=>> Building biology/py-macs2 build started at Wed Jul 8 15:27:13 JST 2026 port directory: /usr/ports/biology/py-macs2 package name: py312-macs2-2.2.9.1_3 building for: FreeBSD s15amd64-setuptools2-job-06 15.1-STABLE FreeBSD 15.1-STABLE 1501501 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1113 Jul 5 18:52 /usr/ports/biology/py-macs2/Makefile Ports top last git commit: 18628b9022c9c1c0e7cb5e71c2aa1e1e563ca34a Ports top unclean checkout: yes Port dir last git commit: 88271a10b53bcfac8011adb74cf721fce4ec6fb8 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8 Host OSVERSION: 1501501 Jail OSVERSION: 1501501 Job Id: 06 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1501501 UNAME_v=FreeBSD 15.1-STABLE 1501501 UNAME_r=15.1-STABLE 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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.8 MASTERMNT=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=s15amd64-setuptools2 SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/s15amd64-setuptools2/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py312 MAKE_ARGS= FLAVOR=py312 ---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/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312/.cache HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/work-py312/.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-py312/.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-py312 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312/.cache HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/work-py312/.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-py312/.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=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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/python3.12 PYTHON_LIBDIR=lib/python3.12 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" OSREL=15.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py312-macs2" EXAMPLESDIR="share/examples/py312-macs2" DATADIR="share/py312-macs2" WWWDIR="www/py312-macs2" ETCDIR="etc/py312-macs2" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.12 PYTHON_LIBDIR=/usr/local/lib/python3.12 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.12/site-packages PYTHON_SUFFIX=312 PYTHON_BASESUFFIX=312 PYTHON_TAG=.cpython-312 PYTHON_SOABI=.cpython-312 PYTHON_VER=3.12 PYTHON_BASEVER=3.12 PYTHON_VERSION=python3.12 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py312-macs2 DOCSDIR=/usr/local/share/doc/py312-macs2 EXAMPLESDIR=/usr/local/share/examples/py312-macs2 WWWDIR=/usr/local/www/py312-macs2 ETCDIR=/usr/local/etc/py312-macs2 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles OVERLAYS+=/overlays/overlay_setuptools FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### LICENSES_ACCEPTED= EULA ISC MPEG2ENC DEFAULT_VERSIONS+= magick=7 DEFAULT_VERSIONS+= pgsql=18 DEFAULT_VERSIONS+= samba=4.23 DEFAULT_VERSIONS+= ssl=openssl japanese_fcitx5-mozc_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_SET= EDICT2 PERSONALNAME PLACENAME SUDACHIDICT UTDIC japanese_mozc_server_UNSET= JAWIKI x11_wm_hikari_SET= INPUTMETHOD GAMMA LAYERSHELL SCREENCOPY VIRTUALINPUT X11 .if $(.CURDIR:M*/x11-wm/hikari) WITH_DEBUG= YES .endif #### #### devel_gamin_set= LIBINOTIFY #### Misc Poudriere #### .include "/etc/make.conf.ports_env" DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 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) 8192 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 pipebuf (kbytes, -y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired lang/cython0. It is scheduled to be removed on or after 2026-09-15. ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-macs2-2.2.9.1_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.7.5.pkg [s15amd64-setuptools2-job-06] Installing pkg-2.7.5... [s15amd64-setuptools2-job-06] Extracting pkg-2.7.5: .......... done ===> py312-macs2-2.2.9.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py312-macs2-2.2.9.1_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired lang/cython0. It is scheduled to be removed on or after 2026-09-15. ===> License BSD3CLAUSE accepted by the user => taoliu-MACS-v2.2.9.1_GH0.tar.gz doesn't seem to exist in /portdistfiles. => Attempting to fetch https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.9.1?dummy=/taoliu-MACS-v2.2.9.1_GH0.tar.gz fetch: https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.9.1?dummy=/taoliu-MACS-v2.2.9.1_GH0.tar.gz: size unknown fetch: https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.9.1?dummy=/taoliu-MACS-v2.2.9.1_GH0.tar.gz: size of remote file is not known taoliu-MACS-v2.2.9.1_GH0.tar.gz 126 MB 9 MBps 12s ===> Fetching all distfiles required by py312-macs2-2.2.9.1_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired lang/cython0. It is scheduled to be removed on or after 2026-09-15. ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py312-macs2-2.2.9.1_3 for building => SHA256 Checksum OK for taoliu-MACS-v2.2.9.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Depends on expired lang/cython0. It is scheduled to be removed on or after 2026-09-15. ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py312-macs2-2.2.9.1_3 for building ===> Extracting for py312-macs2-2.2.9.1_3 => SHA256 Checksum OK for taoliu-MACS-v2.2.9.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for py312-macs2-2.2.9.1_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> py312-macs2-2.2.9.1_3 depends on package: py312-numpy>=1.16 - not found ===> Installing existing package /packages/All/py312-numpy-2.4.6_1,1.pkg [s15amd64-setuptools2-job-06] Installing py312-numpy-2.4.6_1,1... [s15amd64-setuptools2-job-06] `-- Installing gcc14-14.2.0_6... [s15amd64-setuptools2-job-06] | `-- Installing binutils-2.44,1... [s15amd64-setuptools2-job-06] | | `-- Installing indexinfo-0.3.1_1... [s15amd64-setuptools2-job-06] | | `-- Extracting indexinfo-0.3.1_1: .... done [s15amd64-setuptools2-job-06] | | `-- Installing zstd-1.5.7_2... [s15amd64-setuptools2-job-06] | | `-- Installing liblz4-1.10.0_2,1... [s15amd64-setuptools2-job-06] | | `-- Extracting liblz4-1.10.0_2,1: .......... done [s15amd64-setuptools2-job-06] | | `-- Extracting zstd-1.5.7_2: .......... done [s15amd64-setuptools2-job-06] | `-- Extracting binutils-2.44,1: .......... done [s15amd64-setuptools2-job-06] | `-- Installing gmp-6.3.0... [s15amd64-setuptools2-job-06] | `-- Extracting gmp-6.3.0: .......... done [s15amd64-setuptools2-job-06] | `-- Installing mpc-1.4.1... [s15amd64-setuptools2-job-06] | | `-- Installing mpfr-4.2.2,1... [s15amd64-setuptools2-job-06] | | `-- Extracting mpfr-4.2.2,1: .......... done [s15amd64-setuptools2-job-06] | `-- Extracting mpc-1.4.1: .......... done [s15amd64-setuptools2-job-06] `-- Extracting gcc14-14.2.0_6: .......... done [s15amd64-setuptools2-job-06] `-- Installing openblas-0.3.33,2... [s15amd64-setuptools2-job-06] `-- Extracting openblas-0.3.33,2: .......... done [s15amd64-setuptools2-job-06] `-- Installing python312-3.12.13_3... [s15amd64-setuptools2-job-06] | `-- Installing expat-2.8.2... [s15amd64-setuptools2-job-06] | `-- Extracting expat-2.8.2: .......... done [s15amd64-setuptools2-job-06] | `-- Installing gettext-runtime-1.0_1... [s15amd64-setuptools2-job-06] | `-- Extracting gettext-runtime-1.0_1: .......... done [s15amd64-setuptools2-job-06] | `-- Installing libffi-3.6.0... [s15amd64-setuptools2-job-06] | `-- Extracting libffi-3.6.0: .......... done [s15amd64-setuptools2-job-06] | `-- Installing mpdecimal-4.0.1... [s15amd64-setuptools2-job-06] | `-- Extracting mpdecimal-4.0.1: .......... done [s15amd64-setuptools2-job-06] | `-- Installing openssl-3.0.21,1... [s15amd64-setuptools2-job-06] | `-- Extracting openssl-3.0.21,1: .......... done [s15amd64-setuptools2-job-06] | `-- Installing readline-8.3.3... [s15amd64-setuptools2-job-06] | `-- Extracting readline-8.3.3: .......... done [s15amd64-setuptools2-job-06] `-- Extracting python312-3.12.13_3: .......... done [s15amd64-setuptools2-job-06] Extracting py312-numpy-2.4.6_1,1: .......... done ===== Message from gcc14-14.2.0_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/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from openssl-3.0.21,1: -- This port (security/openssl) will update from 3.0 to 3.5 per 2026-07-01 (2026Q3) in anticipation of the End-of-Life of OpenSSL 3.0. A new port (security/openssl30) will be created for the remainder of the lifespan of OpenSSL 3.0 and FreeBSD 14. See: https://openssl-library.org/roadmap/index.html ===== Message from python312-3.12.13_3: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py312-gdbm databases/py-gdbm@py312 py312-sqlite3 databases/py-sqlite3@py312 py312-tkinter x11-toolkits/py-tkinter@py312 ===> py312-macs2-2.2.9.1_3 depends on package: py312-numpy>=1.16 - found ===> Returning to build of py312-macs2-2.2.9.1_3 ===> py312-macs2-2.2.9.1_3 depends on package: py312-cython0>=0.29.37<3 - not found ===> Installing existing package /packages/All/py312-cython0-0.29.37.pkg [s15amd64-setuptools2-job-06] Installing py312-cython0-0.29.37... [s15amd64-setuptools2-job-06] Extracting py312-cython0-0.29.37: .......... done ===== Message from py312-cython0-0.29.37: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Legacy version. Does not work with newer Python versions. Use lang/cython instead. It is scheduled to be removed on or after 2026-06-30. ===> py312-macs2-2.2.9.1_3 depends on package: py312-cython0>=0.29.37<3 - found ===> Returning to build of py312-macs2-2.2.9.1_3 ===> py312-macs2-2.2.9.1_3 depends on package: py312-setuptools>=63.1.0 - not found ===> Installing existing package /packages/All/py312-setuptools-81.0.0.pkg [s15amd64-setuptools2-job-06] Installing py312-setuptools-81.0.0... [s15amd64-setuptools2-job-06] `-- Installing py312-more-itertools-11.1.0... [s15amd64-setuptools2-job-06] `-- Extracting py312-more-itertools-11.1.0: .......... done [s15amd64-setuptools2-job-06] `-- Installing py312-packaging-26.2... [s15amd64-setuptools2-job-06] `-- Extracting py312-packaging-26.2: .......... done [s15amd64-setuptools2-job-06] `-- Installing py312-wheel-0.47.0... [s15amd64-setuptools2-job-06] `-- Extracting py312-wheel-0.47.0: .......... done [s15amd64-setuptools2-job-06] Extracting py312-setuptools-81.0.0: .......... done ===> py312-macs2-2.2.9.1_3 depends on package: py312-setuptools>=63.1.0 - found ===> Returning to build of py312-macs2-2.2.9.1_3 ===> py312-macs2-2.2.9.1_3 depends on file: /usr/local/bin/python3.12 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for py312-macs2-2.2.9.1_3 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 /usr/local/lib/python3.12/site-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for py312-macs2-2.2.9.1_3 /usr/local/lib/python3.12/site-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. This deprecation is overdue, please update your project and remove deprecated calls to avoid build errors in the future. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) /usr/local/lib/python3.12/site-packages/setuptools/_distutils/dist.py:287: UserWarning: Unknown distribution option: 'tests_require' warnings.warn(msg) /usr/local/lib/python3.12/site-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: BSD License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/OptValidator.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/bdgcmp_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/callpeak_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/OutputWriter.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/Constants.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/filterdup_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/diffpeak_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/bdgopt_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/bdgpeakcall_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/predictd_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/randsample_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/refinepeak_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/cmbreps_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/bdgbroadcall_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/bdgdiff_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/pileup_cmd.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 creating build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2/IO copying MACS2/IO/__init__.py -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2/IO copying MACS2/khash.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 copying MACS2/cPosValCalculation.pxd -> build/lib.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 running build_ext building 'MACS2.Prob' extension creating build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MACS2 cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.12/site-packages/numpy/_core/include -I/usr/local/include/python3.12 -c MACS2/Prob.c -o build/temp.freebsd-15.1-STABLE-amd64-cpython-312/MACS2/Prob.o -w -O3 -ffast-math -g0 MACS2/Prob.c:2434:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2434 | __Pyx_TraceCall("pnorm", __pyx_f[0], 44, 0, __PYX_ERR(0, 44, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1535:15: note: expanded from macro '__Pyx_TraceCall' 1535 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2434:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2434 | __Pyx_TraceCall("pnorm", __pyx_f[0], 44, 0, __PYX_ERR(0, 44, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1543:11: note: expanded from macro '__Pyx_TraceCall' 1543 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2501:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2501 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1594:19: note: expanded from macro '__Pyx_TraceReturn' 1594 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2501:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2501 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1601:15: note: expanded from macro '__Pyx_TraceReturn' 1601 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2591:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2591 | __Pyx_TraceCall("pnorm (wrapper)", __pyx_f[0], 44, 0, __PYX_ERR(0, 44, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1535:15: note: expanded from macro '__Pyx_TraceCall' 1535 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2591:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2591 | __Pyx_TraceCall("pnorm (wrapper)", __pyx_f[0], 44, 0, __PYX_ERR(0, 44, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1543:11: note: expanded from macro '__Pyx_TraceCall' 1543 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2606:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2606 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1594:19: note: expanded from macro '__Pyx_TraceReturn' 1594 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2606:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2606 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1601:15: note: expanded from macro '__Pyx_TraceReturn' 1601 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2635:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2635 | __Pyx_TraceCall("factorial", __pyx_f[0], 53, 0, __PYX_ERR(0, 53, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1535:15: note: expanded from macro '__Pyx_TraceCall' 1535 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2635:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2635 | __Pyx_TraceCall("factorial", __pyx_f[0], 53, 0, __PYX_ERR(0, 53, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1543:11: note: expanded from macro '__Pyx_TraceCall' 1543 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2728:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2728 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1594:19: note: expanded from macro '__Pyx_TraceReturn' 1594 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2728:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2728 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1601:15: note: expanded from macro '__Pyx_TraceReturn' 1601 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2769:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2769 | __Pyx_TraceCall("factorial (wrapper)", __pyx_f[0], 53, 0, __PYX_ERR(0, 53, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1535:15: note: expanded from macro '__Pyx_TraceCall' 1535 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2769:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2769 | __Pyx_TraceCall("factorial (wrapper)", __pyx_f[0], 53, 0, __PYX_ERR(0, 53, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1543:11: note: expanded from macro '__Pyx_TraceCall' 1543 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2784:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2784 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1594:19: note: expanded from macro '__Pyx_TraceReturn' 1594 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2784:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2784 | __Pyx_TraceReturn(__pyx_r, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1601:15: note: expanded from macro '__Pyx_TraceReturn' 1601 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2815:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2815 | __Pyx_TraceCall("poz", __pyx_f[0], 65, 0, __PYX_ERR(0, 65, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1535:15: note: expanded from macro '__Pyx_TraceCall' 1535 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:2815:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 2815 | __Pyx_TraceCall("poz", __pyx_f[0], 65, 0, __PYX_ERR(0, 65, __pyx_L1_error)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1543:11: note: expanded from macro '__Pyx_TraceCall' 1543 | if (__Pyx_IsTracing(tstate, 1, 1)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ MACS2/Prob.c:3038:3: error: no member named 'use_tracing' in 'struct _PyCFrame' 3038 | __Pyx_TraceReturn(Py_None, 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1594:19: note: expanded from macro '__Pyx_TraceReturn' 1594 | if (__Pyx_IsTracing(tstate, 0, 0)) {\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MACS2/Prob.c:1496:34: note: expanded from macro '__Pyx_IsTracing' 1496 | (unlikely((tstate)->cframe->use_tracing) &&\ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ MACS2/Prob.c:981:43: note: expanded from macro 'unlikely' 981 | #define unlikely(x) __builtin_expect(!!(x), 0) | ^ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. error: command '/usr/bin/cc' failed with exit code 1 *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/py-macs2 =>> Cleaning up wrkdir ===> Cleaning for py312-macs2-2.2.9.1_3 build of biology/py-macs2@py312 | py312-macs2-2.2.9.1_3 ended at Wed Jul 8 15:30:16 JST 2026 build time: 00:03:15 !!! build failure encountered !!!