=> 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 py312-macs2-2.2.9.1nb2 ========================================================================== The following variables will affect the build process of this package, py312-macs2-2.2.9.1nb2. Their current value is shown below: * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp * PYTHON_VERSION_DEFAULT = 313 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 = python312 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 py312-cython-[0-9]*: found py312-cython-3.3.0 => Tool dependency py312-setuptools>=78: found py312-setuptools-84.0.0 => Tool dependency py312-build>=0: found py312-build-1.5.1 => Tool dependency py312-installer>=0.7.0nb1: found py312-installer-1.0.1 => Tool dependency mktools-[0-9]*: found mktools-20250213 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Full dependency py312-numpy>=1.20.3nb1: found py312-numpy-2.5.2nb1 => Full dependency python312>=3.12.0: found python312-3.12.14 ===> 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 py312-macs2-2.2.9.1nb2 ===> Extracting for py312-macs2-2.2.9.1nb2 ===> Patching for py312-macs2-2.2.9.1nb2 => Applying pkgsrc patches for py312-macs2-2.2.9.1nb2 ===> Creating toolchain wrappers for py312-macs2-2.2.9.1nb2 /bin/ln -s /usr/pkg/lib/python3.12/site-packages/numpy/_core/lib/pkgconfig/numpy.pc /pbulk/work/biology/py-macs2/work/.buildlink/lib/pkgconfig/numpy.pc ===> Configuring for py312-macs2-2.2.9.1nb2 mv -f /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/cPosValCalculation.c /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1 /bin/rm -f /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*.c /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*/*.c cd /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1 && /usr/pkg/bin/cythonize-3.12 /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakDetect.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/PeakModel.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Pileup.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Prob.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Signal.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Signal.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Statistics.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/Statistics.pyx cd /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1 && /usr/pkg/bin/cythonize-3.12 /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/*/*.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraph.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraph.pyx Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraphIO.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/BedGraphIO.pyx Error compiling Cython file: ------------------------------------------------------------ ... np.ndarray adjusted_summits, passflags if self.PE_mode: return None pchrnames = sorted(peaks.get_chr_names()) ^ ------------------------------------------------------------ MACS2/IO/CallPeakUnit.pyx:1864:26: Cannot assign type 'list object' to 'set object' Compiling /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx because it changed. [1/1] Cythonizing /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx Traceback (most recent call last): File "/usr/pkg/bin/cythonize-3.12", line 8, in sys.exit(main()) ^^^^^^ File "/usr/pkg/lib/python3.12/site-packages/Cython/Build/Cythonize.py", line 324, in main ext_modules_by_basedir = _cython_compile_files(all_paths, options) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/pkg/lib/python3.12/site-packages/Cython/Build/Cythonize.py", line 51, in _cython_compile_files ext_modules = cythonize( ^^^^^^^^^^ File "/usr/pkg/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1153, in cythonize cythonize_one(*args) File "/usr/pkg/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1264, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: /pbulk/work/biology/py-macs2/work/MACS-2.2.9.1/MACS2/IO/CallPeakUnit.pyx *** Error code 1 Stop. make[1]: stopped in /usr/pkgsrc/biology/py-macs2 *** Error code 1 Stop. make: stopped in /usr/pkgsrc/biology/py-macs2