[package - 132arm64-default][biology/py-macs2] Failed for py39-macs2-2.2.9.1 in build/runaway
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Date: Thu, 12 Oct 2023 13:02:41 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere3/data/132arm64-default/08943441f26e/logs/py39-macs2-2.2.9.1.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=08943441f26e Log: =>> Building biology/py-macs2 build started at Thu Oct 12 10:49:41 UTC 2023 port directory: /usr/ports/biology/py-macs2 package name: py39-macs2-2.2.9.1 building for: FreeBSD 132arm64-default-job-11 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 arm64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1500000 Jail OSVERSION: 1302001 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p4 UNAME_r=13.2-RELEASE-p4 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/132arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/132arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=132arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/132arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py39 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py39 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-macs2/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-macs2/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py39-macs2" EXAMPLESDIR="share/examples/py39-macs2" DATADIR="share/py39-macs2" WWWDIR="www/py39-macs2" ETCDIR="etc/py39-macs2" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py39-macs2 DOCSDIR=/usr/local/share/doc/py39-macs2 EXAMPLESDIR=/usr/local/share/examples/py39-macs2 WWWDIR=/usr/local/www/py39-macs2 ETCDIR=/usr/local/etc/py39-macs2 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=3 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: aarch64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: aarch64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: aarch64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.2-RELEASE-p4 OSREL=13.2 OSVERSION=1302001 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py39-macs2-2.2.9.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.7.pkg [132arm64-default-job-11] Installing pkg-1.20.7... [132arm64-default-job-11] Extracting pkg-1.20.7: .......... done ===> py39-macs2-2.2.9.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-macs2-2.2.9.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py39-macs2-2.2.9.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py39-macs2-2.2.9.1 for building => SHA256 Checksum OK for taoliu-MACS-v2.2.9.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py39-macs2-2.2.9.1 for building ===> Extracting for py39-macs2-2.2.9.1 => SHA256 Checksum OK for taoliu-MACS-v2.2.9.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py39-macs2-2.2.9.1 =========================================================================== =======================<phase: build-depends >============================ ===> py39-macs2-2.2.9.1 depends on package: py39-numpy>=1.16,1<1.26,1 - not found ===> Installing existing package /packages/All/py39-numpy-1.25.0_1,1.pkg [132arm64-default-job-11] Installing py39-numpy-1.25.0_1,1... [132arm64-default-job-11] `-- Installing gcc12-12.2.0_6... [132arm64-default-job-11] | `-- Installing binutils-2.40_4,1... [132arm64-default-job-11] | | `-- Installing gettext-runtime-0.22_1... [132arm64-default-job-11] | | `-- Installing indexinfo-0.3.1... [132arm64-default-job-11] | | `-- Extracting indexinfo-0.3.1: .... done [132arm64-default-job-11] | | `-- Extracting gettext-runtime-0.22_1: .......... done [132arm64-default-job-11] | | `-- Installing zstd-1.5.5... [132arm64-default-job-11] | | `-- Installing liblz4-1.9.4,1... [132arm64-default-job-11] | | `-- Extracting liblz4-1.9.4,1: .......... done [132arm64-default-job-11] | | `-- Extracting zstd-1.5.5: .......... done [132arm64-default-job-11] | `-- Extracting binutils-2.40_4,1: .......... done [132arm64-default-job-11] | `-- Installing gmp-6.3.0... [132arm64-default-job-11] | `-- Extracting gmp-6.3.0: .......... done [132arm64-default-job-11] | `-- Installing mpc-1.3.1_1... [132arm64-default-job-11] | | `-- Installing mpfr-4.2.1,1... [132arm64-default-job-11] | | `-- Extracting mpfr-4.2.1,1: .......... done [132arm64-default-job-11] | `-- Extracting mpc-1.3.1_1: ......... done [132arm64-default-job-11] `-- Extracting gcc12-12.2.0_6: .......... done [132arm64-default-job-11] `-- Installing openblas-0.3.24,1... [132arm64-default-job-11] `-- Extracting openblas-0.3.24,1: .......... done [132arm64-default-job-11] `-- Installing py39-setuptools-63.1.0_1... [132arm64-default-job-11] | `-- Installing python39-3.9.18... [132arm64-default-job-11] | | `-- Installing libffi-3.4.4... [132arm64-default-job-11] | | `-- Extracting libffi-3.4.4: .......... done [132arm64-default-job-11] | | `-- Installing mpdecimal-2.5.1... [132arm64-default-job-11] | | `-- Extracting mpdecimal-2.5.1: .......... done [132arm64-default-job-11] | | `-- Installing readline-8.2.1... [132arm64-default-job-11] | | `-- Extracting readline-8.2.1: .......... done [132arm64-default-job-11] | `-- Extracting python39-3.9.18: .......... done [132arm64-default-job-11] `-- Extracting py39-setuptools-63.1.0_1: .......... done [132arm64-default-job-11] `-- Installing suitesparse-umfpack-6.2.0... [132arm64-default-job-11] | `-- Installing suitesparse-amd-3.2.0... [132arm64-default-job-11] | | `-- Installing suitesparse-config-7.2.0... [132arm64-default-job-11] | | `-- Extracting suitesparse-config-7.2.0: .......... done [132arm64-default-job-11] | `-- Extracting suitesparse-amd-3.2.0: .......... done [132arm64-default-job-11] | `-- Installing suitesparse-camd-3.2.0... [132arm64-default-job-11] | `-- Extracting suitesparse-camd-3.2.0: .......... done [132arm64-default-job-11] | `-- Installing suitesparse-ccolamd-3.2.0... [132arm64-default-job-11] | `-- Extracting suitesparse-ccolamd-3.2.0: .......... done [132arm64-default-job-11] | `-- Installing suitesparse-cholmod-4.2.0... [132arm64-default-job-11] | | `-- Installing suitesparse-colamd-3.2.0... [132arm64-default-job-11] | | `-- Extracting suitesparse-colamd-3.2.0: .......... done [132arm64-default-job-11] | `-- Extracting suitesparse-cholmod-4.2.0: .......... done [132arm64-default-job-11] `-- Extracting suitesparse-umfpack-6.2.0: .......... done [132arm64-default-job-11] Extracting py39-numpy-1.25.0_1,1: .......... done ===== Message from gcc12-12.2.0_6: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python39-3.9.18: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> py39-macs2-2.2.9.1 depends on package: py39-numpy>=1.16,1<1.26,1 - found ===> Returning to build of py39-macs2-2.2.9.1 ===> py39-macs2-2.2.9.1 depends on executable: cython-3.9 - not found ===> Installing existing package /packages/All/py39-cython-0.29.36.pkg [132arm64-default-job-11] Installing py39-cython-0.29.36... [132arm64-default-job-11] Extracting py39-cython-0.29.36: .......... done ===> py39-macs2-2.2.9.1 depends on executable: cython-3.9 - found ===> Returning to build of py39-macs2-2.2.9.1 ===> py39-macs2-2.2.9.1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-macs2-2.2.9.1 depends on file: /usr/local/bin/python3.9 - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for py39-macs2-2.2.9.1 Compiling MACS2/Prob.pyx because it changed. Compiling MACS2/IO/Parser.pyx because it changed. Compiling MACS2/Pileup.pyx because it changed. Compiling MACS2/PeakModel.pyx because it changed. Compiling MACS2/PeakDetect.pyx because it changed. Compiling MACS2/Signal.pyx because it changed. Compiling MACS2/IO/PeakIO.pyx because it changed. Compiling MACS2/IO/BedGraphIO.pyx because it changed. Compiling MACS2/IO/FixWidthTrack.pyx because it changed. Compiling MACS2/IO/PairedEndTrack.pyx because it changed. Compiling MACS2/IO/BedGraph.pyx because it changed. Compiling MACS2/IO/ScoreTrack.pyx because it changed. Compiling MACS2/IO/CallPeakUnit.pyx because it changed. [ 1/13] Cythonizing MACS2/IO/BedGraph.pyx [ 2/13] Cythonizing MACS2/IO/BedGraphIO.pyx [ 3/13] Cythonizing MACS2/IO/CallPeakUnit.pyx [ 4/13] Cythonizing MACS2/IO/FixWidthTrack.pyx [ 5/13] Cythonizing MACS2/IO/PairedEndTrack.pyx [ 6/13] Cythonizing MACS2/IO/Parser.pyx [ 7/13] Cythonizing MACS2/IO/PeakIO.pyx [ 8/13] Cythonizing MACS2/IO/ScoreTrack.pyx [ 9/13] Cythonizing MACS2/PeakDetect.pyx [10/13] Cythonizing MACS2/PeakModel.pyx [11/13] Cythonizing MACS2/Pileup.pyx [12/13] Cythonizing MACS2/Prob.pyx [13/13] Cythonizing MACS2/Signal.pyx running config =========================================================================== =======================<phase: build >============================ ===> Building for py39-macs2-2.2.9.1 running build running build_py creating build creating build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39 creating build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/OptValidator.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/bdgcmp_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/callpeak_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/OutputWriter.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/Constants.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/filterdup_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/__init__.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/diffpeak_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/bdgopt_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/bdgpeakcall_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/predictd_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/randsample_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/refinepeak_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/cmbreps_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/bdgbroadcall_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/bdgdiff_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/pileup_cmd.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 creating build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO copying MACS2/IO/__init__.py -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO copying MACS2/khash.pxd -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 copying MACS2/cPosValCalculation.pxd -> build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 running build_ext building 'MACS2.Prob' extension creating build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39 creating build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2 cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/Prob.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Prob.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Prob.o -L/usr/local/lib -lm -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Prob.cpython-39.so building 'MACS2.IO.Parser' extension creating build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/IO/Parser.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/Parser.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/Parser.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/Parser.cpython-39.so building 'MACS2.Pileup' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I./MACS2 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/Pileup.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Pileup.o -w -O3 -ffast-math -g0 cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I./MACS2 -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/cPosValCalculation.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/cPosValCalculation.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Pileup.o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/cPosValCalculation.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Pileup.cpython-39.so building 'MACS2.PeakModel' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/PeakModel.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/PeakModel.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/PeakModel.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/PeakModel.cpython-39.so building 'MACS2.PeakDetect' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/PeakDetect.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/PeakDetect.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/PeakDetect.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/PeakDetect.cpython-39.so building 'MACS2.Signal' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/Signal.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Signal.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Signal.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/Signal.cpython-39.so building 'MACS2.IO.PeakIO' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/IO/PeakIO.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/PeakIO.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/PeakIO.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/PeakIO.cpython-39.so building 'MACS2.IO.BedGraphIO' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/IO/BedGraphIO.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/BedGraphIO.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/BedGraphIO.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/BedGraphIO.cpython-39.so building 'MACS2.IO.FixWidthTrack' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/IO/FixWidthTrack.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/FixWidthTrack.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/FixWidthTrack.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/FixWidthTrack.cpython-39.so building 'MACS2.IO.PairedEndTrack' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/IO/PairedEndTrack.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/PairedEndTrack.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/PairedEndTrack.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/PairedEndTrack.cpython-39.so building 'MACS2.IO.BedGraph' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/IO/BedGraph.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/BedGraph.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/BedGraph.o -L/usr/local/lib -lm -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/BedGraph.cpython-39.so building 'MACS2.IO.ScoreTrack' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/IO/ScoreTrack.c -o build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/ScoreTrack.o -w -O3 -ffast-math -g0 cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/ScoreTrack.o -L/usr/local/lib -o build/lib.freebsd-13.2-RELEASE-p4-arm64-cpython-39/MACS2/IO/ScoreTrack.cpython-39.so =>> Killing runaway build after 7200 seconds with no output