=> 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/bin/make 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 cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency python311>=3.11.0: found python311-3.11.6nb4 => Full dependency py311-numpy>=1.20.3nb1: found py311-numpy-1.26.2nb1 ===> 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 py311-macs2-2.2.8 ===> Extracting for py311-macs2-2.2.8 mv -f /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/cPosValCalculation.c /tmp/biology/py-macs2/work/MACS-2.2.8 /bin/rm -f /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*.c /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*/*.c cd /tmp/biology/py-macs2/work/MACS-2.2.8 && /usr/pkg/bin/cythonize-3.11 /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakDetect.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/PeakModel.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Pileup.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Prob.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Signal.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/Statistics.pyx cd /tmp/biology/py-macs2/work/MACS-2.2.8 && /usr/pkg/bin/cythonize-3.11 /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/*/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraph.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/BedGraphIO.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 /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /tmp/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: /tmp/biology/py-macs2/work/MACS-2.2.8/MACS2/IO/CallPeakUnit.pyx *** Error code 1 Stop. make[1]: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/py-macs2 *** Error code 1 Stop. make: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/biology/py-macs2