------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/biology/py-macs2 XDG_CONFIG_HOME=/construction/biology/py-macs2 XDG_CACHE_HOME=/construction/biology/py-macs2/.cache HOME=/construction/biology/py-macs2 TMPDIR="/tmp" PATH=/construction/biology/py-macs2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-macs2/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-macs2 XDG_CONFIG_HOME=/construction/biology/py-macs2 XDG_CACHE_HOME=/construction/biology/py-macs2/.cache HOME=/construction/biology/py-macs2 TMPDIR="/tmp" PATH=/construction/biology/py-macs2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-macs2/.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 CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-macs2/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 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=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/py39-macs2" EXAMPLESDIR="share/examples/py39-macs2" DATADIR="share/py39-macs2" WWWDIR="www/py39-macs2" ETCDIR="etc/py39-macs2" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_9.pkg ===== Message from metis-5.1.0_9: -- ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gmp-6.2.1.pkg Installing /packages/All/mpfr-4.2.0_1,1.pkg Installing /packages/All/mpc-1.3.1_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/liblz4-1.9.4,1.pkg Installing /packages/All/zstd-1.5.5.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/binutils-2.40_4,1.pkg Installing /packages/All/gcc12-12.2.0_6.pkg ===== 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. Installing /packages/All/openblas-0.3.20_1,1.pkg Installing /packages/All/suitesparse-config-7.0.1_1.pkg Installing /packages/All/suitesparse-amd-3.0.3_1.pkg Installing /packages/All/suitesparse-camd-3.0.3_1.pkg Installing /packages/All/suitesparse-colamd-3.0.3_1.pkg Installing /packages/All/suitesparse-ccolamd-3.0.3_1.pkg Installing /packages/All/suitesparse-cholmod-4.0.3_1.pkg Installing /packages/All/suitesparse-umfpack-6.1.0_1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- 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 Installing /packages/All/py39-setuptools-63.1.0_1.pkg Installing /packages/All/py39-numpy-1.24.1_4,1.pkg Installing /packages/All/py39-cython-0.29.35.pkg Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) create symlink for gcc12 create symlink for gcc12 (world) create symlink for g++12 create symlink for g++12 (world) create symlink for cpp12 create symlink for cpp12 (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on file: /usr/local/sbin/pkg - found => taoliu-MACS-v2.2.8_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.8?dummy=/taoliu-MACS-v2.2.8_GH0.tar.gz fetch: https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.8?dummy=/taoliu-MACS-v2.2.8_GH0.tar.gz: size unknown fetch: https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.8?dummy=/taoliu-MACS-v2.2.8_GH0.tar.gz: size of remote file is not known taoliu-MACS-v2.2.8_GH0.tar.gz 0 B 0 Bps taoliu-MACS-v2.2.8_GH0.tar.gz 256 kB 717 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 2688 kB 2392 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 8288 kB 5758 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 13 MB 5106 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 17 MB 4723 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 21 MB 3529 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 24 MB 3838 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 28 MB 3971 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 32 MB 4095 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 36 MB 4188 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 41 MB 4452 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 45 MB 4706 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 50 MB 4752 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 55 MB 5052 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 60 MB 5417 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 64 MB 4368 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 68 MB 3659 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 72 MB 3906 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 76 MB 4101 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 80 MB 4142 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 84 MB 4260 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 89 MB 4526 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 93 MB 4651 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 98 MB 4867 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 103 MB 5105 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 108 MB 5365 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 114 MB 6160 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 121 MB 7337 kBps taoliu-MACS-v2.2.8_GH0.tar.gz 126 MB 4646 kBps 28s ===> Fetching all distfiles required by py39-macs2-2.2.8 for building SUCCEEDED 00:00:28 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-macs2-2.2.8 for building => SHA256 Checksum OK for taoliu-MACS-v2.2.8_GH0.tar.gz. SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-macs2-2.2.8 for building ===> Extracting for py39-macs2-2.2.8 => SHA256 Checksum OK for taoliu-MACS-v2.2.8_GH0.tar.gz. Extracted Memory Use: 297.71M SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-macs2-2.2.8 ===> Applying ports patches for py39-macs2-2.2.8 from /xports/biology/py-macs2/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-macs2-2.2.8 depends on executable: cython-3.9 - found ===> py39-macs2-2.2.8 depends on package: py39-setuptools>=63.1.0 - found ===> py39-macs2-2.2.8 depends on file: /usr/local/bin/python3.9 - found ===> py39-macs2-2.2.8 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-macs2-2.2.8 depends on executable: cython-3.9 - found ===> py39-macs2-2.2.8 depends on package: py39-setuptools>=63.1.0 - found ===> py39-macs2-2.2.8 depends on file: /usr/local/bin/python3.9 - found ===> py39-macs2-2.2.8 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-macs2-2.2.8 running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-macs2-2.2.8 running build running build_py creating build creating build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/Constants.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/OptValidator.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/OutputWriter.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/bdgbroadcall_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/bdgcmp_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/bdgdiff_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/bdgopt_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/bdgpeakcall_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/callpeak_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/cmbreps_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/diffpeak_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/filterdup_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/pileup_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/predictd_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/randsample_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/refinepeak_cmd.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 creating build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO copying MACS2/IO/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO copying MACS2/cPosValCalculation.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 copying MACS2/khash.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2 running build_ext cythoning MACS2/Prob.pyx to MACS2/Prob.c cythoning MACS2/IO/Parser.pyx to MACS2/IO/Parser.c cythoning MACS2/Pileup.pyx to MACS2/Pileup.c cythoning MACS2/PeakModel.pyx to MACS2/PeakModel.c cythoning MACS2/PeakDetect.pyx to MACS2/PeakDetect.c cythoning MACS2/Signal.pyx to MACS2/Signal.c cythoning MACS2/IO/PeakIO.pyx to MACS2/IO/PeakIO.c cythoning MACS2/IO/BedGraphIO.pyx to MACS2/IO/BedGraphIO.c cythoning MACS2/IO/FixWidthTrack.pyx to MACS2/IO/FixWidthTrack.c cythoning MACS2/IO/PairedEndTrack.pyx to MACS2/IO/PairedEndTrack.c cythoning MACS2/IO/BedGraph.pyx to MACS2/IO/BedGraph.c cythoning MACS2/IO/ScoreTrack.pyx to MACS2/IO/ScoreTrack.c cythoning MACS2/IO/CallPeakUnit.pyx to MACS2/IO/CallPeakUnit.c building 'MACS2.Prob' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2 cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/Prob.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/Prob.o -L/usr/local/lib -lm -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Prob.cpython-39.so building 'MACS2.IO.Parser' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/Parser.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/Parser.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/Parser.cpython-39.so building 'MACS2.Pileup' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/Pileup.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/Pileup.o -w -O3 -ffast-math -g0 cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/cPosValCalculation.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/cPosValCalculation.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/Pileup.o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/cPosValCalculation.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Pileup.cpython-39.so building 'MACS2.PeakModel' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakModel.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakModel.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakModel.cpython-39.so building 'MACS2.PeakDetect' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/PeakDetect.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakDetect.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakDetect.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakDetect.cpython-39.so building 'MACS2.Signal' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/Signal.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/Signal.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Signal.cpython-39.so building 'MACS2.IO.PeakIO' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/IO/PeakIO.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PeakIO.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PeakIO.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PeakIO.cpython-39.so building 'MACS2.IO.BedGraphIO' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/IO/BedGraphIO.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraphIO.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraphIO.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraphIO.cpython-39.so building 'MACS2.IO.FixWidthTrack' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/FixWidthTrack.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/FixWidthTrack.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/FixWidthTrack.cpython-39.so building 'MACS2.IO.PairedEndTrack' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PairedEndTrack.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PairedEndTrack.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PairedEndTrack.cpython-39.so building 'MACS2.IO.BedGraph' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c MACS2/IO/BedGraph.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraph.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraph.o -L/usr/local/lib -lm -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraph.cpython-39.so building 'MACS2.IO.ScoreTrack' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -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.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/ScoreTrack.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/ScoreTrack.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/ScoreTrack.cpython-39.so building 'MACS2.IO.CallPeakUnit' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c MACS2/IO/CallPeakUnit.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/CallPeakUnit.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/CallPeakUnit.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/CallPeakUnit.cpython-39.so running build_scripts creating build/scripts-3.9 copying and adjusting bin/macs2 -> build/scripts-3.9 changing mode of build/scripts-3.9/macs2 from 644 to 755 SUCCEEDED 00:03:36 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-macs2-2.2.8 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-macs2-2.2.8 depends on package: py39-setuptools>=63.1.0 - found ===> py39-macs2-2.2.8 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-macs2-2.2.8 ===> py39-macs2-2.2.8 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-macs2-2.2.8 depends on package: py39-setuptools>=63.1.0 - found ===> py39-macs2-2.2.8 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext skipping 'MACS2/Prob.c' Cython extension (up-to-date) skipping 'MACS2/IO/Parser.c' Cython extension (up-to-date) skipping 'MACS2/Pileup.c' Cython extension (up-to-date) skipping 'MACS2/PeakModel.c' Cython extension (up-to-date) skipping 'MACS2/PeakDetect.c' Cython extension (up-to-date) skipping 'MACS2/Signal.c' Cython extension (up-to-date) skipping 'MACS2/IO/PeakIO.c' Cython extension (up-to-date) skipping 'MACS2/IO/BedGraphIO.c' Cython extension (up-to-date) skipping 'MACS2/IO/FixWidthTrack.c' Cython extension (up-to-date) skipping 'MACS2/IO/PairedEndTrack.c' Cython extension (up-to-date) skipping 'MACS2/IO/BedGraph.c' Cython extension (up-to-date) skipping 'MACS2/IO/ScoreTrack.c' Cython extension (up-to-date) skipping 'MACS2/IO/CallPeakUnit.c' Cython extension (up-to-date) running build_scripts running install_lib creating /construction/biology/py-macs2/stage/usr/local/lib/python3.9 creating /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages creating /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakModel.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Pileup.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/PeakDetect.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Signal.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Constants.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/OptValidator.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/OutputWriter.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/__init__.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/bdgbroadcall_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/bdgcmp_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/bdgdiff_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/bdgopt_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/bdgpeakcall_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/callpeak_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/cmbreps_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/diffpeak_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/filterdup_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/pileup_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/predictd_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/randsample_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/refinepeak_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 creating /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PairedEndTrack.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/FixWidthTrack.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/CallPeakUnit.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/ScoreTrack.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/__init__.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/Parser.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraphIO.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/BedGraph.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/IO/PeakIO.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/cPosValCalculation.pxd -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/khash.pxd -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 copying build/lib.dragonfly-6.5-x86_64-cpython-39/MACS2/Prob.cpython-39.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2 byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/Constants.py to Constants.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/OptValidator.py to OptValidator.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/OutputWriter.py to OutputWriter.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/bdgbroadcall_cmd.py to bdgbroadcall_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/bdgcmp_cmd.py to bdgcmp_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/bdgdiff_cmd.py to bdgdiff_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/bdgopt_cmd.py to bdgopt_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/bdgpeakcall_cmd.py to bdgpeakcall_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/callpeak_cmd.py to callpeak_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/cmbreps_cmd.py to cmbreps_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/diffpeak_cmd.py to diffpeak_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/filterdup_cmd.py to filterdup_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/pileup_cmd.py to pileup_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/predictd_cmd.py to predictd_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/randsample_cmd.py to randsample_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/refinepeak_cmd.py to refinepeak_cmd.cpython-39.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/IO/__init__.py to __init__.cpython-39.pyc writing byte-compilation script '/tmp/tmp51xxq2pn.py' /usr/local/bin/python3.9 /tmp/tmp51xxq2pn.py removing /tmp/tmp51xxq2pn.py running install_egg_info running egg_info creating MACS2.egg-info writing MACS2.egg-info/PKG-INFO writing dependency_links to MACS2.egg-info/dependency_links.txt writing requirements to MACS2.egg-info/requires.txt writing top-level names to MACS2.egg-info/top_level.txt writing manifest file 'MACS2.egg-info/SOURCES.txt' reading manifest file 'MACS2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files found matching '.gitignore' warning: no previously-included files found matching '.travis.yml' no previously-included directories found matching '.github' no previously-included directories found matching 'DOCKER' adding license file 'LICENSE' writing manifest file 'MACS2.egg-info/SOURCES.txt' Copying MACS2.egg-info to /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2-2.2.8-py3.9.egg-info running install_scripts copying build/scripts-3.9/macs2 -> /construction/biology/py-macs2/stage/usr/local/bin changing mode of /construction/biology/py-macs2/stage/usr/local/bin/macs2 to 755 writing list of installed files to '/construction/biology/py-macs2/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX Move: bin/macs2 --> bin/macs2-3.9 Link: @bin/macs2 --> bin/macs2-3.9 /usr/bin/strip /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/*.so /construction/biology/py-macs2/stage/usr/local/lib/python3.9/site-packages/MACS2/*/*.so ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-macs2-2.2.8 file sizes/checksums [76]: 0% file sizes/checksums [76]: 100% Service unavailablepacking files [76]: 0% packing files [76]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:04:26