047 +0000
|+++ MACS3/fermi-lite/ksw.c
--------------------------
Patching file MACS3/fermi-lite/ksw.c using Plan A...
Hunk #1 succeeded at 28.
done
===> Creating toolchain wrappers for py311-macs3-3.0.2nb2
===> Configuring for py311-macs3-3.0.2nb2
=> Replacing bash interpreter in test/cmdlinetest* test/prockreport test/*.py test/pyprofile*.
INFO: [replace-interpreter] Nothing changed in test/cmdlinetest.
INFO: [replace-interpreter] Nothing changed in test/cmdlinetest-nohmmratac.
INFO: [replace-interpreter] Nothing changed in test/prockreport.
INFO: [replace-interpreter] Nothing changed in test/jaccard.py.
INFO: [replace-interpreter] Nothing changed in test/test_BAMBAI.py.
INFO: [replace-interpreter] Nothing changed in test/test_BedGraph.py.
INFO: [replace-interpreter] Nothing changed in test/test_BedGraphIO.py.
INFO: [replace-interpreter] Nothing changed in test/test_CallPeakUnit.py.
INFO: [replace-interpreter] Nothing changed in test/test_FixWidthTrack.py.
INFO: [replace-interpreter] Nothing changed in test/test_HMMR_HMM.py.
INFO: [replace-interpreter] Nothing changed in test/test_HMMR_poisson.py.
INFO: [replace-interpreter] Nothing changed in test/test_PairedEndTrack.py.
INFO: [replace-interpreter] Nothing changed in test/test_Parser.py.
INFO: [replace-interpreter] Nothing changed in test/test_PeakDetect.py.
INFO: [replace-interpreter] Nothing changed in test/test_PeakIO.py.
INFO: [replace-interpreter] Nothing changed in test/test_PeakModel.py.
INFO: [replace-interpreter] Nothing changed in test/test_Pileup.py.
INFO: [replace-interpreter] Nothing changed in test/test_Prob.py.
INFO: [replace-interpreter] Nothing changed in test/test_Region.py.
INFO: [replace-interpreter] Nothing changed in test/test_ScoreTrack.py.
INFO: [replace-interpreter] Nothing changed in test/test_SignalProcessing.py.
INFO: [replace-interpreter] Nothing changed in test/test_online.py.
INFO: [replace-interpreter] Nothing changed in test/pyprofile_stat.
=> Checking for portability problems in extracted files