=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> 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'. ===> Building for py310-macs3-3.0.1 * Building wheel... Compiling MACS3/Signal/HMMR_EM.pyx because it changed. Compiling MACS3/Signal/HMMR_Signal_Processing.pyx because it changed. Compiling MACS3/Signal/HMMR_HMM.pyx because it changed. Compiling MACS3/Signal/Prob.pyx because it changed. Compiling MACS3/Signal/Region.pyx because it changed. Compiling MACS3/Signal/Pileup.pyx because it changed. Compiling MACS3/Signal/PileupV2.pyx because it changed. Compiling MACS3/Signal/PeakModel.pyx because it changed. Compiling MACS3/Signal/PeakDetect.pyx because it changed. Compiling MACS3/Signal/SignalProcessing.pyx because it changed. Compiling MACS3/Signal/FixWidthTrack.pyx because it changed. Compiling MACS3/Signal/PairedEndTrack.pyx because it changed. Compiling MACS3/Signal/BedGraph.pyx because it changed. Compiling MACS3/Signal/ScoreTrack.pyx because it changed. Compiling MACS3/Signal/CallPeakUnit.pyx because it changed. Compiling MACS3/Signal/VariantStat.pyx because it changed. Compiling MACS3/Signal/ReadAlignment.pyx because it changed. Compiling MACS3/Signal/RACollection.pyx because it changed. Compiling MACS3/Signal/UnitigRACollection.pyx because it changed. Compiling MACS3/Signal/PosReadsInfo.pyx because it changed. Compiling MACS3/Signal/PeakVariants.pyx because it changed. Compiling MACS3/IO/Parser.pyx because it changed. Compiling MACS3/IO/PeakIO.pyx because it changed. Compiling MACS3/IO/BedGraphIO.pyx because it changed. Compiling MACS3/IO/BAM.pyx because it changed. [ 1/25] Cythonizing MACS3/IO/BAM.pyx [ 2/25] Cythonizing MACS3/IO/BedGraphIO.pyx [ 3/25] Cythonizing MACS3/IO/Parser.pyx [ 4/25] Cythonizing MACS3/IO/PeakIO.pyx [ 5/25] Cythonizing MACS3/Signal/BedGraph.pyx [ 6/25] Cythonizing MACS3/Signal/CallPeakUnit.pyx [ 7/25] Cythonizing MACS3/Signal/FixWidthTrack.pyx [ 8/25] Cythonizing MACS3/Signal/HMMR_EM.pyx [ 9/25] Cythonizing MACS3/Signal/HMMR_HMM.pyx [10/25] Cythonizing MACS3/Signal/HMMR_Signal_Processing.pyx [11/25] Cythonizing MACS3/Signal/PairedEndTrack.pyx [12/25] Cythonizing MACS3/Signal/PeakDetect.pyx [13/25] Cythonizing MACS3/Signal/PeakModel.pyx [14/25] Cythonizing MACS3/Signal/PeakVariants.pyx [15/25] Cythonizing MACS3/Signal/Pileup.pyx [16/25] Cythonizing MACS3/Signal/PileupV2.pyx [17/25] Cythonizing MACS3/Signal/PosReadsInfo.pyx [18/25] Cythonizing MACS3/Signal/Prob.pyx [19/25] Cythonizing MACS3/Signal/RACollection.pyx [20/25] Cythonizing MACS3/Signal/ReadAlignment.pyx [21/25] Cythonizing MACS3/Signal/Region.pyx [22/25] Cythonizing MACS3/Signal/ScoreTrack.pyx [23/25] Cythonizing MACS3/Signal/SignalProcessing.pyx [24/25] Cythonizing MACS3/Signal/UnitigRACollection.pyx [25/25] Cythonizing MACS3/Signal/VariantStat.pyx running bdist_wheel running build running build_py creating build creating build/lib.netbsd-9.3-amd64-cpython-310 creating build/lib.netbsd-9.3-amd64-cpython-310/MACS3 copying MACS3/__init__.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3 creating build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO copying MACS3/IO/OutputWriter.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO copying MACS3/IO/__init__.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO creating build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal copying MACS3/Signal/__init__.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal creating build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/__init__.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/bdgbroadcall_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/bdgcmp_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/bdgdiff_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/bdgopt_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/bdgpeakcall_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/callpeak_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/callvar_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/cmbreps_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/diffpeak_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/filterdup_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/hmmratac_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/pileup_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/predictd_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/randsample_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands copying MACS3/Commands/refinepeak_cmd.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands creating build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities copying MACS3/Utilities/Constants.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities copying MACS3/Utilities/Logger.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities copying MACS3/Utilities/OptValidator.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities copying MACS3/Utilities/__init__.py -> build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities running build_ext building 'MACS3.Signal.HMMR_EM' extension creating build/temp.netbsd-9.3-amd64-cpython-310 creating build/temp.netbsd-9.3-amd64-cpython-310/MACS3 creating build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/HMMR_EM.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_EM.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/HMMR_EM.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_EM.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_EM.so building 'MACS3.Signal.HMMR_Signal_Processing' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/HMMR_Signal_Processing.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_Signal_Processing.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/HMMR_Signal_Processing.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_Signal_Processing.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_Signal_Processing.so building 'MACS3.Signal.HMMR_HMM' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/HMMR_HMM.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_HMM.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/HMMR_HMM.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_HMM.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_HMM.so building 'MACS3.Signal.Prob' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/Prob.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Prob.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/Prob.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ MACS3/Signal/Prob.c: In function '__pyx_f_5MACS3_6Signal_4Prob_factorial': MACS3/Signal/Prob.c:6305:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_4 = 2; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { ^ MACS3/Signal/Prob.c: In function '__pyx_f_5MACS3_6Signal_4Prob___poisson_cdf_large_lambda': MACS3/Signal/Prob.c:8693:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_8; __pyx_t_4+=1) { ^ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Prob.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Prob.so building 'MACS3.Signal.Region' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/Region.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Region.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Region.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Region.so building 'MACS3.Signal.Pileup' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/Pileup.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Pileup.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/Pileup.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/cPosValCalculation.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/cPosValCalculation.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Pileup.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/cPosValCalculation.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Pileup.so building 'MACS3.Signal.PileupV2' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/PileupV2.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PileupV2.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/PileupV2.c:1241: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ MACS3/Signal/PileupV2.c: In function '__pyx_f_5MACS3_6Signal_8PileupV2_make_PV_from_PN': MACS3/Signal/PileupV2.c:7104:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] __pyx_t_2 = (__pyx_v_l_PN == (__pyx_t_1[0])); ^~ MACS3/Signal/PileupV2.c: In function '__pyx_f_5MACS3_6Signal_8PileupV2_pileup_PV': MACS3/Signal/PileupV2.c:7486:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) { ^ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PileupV2.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PileupV2.so building 'MACS3.Signal.PeakModel' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/PeakModel.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakModel.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/PeakModel.c:1252: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakModel.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakModel.so building 'MACS3.Signal.PeakDetect' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/include/python3.10 -c MACS3/Signal/PeakDetect.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakDetect.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakDetect.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakDetect.so building 'MACS3.Signal.SignalProcessing' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/SignalProcessing.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/SignalProcessing.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/SignalProcessing.c:1241: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/SignalProcessing.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/SignalProcessing.so building 'MACS3.Signal.FixWidthTrack' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/FixWidthTrack.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/FixWidthTrack.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/FixWidthTrack.c:1243: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/FixWidthTrack.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/FixWidthTrack.so building 'MACS3.Signal.PairedEndTrack' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/PairedEndTrack.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PairedEndTrack.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/PairedEndTrack.c:1241: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PairedEndTrack.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PairedEndTrack.so building 'MACS3.Signal.BedGraph' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/BedGraph.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/BedGraph.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/BedGraph.c:1255: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/BedGraph.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/BedGraph.so building 'MACS3.Signal.ScoreTrack' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/ScoreTrack.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ScoreTrack.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/ScoreTrack.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ScoreTrack.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ScoreTrack.so building 'MACS3.Signal.CallPeakUnit' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/CallPeakUnit.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/CallPeakUnit.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/CallPeakUnit.c:1244: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/CallPeakUnit.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/CallPeakUnit.so building 'MACS3.Signal.VariantStat' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/VariantStat.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/VariantStat.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/VariantStat.c:1246: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/VariantStat.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/VariantStat.so building 'MACS3.Signal.ReadAlignment' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/ReadAlignment.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ReadAlignment.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ReadAlignment.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ReadAlignment.so building 'MACS3.Signal.RACollection' extension creating build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/Signal/RACollection.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/RACollection.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/RACollection.c:1272: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/Signal/swalign.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/swalign.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/bfc.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/bfc.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP In file included from MACS3/fermi-lite/bfc.c:147:0: MACS3/fermi-lite/bfc.c: In function 'bfc_seq_conv': MACS3/fermi-lite/kvec.h:64:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((v).m < (s)) { \ ^ MACS3/fermi-lite/bfc.c:162:2: note: in expansion of macro 'kv_resize' kv_resize(ecbase_t, *seq, l); ^~~~~~~~~ MACS3/fermi-lite/bfc.c: In function 'bfc_seq_revcomp': MACS3/fermi-lite/bfc.c:185:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < seq->n>>1; ++i) { ^ MACS3/fermi-lite/bfc.c: In function 'bfc_ec_first_kmer': MACS3/fermi-lite/bfc.c:221:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = start, l = 0; i < s->n; ++i) { ^ MACS3/fermi-lite/bfc.c: In function 'bfc_ec_kcov': MACS3/fermi-lite/bfc.c:235:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = l = 0; i < s->n; ++i) { ^ MACS3/fermi-lite/bfc.c: In function 'bfc_ec_best_island': MACS3/fermi-lite/bfc.c:257:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = k - 1, max = l = 0, max_i = -1; i < s->n; ++i) { ^ In file included from MACS3/fermi-lite/bfc.c:271:0: MACS3/fermi-lite/bfc.c: In function 'ks_sample_ec': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/bfc.c:315:1: note: in expansion of macro 'KSORT_INIT' KSORT_INIT(ec, echeap1_t, heap_lt) ^~~~~~~~~~ MACS3/fermi-lite/bfc.c: In function 'buf_backtrack': MACS3/fermi-lite/bfc.c:371:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ((i = s[end].i) < seq->n) { ^ MACS3/fermi-lite/bfc.c: In function 'bfc_ec1dir': MACS3/fermi-lite/bfc.c:404:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < seq->n; ++i) ec->a[i].b = seq->a[i].b, ec->a[i].ob = seq->a[i].ob; ^ MACS3/fermi-lite/bfc.c:408:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] *max_heap = *max_heap > 255? 255 : *max_heap > e->heap.n? *max_heap : e->heap.n; ^ MACS3/fermi-lite/bfc.c:408:71: warning: signed and unsigned type in conditional expression [-Wsign-compare] *max_heap = *max_heap > 255? 255 : *max_heap > e->heap.n? *max_heap : e->heap.n; ^ MACS3/fermi-lite/bfc.c:419:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] ecbase_t *c = z.i < seq->n? &seq->a[z.i] : 0; ^ MACS3/fermi-lite/bfc.c:465:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (n_failures > seq->n * 2) { ^ MACS3/fermi-lite/bfc.c:470:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (n_added > 1 && e->heap.n > e->opt->max_heap) { // to prevent heap explosion ^ MACS3/fermi-lite/bfc.c:498:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < ec->n; ++i) // mask out uncorrected regions ^ MACS3/fermi-lite/bfc.c: In function 'bfc_ec1': MACS3/fermi-lite/bfc.c:511:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < e->seq.n; ++i) ^ MACS3/fermi-lite/bfc.c:522:67: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while ((end = bfc_ec_first_kmer(e->opt->k, &e->seq, start, &x)) < e->seq.n) { ^ MACS3/fermi-lite/bfc.c:525:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (end + (e->opt->k>>1) >= e->seq.n) break; ^~ MACS3/fermi-lite/bfc.c:550:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < e->seq.n; ++i) { ^ MACS3/fermi-lite/bfc.c:558:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < e->seq.n; ++i) { ^ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/bseq.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/bseq.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/bubble.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/bubble.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP MACS3/fermi-lite/bubble.c: In function 'mag_vh_simplify_bubble': MACS3/fermi-lite/bubble.c:116:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) { ^ MACS3/fermi-lite/bubble.c:142:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (++tiptr(q)->cnt[y&1] == q->nei[y&1].n) { // all q's predecessors have been processed; then push ^~ MACS3/fermi-lite/bubble.c: In function 'mag_g_simplify_bubble': MACS3/fermi-lite/bubble.c:171:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/bubble.c: In function 'mag_g_pop_simple': MACS3/fermi-lite/bubble.c:261:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/bubble.c: In function 'mag_v_pop_open': MACS3/fermi-lite/bubble.c:296:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (l = 0; l < s->n; ++l) { // if we use "if (p->nei[0].n + p->nei[1].n != 1)", s->n == 1 ^ MACS3/fermi-lite/bubble.c:319:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) { ^ MACS3/fermi-lite/bubble.c:343:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (i != r->n) { ^~ MACS3/fermi-lite/bubble.c:346:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) ^ MACS3/fermi-lite/bubble.c:353:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < s->n; ++i) ^ MACS3/fermi-lite/bubble.c:355:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (i == s->n) mag_v_del(g, p); // p is not connected to any other vertices ^~ MACS3/fermi-lite/bubble.c: In function 'mag_g_pop_open': MACS3/fermi-lite/bubble.c:361:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) ^ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/htab.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/htab.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP MACS3/fermi-lite/htab.c: In function 'bfc_ch_get': MACS3/fermi-lite/htab.c:91:30: warning: signed and unsigned type in conditional expression [-Wsign-compare] return itr == kh_end(h)? -1 : kh_key(h, itr) & 0x3fff; ^ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/ksw.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/ksw.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/kthread.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/kthread.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/mag.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/mag.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP In file included from MACS3/fermi-lite/mag.c:23:0: MACS3/fermi-lite/mag.c: In function 'ks_sample_128x': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/mag.c:24:1: note: in expansion of macro 'KSORT_INIT' KSORT_INIT(128x, ku128_t, ku128_xlt) ^~~~~~~~~~ MACS3/fermi-lite/mag.c: In function 'ks_sample_128y': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/mag.c:25:1: note: in expansion of macro 'KSORT_INIT' KSORT_INIT(128y, ku128_t, ku128_ylt) ^~~~~~~~~~ MACS3/fermi-lite/mag.c: In function 'ks_sample_uint64_t': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/ksort.h:306:36: note: in expansion of macro 'KSORT_INIT' #define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic) ^~~~~~~~~~ MACS3/fermi-lite/mag.c:26:1: note: in expansion of macro 'KSORT_INIT_GENERIC' KSORT_INIT_GENERIC(uint64_t) ^~~~~~~~~~~~~~~~~~ MACS3/fermi-lite/mag.c: In function 'v128_clean': MACS3/fermi-lite/mag.c:40:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = j = 0; i < r->n; ++i) ^ MACS3/fermi-lite/mag.c: In function 'v128_rmdup': MACS3/fermi-lite/mag.c:58:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (l = cnt = 0; l < r->n; ++l) // jump to the first node to be retained ^ MACS3/fermi-lite/mag.c:61:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (l == r->n) { // no good arcs ^~ MACS3/fermi-lite/mag.c:66:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (++l; l < r->n; ++l) { // mark duplicated node ^ MACS3/fermi-lite/mag.c: In function 'v128_cap': MACS3/fermi-lite/mag.c:77:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (r->n <= max) return; ^~ MACS3/fermi-lite/mag.c:80:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) ^ MACS3/fermi-lite/mag.c:81:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (r->a[i].y == thres) break; ^~ MACS3/fermi-lite/mag.c: In function 'mag_g_build_hash': MACS3/fermi-lite/mag.c:95:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/mag.c: In function 'mag_g_amend': MACS3/fermi-lite/mag.c:124:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/mag.c:128:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (l = 0; l < p->nei[j].n; ++l) { ^ MACS3/fermi-lite/mag.c:137:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (ll = 0, z = p->k[j]; ll < r->n; ++ll) ^ MACS3/fermi-lite/mag.c:139:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (ll == r->n) // not in neighbor's neighor ^~ MACS3/fermi-lite/mag.c: In function 'mag_v_write': MACS3/fermi-lite/mag.c:161:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (k = 0; k < r->n; ++k) { ^ MACS3/fermi-lite/mag.c: In function 'mag_g_print': MACS3/fermi-lite/mag.c:183:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/mag.c: In function 'mag_g_destroy': MACS3/fermi-lite/mag.c:208:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) ^ MACS3/fermi-lite/mag.c: In function 'mag_eh_add': MACS3/fermi-lite/mag.c:234:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) // no multi-edges ^ MACS3/fermi-lite/mag.c: In function 'mag_eh_markdel': MACS3/fermi-lite/mag.c:247:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) ^ MACS3/fermi-lite/mag.c: In function 'mag_v_del': MACS3/fermi-lite/mag.c:258:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0; j < r->n; ++j) ^ MACS3/fermi-lite/mag.c: In function 'mag_v_transdel': MACS3/fermi-lite/mag.c:273:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < p->nei[0].n; ++i) { ^ MACS3/fermi-lite/mag.c:275:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0; j < p->nei[1].n; ++j) { ^ MACS3/fermi-lite/mag.c: In function 'mag_vh_merge_try': MACS3/fermi-lite/mag.c:338:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (new_l + 1 > p->max_len) { // then double p->seq and p->cov ^ MACS3/fermi-lite/mag.c: In function 'mag_g_merge': MACS3/fermi-lite/mag.c:371:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { // remove multiedges; FIXME: should we do that? ^ MACS3/fermi-lite/mag.c:380:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ In file included from MACS3/fermi-lite/mag.c:23:0: MACS3/fermi-lite/mag.c: In function 'ks_sample_vlt1': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/mag.c:398:1: note: in expansion of macro 'KSORT_INIT' KSORT_INIT(vlt1, magv_p, mag_vlt1) ^~~~~~~~~~ MACS3/fermi-lite/mag.c: In function 'ks_sample_vlt2': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/mag.c:401:1: note: in expansion of macro 'KSORT_INIT' KSORT_INIT(vlt2, magv_p, mag_vlt2) ^~~~~~~~~~ MACS3/fermi-lite/mag.c: In function 'mag_g_rm_vext': MACS3/fermi-lite/mag.c:408:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/mag.c:415:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < a.n; ++i) mag_v_del(g, a.a[i]); ^ MACS3/fermi-lite/mag.c: In function 'mag_g_rm_vint': MACS3/fermi-lite/mag.c:427:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/mag.c:433:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < a.n; ++i) mag_v_transdel(g, a.a[i], min_ovlp); ^ MACS3/fermi-lite/mag.c: In function 'mag_g_rm_edge': MACS3/fermi-lite/mag.c:446:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) { ^ MACS3/fermi-lite/mag.c:461:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (k = 0; k < r->n; ++k) // get the max overlap length ^ MACS3/fermi-lite/mag.c:462:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (max_ovlp < r->a[k].y) ^ MACS3/fermi-lite/mag.c:470:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (k = 0; k < r->n; ++k) { ^ MACS3/fermi-lite/mag.c:472:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (r->a[k].y < min_ovlp || (double)r->a[k].y / max_ovlp < min_ratio) { ^ MACS3/fermi-lite/mag.c: In function 'mag_cal_rdist': MACS3/fermi-lite/mag.c:501:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0, sum_n_all = 0; i < v->n; ++i) { ^ MACS3/fermi-lite/mag.c: In function 'mag_v_trim_open': MACS3/fermi-lite/mag.c:596:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < r->n; ++i) ^ MACS3/fermi-lite/mag.c:597:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] max_ovlp = max_ovlp > r->a[i].y? max_ovlp : r->a[i].y; ^ MACS3/fermi-lite/mag.c:597:46: warning: signed and unsigned type in conditional expression [-Wsign-compare] max_ovlp = max_ovlp > r->a[i].y? max_ovlp : r->a[i].y; ^ MACS3/fermi-lite/mag.c: In function 'mag_g_trim_open': MACS3/fermi-lite/mag.c:618:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < g->v.n; ++i) ^ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/misc.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/misc.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP MACS3/fermi-lite/misc.c: In function 'fml_mag2utg': MACS3/fermi-lite/misc.c:183:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (b = q->n_ovlp[from] = 0; b < r->n; ++b) ^ MACS3/fermi-lite/misc.c:189:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (b = 0; b < r->n; ++b) { ^ MACS3/fermi-lite/misc.c: In function 'fml_utg_print_gfa': MACS3/fermi-lite/misc.c:256:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (i < o->id_) ^ gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/mrope.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/mrope.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/rld0.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/rld0.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/rle.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/rle.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/rope.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/rope.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -IMACS3/Signal -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I./ -I./MACS3/fermi-lite/ -I./MACS3/Signal/ -I/usr/pkg/include/python3.10 -c MACS3/fermi-lite/unitig.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/unitig.o -w -Ofast -g0 -std=gnu99 -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -DSIMDE_ENABLE_OPENMP In file included from MACS3/fermi-lite/unitig.c:67:0: MACS3/fermi-lite/unitig.c: In function 'ks_sample_infocmp': MACS3/fermi-lite/ksort.h:287:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (k != n - pop - 1) tmp = a[k], a[k] = a[n-pop-1], a[n-pop-1] = tmp; \ ^ MACS3/fermi-lite/unitig.c:68:1: note: in expansion of macro 'KSORT_INIT' KSORT_INIT(infocmp, rldintv_t, info_lt) ^~~~~~~~~~ MACS3/fermi-lite/unitig.c: In function 'fm6_get_nei': MACS3/fermi-lite/unitig.c:152:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0; j < prev->n; ++j) prev->a[j].info += beg; ^ MACS3/fermi-lite/unitig.c:155:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0; j < prev->n; ++j) cat->a[j] = 0; // only one interval; all point to 0 ^ MACS3/fermi-lite/unitig.c:157:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0, curr->n = 0; j < prev->n; ++j) { ^ MACS3/fermi-lite/unitig.c:161:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (ok[0].x[2] && ori_l != s->l) { // some (partial) reads end here ^~ MACS3/fermi-lite/unitig.c:168:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = j; i < prev->n && cat->a[i] == cat0; ++i) cat->a[i] = -1; // mask out other intervals of the same cat ^ MACS3/fermi-lite/unitig.c:193:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 1, cat0 = 0; j < curr->n; ++j) { // this loop recalculate cat ^ MACS3/fermi-lite/unitig.c:211:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = ori_l; i < s->l; ++i) { ^ MACS3/fermi-lite/unitig.c: In function 'check_left_simple': MACS3/fermi-lite/unitig.c:241:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (j = 0, curr->n = 0; j < prev->n; ++j) { ^ MACS3/fermi-lite/unitig.c: In function 'unitig_unidir': MACS3/fermi-lite/unitig.c:305:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = ori_l; i < s->l; ++i) cov->s[i] = '"'; ^ MACS3/fermi-lite/unitig.c: In function 'copy_nei': MACS3/fermi-lite/unitig.c:315:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (i = 0; i < src->n; ++i) { ^ MACS3/fermi-lite/unitig.c: In function 'unitig1': MACS3/fermi-lite/unitig.c:336:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (intv0.x[2] > 1 && k != intv0.x[0]) return -3; // duplicated, but not the first ^~ MACS3/fermi-lite/unitig.c:340:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (s->l <= a->min_match) return -1; // too short ^~ MACS3/fermi-lite/unitig.c: In function 'worker': MACS3/fermi-lite/unitig.c:394:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (d->max_l < d->str.m) { ^ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/RACollection.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/swalign.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/bfc.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/bseq.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/bubble.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/htab.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/ksw.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/kthread.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/mag.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/misc.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/mrope.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/rld0.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/rle.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/rope.o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/fermi-lite/unitig.o -L/usr/pkg/lib -lm -lz -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/RACollection.so building 'MACS3.Signal.UnitigRACollection' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/UnitigRACollection.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/UnitigRACollection.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/UnitigRACollection.c:1246: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/UnitigRACollection.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/UnitigRACollection.so building 'MACS3.Signal.PosReadsInfo' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/PosReadsInfo.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PosReadsInfo.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/Signal/PosReadsInfo.c:1246: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PosReadsInfo.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PosReadsInfo.so building 'MACS3.Signal.PeakVariants' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/Signal/PeakVariants.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakVariants.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakVariants.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakVariants.so building 'MACS3.IO.Parser' extension creating build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/IO/Parser.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/Parser.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/IO/Parser.c:1243: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/Parser.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/Parser.so building 'MACS3.IO.PeakIO' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/include/python3.10 -c MACS3/IO/PeakIO.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/PeakIO.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/PeakIO.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/PeakIO.so building 'MACS3.IO.BedGraphIO' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/include/python3.10 -c MACS3/IO/BedGraphIO.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/BedGraphIO.o -w -Ofast -g0 gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/BedGraphIO.o -L/usr/pkg/lib -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/BedGraphIO.so building 'MACS3.IO.BAM' extension gcc -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -fPIC -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/pkg/include/python3.10 -c MACS3/IO/BAM.c -o build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/BAM.o -w -Ofast -g0 In file included from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h:1929:0, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h:5, from MACS3/IO/BAM.c:1246: /tmp/biology/py-macs3/work/.buildlink/lib/python3.10/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ gcc -shared -L. -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -Wl,-zrelro -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include -I/usr/include -I/usr/pkg/include/python3.10 -I/usr/pkg/include build/temp.netbsd-9.3-amd64-cpython-310/MACS3/IO/BAM.o -L/usr/pkg/lib -lm -o build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/BAM.so running build_scripts creating build/scripts-3.10 copying and adjusting bin/macs3 -> build/scripts-3.10 changing mode of build/scripts-3.10/macs3 from 644 to 755 installing to build/bdist.netbsd-9.3-amd64/wheel running install running install_lib creating build/bdist.netbsd-9.3-amd64 creating build/bdist.netbsd-9.3-amd64/wheel creating build/bdist.netbsd-9.3-amd64/wheel/MACS3 copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/__init__.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3 creating build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/OutputWriter.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/__init__.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/Parser.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/PeakIO.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/BedGraphIO.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/IO/BAM.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/IO creating build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/__init__.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_EM.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_Signal_Processing.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/HMMR_HMM.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Prob.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Region.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/Pileup.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PileupV2.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakModel.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakDetect.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/SignalProcessing.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/FixWidthTrack.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PairedEndTrack.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/BedGraph.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ScoreTrack.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/CallPeakUnit.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/VariantStat.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/ReadAlignment.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/RACollection.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/UnitigRACollection.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PosReadsInfo.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Signal/PeakVariants.so -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Signal creating build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/__init__.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/bdgbroadcall_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/bdgcmp_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/bdgdiff_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/bdgopt_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/bdgpeakcall_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/callpeak_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/callvar_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/cmbreps_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/diffpeak_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/filterdup_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/hmmratac_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/pileup_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/predictd_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/randsample_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Commands/refinepeak_cmd.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Commands creating build/bdist.netbsd-9.3-amd64/wheel/MACS3/Utilities copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities/Constants.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Utilities copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities/Logger.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Utilities copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities/OptValidator.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Utilities copying build/lib.netbsd-9.3-amd64-cpython-310/MACS3/Utilities/__init__.py -> build/bdist.netbsd-9.3-amd64/wheel/MACS3/Utilities running install_egg_info running egg_info creating MACS3.egg-info writing MACS3.egg-info/PKG-INFO writing dependency_links to MACS3.egg-info/dependency_links.txt writing requirements to MACS3.egg-info/requires.txt writing top-level names to MACS3.egg-info/top_level.txt writing manifest file 'MACS3.egg-info/SOURCES.txt' dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/arrayscalars.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarrayobject.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ndarraytypes.h won't be automatically included in the manifest: the path must be relative dependency /usr/pkg/lib/python3.10/site-packages/numpy/core/include/numpy/ufuncobject.h won't be automatically included in the manifest: the path must be relative reading manifest file 'MACS3.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'make_docker_base.sh' warning: no previously-included files matching '.ipynb_checkpoints/*' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'MACS3.egg-info/SOURCES.txt' Copying MACS3.egg-info to build/bdist.netbsd-9.3-amd64/wheel/MACS3-3.0.1-py3.10.egg-info running install_scripts creating build/bdist.netbsd-9.3-amd64/wheel/MACS3-3.0.1.data creating build/bdist.netbsd-9.3-amd64/wheel/MACS3-3.0.1.data/scripts copying build/scripts-3.10/macs3 -> build/bdist.netbsd-9.3-amd64/wheel/MACS3-3.0.1.data/scripts changing mode of build/bdist.netbsd-9.3-amd64/wheel/MACS3-3.0.1.data/scripts/macs3 to 755 creating build/bdist.netbsd-9.3-amd64/wheel/MACS3-3.0.1.dist-info/WHEEL creating '/tmp/biology/py-macs3/work/MACS-3.0.1/dist/.tmp-1ivtvd6c/MACS3-3.0.1-cp310-cp310-netbsd_9_3_amd64.whl' and adding 'build/bdist.netbsd-9.3-amd64/wheel' to it adding 'MACS3/__init__.py' adding 'MACS3/Commands/__init__.py' adding 'MACS3/Commands/bdgbroadcall_cmd.py' adding 'MACS3/Commands/bdgcmp_cmd.py' adding 'MACS3/Commands/bdgdiff_cmd.py' adding 'MACS3/Commands/bdgopt_cmd.py' adding 'MACS3/Commands/bdgpeakcall_cmd.py' adding 'MACS3/Commands/callpeak_cmd.py' adding 'MACS3/Commands/callvar_cmd.py' adding 'MACS3/Commands/cmbreps_cmd.py' adding 'MACS3/Commands/diffpeak_cmd.py' adding 'MACS3/Commands/filterdup_cmd.py' adding 'MACS3/Commands/hmmratac_cmd.py' adding 'MACS3/Commands/pileup_cmd.py' adding 'MACS3/Commands/predictd_cmd.py' adding 'MACS3/Commands/randsample_cmd.py' adding 'MACS3/Commands/refinepeak_cmd.py' adding 'MACS3/IO/BAM.so' adding 'MACS3/IO/BedGraphIO.so' adding 'MACS3/IO/OutputWriter.py' adding 'MACS3/IO/Parser.so' adding 'MACS3/IO/PeakIO.so' adding 'MACS3/IO/__init__.py' adding 'MACS3/Signal/BedGraph.so' adding 'MACS3/Signal/CallPeakUnit.so' adding 'MACS3/Signal/FixWidthTrack.so' adding 'MACS3/Signal/HMMR_EM.so' adding 'MACS3/Signal/HMMR_HMM.so' adding 'MACS3/Signal/HMMR_Signal_Processing.so' adding 'MACS3/Signal/PairedEndTrack.so' adding 'MACS3/Signal/PeakDetect.so' adding 'MACS3/Signal/PeakModel.so' adding 'MACS3/Signal/PeakVariants.so' adding 'MACS3/Signal/Pileup.so' adding 'MACS3/Signal/PileupV2.so' adding 'MACS3/Signal/PosReadsInfo.so' adding 'MACS3/Signal/Prob.so' adding 'MACS3/Signal/RACollection.so' adding 'MACS3/Signal/ReadAlignment.so' adding 'MACS3/Signal/Region.so' adding 'MACS3/Signal/ScoreTrack.so' adding 'MACS3/Signal/SignalProcessing.so' adding 'MACS3/Signal/UnitigRACollection.so' adding 'MACS3/Signal/VariantStat.so' adding 'MACS3/Signal/__init__.py' adding 'MACS3/Utilities/Constants.py' adding 'MACS3/Utilities/Logger.py' adding 'MACS3/Utilities/OptValidator.py' adding 'MACS3/Utilities/__init__.py' adding 'MACS3-3.0.1.data/scripts/macs3' adding 'MACS3-3.0.1.dist-info/LICENSE' adding 'MACS3-3.0.1.dist-info/METADATA' adding 'MACS3-3.0.1.dist-info/WHEEL' adding 'MACS3-3.0.1.dist-info/top_level.txt' adding 'MACS3-3.0.1.dist-info/RECORD' removing build/bdist.netbsd-9.3-amd64/wheel Successfully built MACS3-3.0.1-cp310-cp310-netbsd_9_3_amd64.whl