=> Bootstrap dependency digest>=20211023: found digest-20220214 => Checksum BLAKE2s OK for MACS2-2.2.7.1.tar.gz => Checksum SHA512 OK for MACS2-2.2.7.1.tar.gz ===> Installing dependencies for py38-macs2-2.2.7.1 ========================================================================== The following variables will affect the build process of this package, py38-macs2-2.2.7.1. Their current value is shown below: * PKGSRC_BLAS_TYPES = netlib openblas openblas_pthread openblas_openmp * PYTHON_VERSION_DEFAULT = 310 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 = python38 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 py38-cython-[0-9]*: found py38-cython-0.29.33 => Tool dependency py38-setuptools-[0-9]*: found py38-setuptools-67.3.3 => 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 python38>=3.8.0: found python38-3.8.16 => Full dependency py38-numpy>=1.20.3nb1: found py38-numpy-1.24.2 ===> 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 py38-macs2-2.2.7.1 ===> Extracting for py38-macs2-2.2.7.1 mv -f /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/cPosValCalculation.c /tmp/biology/py-macs2/work/MACS-2.2.7.1 /bin/rm /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*.c /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*/*.c cd /tmp/biology/py-macs2/work/MACS-2.2.7.1 && /usr/pkg/bin/cythonize-3.8 /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/*.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakDetect.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakDetect.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakModel.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/PeakModel.pyx Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Pileup.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Pileup.pyx /usr/pkg/lib/python3.8/site-packages/numpy/__init__.pxd Traceback (most recent call last): File "/usr/pkg/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1218, in cythonize_one File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 731, in compile_single File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Main.py", line 515, in run_pipeline File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 355, in run_pipeline File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 335, in run File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Pipeline.py", line 52, in generate_pyx_code_stage File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/ModuleNode.py", line 143, in process_implementation File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/ModuleNode.py", line 385, in generate_c_code File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 442, in generate_function_definitions File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Nodes.py", line 1793, in generate_function_definitions File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Code.py", line 1865, in putln File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Code.py", line 1891, in emit_marker File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Code.py", line 1900, in _build_marker File "/usr/pkg/lib/python3.8/site-packages/Cython/Compiler/Code.py", line 1623, in commented_file_contents File "Cython/Compiler/Scanning.py", line 236, in Cython.Compiler.Scanning.FileSourceDescriptor.get_lines File "/usr/pkg/lib/python3.8/site-packages/Cython/Utils.py", line 255, in open_source_file FileNotFoundError: /usr/pkg/lib/python3.8/site-packages/numpy/__init__.pxd Compiling /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Prob.pyx because it changed. [1/1] Cythonizing /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Prob.pyx Traceback (most recent call last): File "/usr/pkg/bin/cythonize-3.8", line 33, in File "/usr/pkg/lib/python3.8/site-packages/Cython/Build/Cythonize.py", line 225, in main File "/usr/pkg/lib/python3.8/site-packages/Cython/Build/Cythonize.py", line 97, in cython_compile File "/usr/pkg/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1112, in cythonize File "/usr/pkg/lib/python3.8/site-packages/Cython/Build/Dependencies.py", line 1235, in cythonize_one Cython.Compiler.Errors.CompileError: /tmp/biology/py-macs2/work/MACS-2.2.7.1/MACS2/Prob.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