=> Building biology/py-macs2@py37 Started : Friday, 24 JAN 2020 at 03:51:53 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1284.g34ca1-DEVELOPMENT #20: Fri Jan 17 02:50:51 PST 2020 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/construction/biology/py-macs2 XDG_CONFIG_HOME=/construction/biology/py-macs2 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 SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-macs2 XDG_CONFIG_HOME=/construction/biology/py-macs2 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 NO_PIE=yes 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/py-macs2/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=5.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/py37-macs2" EXAMPLESDIR="share/examples/py37-macs2" DATADIR="share/py37-macs2" WWWDIR="www/py37-macs2" ETCDIR="etc/py37-macs2" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py37-macs2 DOCSDIR=/usr/local/share/doc/py37-macs2 EXAMPLESDIR=/usr/local/share/examples/py37-macs2 WWWDIR=/usr/local/www/py37-macs2 ETCDIR=/usr/local/etc/py37-macs2 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> py37-macs2-2.2.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz Installing pkg-1.12.0... Extracting pkg-1.12.0: .......... done ===> py37-macs2-2.2.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py37-macs2-2.2.6 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- => taoliu-MACS-v2.2.6_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.6?dummy=/taoliu-MACS-v2.2.6_GH0.tar.gz fetch: https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.6?dummy=/taoliu-MACS-v2.2.6_GH0.tar.gz: size unknown fetch: https://codeload.github.com/taoliu/MACS/tar.gz/v2.2.6?dummy=/taoliu-MACS-v2.2.6_GH0.tar.gz: size of remote file is not known taoliu-MACS-v2.2.6_GH0.tar.gz 127 MB 9526 kBps 14s ===> Fetching all distfiles required by py37-macs2-2.2.6 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-macs2-2.2.6 for building => SHA256 Checksum OK for taoliu-MACS-v2.2.6_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by py37-macs2-2.2.6 for building ===> Extracting for py37-macs2-2.2.6 => SHA256 Checksum OK for taoliu-MACS-v2.2.6_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for py37-macs2-2.2.6 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> py37-macs2-2.2.6 depends on package: py37-numpy>0 - not found ===> Installing existing package /packages/All/py37-numpy-1.16.5_3,1.txz Installing py37-numpy-1.16.5_3,1... `-- Installing gcc8-8.3.0_3... | `-- Installing binutils-2.33.1_2,1... | | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: . done | | `-- Extracting gettext-runtime-0.20.1: .......... done | `-- Extracting binutils-2.33.1_2,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ...... done `-- Extracting gcc8-8.3.0_3: .......... done `-- Installing openblas-0.3.7,1... `-- Extracting openblas-0.3.7,1: .......... done `-- Installing py37-setuptools-44.0.0... | `-- Installing python37-3.7.6... | | `-- Installing expat-2.2.8... | | `-- Extracting expat-2.2.8: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | | `-- Installing openssl-1.1.1d,1... | | `-- Extracting openssl-1.1.1d,1: .......... done | | `-- Installing readline-8.0.1... | | `-- Extracting readline-8.0.1: .......... done | `-- Extracting python37-3.7.6: .......... done `-- Extracting py37-setuptools-44.0.0: .......... done `-- Installing suitesparse-5.4.0_4... | `-- Installing metis-5.1.0_8... | `-- Extracting metis-5.1.0_8: .......... done | `-- Installing tbb-2020.0... | `-- Extracting tbb-2020.0: .......... done `-- Extracting suitesparse-5.4.0_4: .......... done Extracting py37-numpy-1.16.5_3,1: .......... done ===== Message from gcc8-8.3.0_3: -- 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from python37-3.7.6: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 ===> py37-macs2-2.2.6 depends on package: py37-numpy>0 - found ===> Returning to build of py37-macs2-2.2.6 ===> py37-macs2-2.2.6 depends on executable: cython-3.7 - not found ===> Installing existing package /packages/All/py37-cython-0.29.13_1.txz Installing py37-cython-0.29.13_1... Extracting py37-cython-0.29.13_1: .......... done ===> py37-macs2-2.2.6 depends on executable: cython-3.7 - found ===> Returning to build of py37-macs2-2.2.6 ===> py37-macs2-2.2.6 depends on package: py37-setuptools>0 - found ===> py37-macs2-2.2.6 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for py37-macs2-2.2.6 running config -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for py37-macs2-2.2.6 running build running build_py creating build creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/Constants.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/OptValidator.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/OutputWriter.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/bdgbroadcall_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/bdgcmp_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/bdgdiff_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/bdgopt_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/bdgpeakcall_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/callpeak_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/cmbreps_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/diffpeak_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/filterdup_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/pileup_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/predictd_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/randsample_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/refinepeak_cmd.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 creating build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO copying MACS2/IO/__init__.py -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO copying MACS2/cPosValCalculation.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 copying MACS2/khash.pxd -> build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2 running build_ext skipping 'MACS2/Prob.c' Cython extension (up-to-date) building 'MACS2.Prob' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7 creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/Prob.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Prob.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Prob.o -L/usr/local/lib -lm -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Prob.so skipping 'MACS2/IO/Parser.c' Cython extension (up-to-date) building 'MACS2.IO.Parser' extension creating build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/IO/Parser.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/Parser.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/Parser.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/Parser.so skipping 'MACS2/Pileup.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/Pileup.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/cPosValCalculation.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/cPosValCalculation.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Pileup.o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/cPosValCalculation.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Pileup.so skipping 'MACS2/PeakModel.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/PeakModel.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakModel.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakModel.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakModel.so skipping 'MACS2/PeakDetect.c' Cython extension (up-to-date) 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/python3.7m -c MACS2/PeakDetect.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakDetect.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakDetect.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakDetect.so skipping 'MACS2/Signal.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/Signal.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Signal.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Signal.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Signal.so skipping 'MACS2/IO/PeakIO.c' Cython extension (up-to-date) 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/python3.7m -c MACS2/IO/PeakIO.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PeakIO.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PeakIO.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PeakIO.so skipping 'MACS2/IO/BedGraphIO.c' Cython extension (up-to-date) 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/python3.7m -c MACS2/IO/BedGraphIO.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraphIO.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraphIO.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraphIO.so skipping 'MACS2/IO/FixWidthTrack.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/IO/FixWidthTrack.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/FixWidthTrack.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/FixWidthTrack.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/FixWidthTrack.so skipping 'MACS2/IO/PairedEndTrack.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/IO/PairedEndTrack.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PairedEndTrack.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PairedEndTrack.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PairedEndTrack.so skipping 'MACS2/IO/BedGraph.c' Cython extension (up-to-date) 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/python3.7m -c MACS2/IO/BedGraph.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraph.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraph.o -L/usr/local/lib -lm -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraph.so skipping 'MACS2/IO/ScoreTrack.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/IO/ScoreTrack.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/ScoreTrack.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/ScoreTrack.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/ScoreTrack.so skipping 'MACS2/IO/CallPeakUnit.c' Cython extension (up-to-date) 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/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/IO/CallPeakUnit.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/CallPeakUnit.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/CallPeakUnit.o -L/usr/local/lib -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/CallPeakUnit.so skipping 'MACS2/Statistics.c' Cython extension (up-to-date) building 'MACS2.Statistics' 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 -IMACS2/ -I/usr/local/lib/python3.7/site-packages/numpy/core/include -I/usr/local/include/python3.7m -c MACS2/Statistics.c -o build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Statistics.o -w -O3 -ffast-math -g0 cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Statistics.o -L/usr/local/lib -lm -lpython3.7m -o build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Statistics.so running build_scripts creating build/scripts-3.7 copying and adjusting bin/macs2 -> build/scripts-3.7 changing mode of build/scripts-3.7/macs2 from 644 to 755 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> py37-macs2-2.2.6 depends on package: py37-setuptools>0 - found ===> py37-macs2-2.2.6 depends on file: /usr/local/bin/python3.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for py37-macs2-2.2.6 ===> Generating temporary packing list running install 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) skipping 'MACS2/Statistics.c' Cython extension (up-to-date) running build_scripts running install_lib creating /construction/biology/py-macs2/stage/usr/local/lib/python3.7 creating /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages creating /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakDetect.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Prob.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Signal.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Pileup.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/bdgdiff_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/bdgopt_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 creating /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/ScoreTrack.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/Parser.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PeakIO.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraphIO.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/PairedEndTrack.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/__init__.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/CallPeakUnit.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/BedGraph.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/IO/FixWidthTrack.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/diffpeak_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/bdgbroadcall_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/__init__.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/OptValidator.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/cPosValCalculation.pxd -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/pileup_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/bdgpeakcall_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/callpeak_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/randsample_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/OutputWriter.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/filterdup_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/bdgcmp_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/refinepeak_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/predictd_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/khash.pxd -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Constants.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/cmbreps_cmd.py -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/Statistics.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 copying build/lib.dragonfly-5.7-SYNTH-x86_64-3.7/MACS2/PeakModel.so -> /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2 byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/bdgdiff_cmd.py to bdgdiff_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/bdgopt_cmd.py to bdgopt_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/IO/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/diffpeak_cmd.py to diffpeak_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/bdgbroadcall_cmd.py to bdgbroadcall_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/__init__.py to __init__.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/OptValidator.py to OptValidator.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/pileup_cmd.py to pileup_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/bdgpeakcall_cmd.py to bdgpeakcall_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/callpeak_cmd.py to callpeak_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/randsample_cmd.py to randsample_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/OutputWriter.py to OutputWriter.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/filterdup_cmd.py to filterdup_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/bdgcmp_cmd.py to bdgcmp_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/refinepeak_cmd.py to refinepeak_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/predictd_cmd.py to predictd_cmd.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/Constants.py to Constants.cpython-37.pyc byte-compiling /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/cmbreps_cmd.py to cmbreps_cmd.cpython-37.pyc writing byte-compilation script '/tmp/tmp6ggamu5h.py' /usr/local/bin/python3.7 /tmp/tmp6ggamu5h.py removing /tmp/tmp6ggamu5h.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' writing manifest file 'MACS2.egg-info/SOURCES.txt' Copying MACS2.egg-info to /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2-2.2.6-py3.7.egg-info running install_scripts copying build/scripts-3.7/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/macs2-3.7 Link: @bin/macs2 --> bin/macs2-3.7 /usr/bin/strip /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/*.so /construction/biology/py-macs2/stage/usr/local/lib/python3.7/site-packages/MACS2/*/*.so ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.7/site-packages/MACS2/IO/BedGraph.so is linked to /usr/local/lib/libintl.so.8 from devel/gettext-runtime but it is not declared as a dependency Warning: you need USES+=gettext-runtime Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for py37-macs2-2.2.6 file sizes/checksums [77]: . done packing files [77]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 24 JAN 2020 at 03:58:16 UTC Duration: 00:06:23