+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/py311-macs2-2.2.8/work.log + su pbulk -c '"$@"' make /usr/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/py311-macs2-2.2.8/work.log => 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 py311-macs2-2.2.8 ========================================================================== The following variables will affect the build process of this package, py311-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 = 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 `/usr/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency py311-cython-[0-9]*: found py311-cython-3.0.6 => Tool dependency py311-setuptools-[0-9]*: found py311-setuptools-69.0.2 => 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 => Build dependency gcc7>=7.5.0nb6: found gcc7-7.5.0nb6 => Full dependency python311>=3.11.0: found python311-3.11.7 => Full dependency py311-numpy>=1.20.3nb1: found py311-numpy-1.26.2nb1 ===> Overriding tools for py311-macs2-2.2.8 ===> Extracting for py311-macs2-2.2.8 /bin/mv /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/cPosValCalculation.c /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8 /bin/rm -f /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/*.c /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/*/*.c cd /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8 && /usr/pkg/bin/cythonize-3.11 /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/*.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakDetect.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakModel.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Pileup.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Prob.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Signal.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/Statistics.pyx cd /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8 && /usr/pkg/bin/cythonize-3.11 /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/*/*.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraphIO.pyx Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraph.pyx Error compiling Cython file: ------------------------------------------------------------ ... crick_right = right_sum(crick, search_start, window_size) wtd_list = np.zeros( search_end - search_start + 1, dtype="float32") i = 0 for j in range(search_start, search_end+1): wtd_list[i] = max((2 * (watson_left * crick_right)**0.5 - watson_right - crick_left),0) # minimum score is 0 ^ ------------------------------------------------------------ MACS2/IO/CallPeakUnit.pyx:200:93: complex types are unordered Compiling /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx Traceback (most recent call last): File "/usr/pkg/bin/cythonize-3.11", line 8, in sys.exit(main()) ^^^^^^ File "/usr/pkg/lib/python3.11/site-packages/Cython/Build/Cythonize.py", line 251, in main _cython_compile_files(all_paths, options) File "/usr/pkg/lib/python3.11/site-packages/Cython/Build/Cythonize.py", line 67, in _cython_compile_files ext_modules = cythonize( ^^^^^^^^^^ File "/usr/pkg/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize cythonize_one(*args) File "/usr/pkg/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: /home/pbulk/build/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx *** Error code 1 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/py-macs2 *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-el7-trunk-x86_64/biology/py-macs2