------------------------------------------------------------------------------- -- 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 ------------------------------------------------------------------------------- ===> The following configuration options are available for py39-pyteomics-4.6: DF=on: DataFrame support GRAPHICS=on: Graphics support TDA=on: Target-decoy approach support UNIMOD=on: Unimod database support XML=on: XML support ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/science/py-pyteomics XDG_CONFIG_HOME=/construction/science/py-pyteomics XDG_CACHE_HOME=/construction/science/py-pyteomics/.cache HOME=/construction/science/py-pyteomics TMPDIR="/tmp" PATH=/construction/science/py-pyteomics/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-pyteomics/.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/science/py-pyteomics XDG_CONFIG_HOME=/construction/science/py-pyteomics XDG_CACHE_HOME=/construction/science/py-pyteomics/.cache HOME=/construction/science/py-pyteomics TMPDIR="/tmp" PATH=/construction/science/py-pyteomics/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/science/py-pyteomics/.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/science/py-pyteomics/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-pyteomics" EXAMPLESDIR="share/examples/py39-pyteomics" DATADIR="share/py39-pyteomics" WWWDIR="www/py39-pyteomics" ETCDIR="etc/py39-pyteomics" 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-pyteomics DOCSDIR=/usr/local/share/doc/py39-pyteomics EXAMPLESDIR=/usr/local/share/examples/py39-pyteomics WWWDIR=/usr/local/www/py39-pyteomics ETCDIR=/usr/local/etc/py39-pyteomics 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/indexinfo-0.3.1.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/gettext-runtime-0.21.1.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/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) ===== 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. Installing /packages/All/py39-cython-0.29.35.pkg 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/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/binutils-2.40_4,1.pkg Installing /packages/All/gcc12-12.2.0_6.pkg 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 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/py39-numpy-1.24.1_4,1.pkg Installing /packages/All/py39-six-1.16.0.pkg Installing /packages/All/py39-dateutil-2.8.2.pkg Installing /packages/All/py39-pytz-2023.3,1.pkg UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default Installing /packages/All/libedit-3.1.20221030,1.pkg Installing /packages/All/sqlite3-3.42.0,1.pkg Installing /packages/All/py39-sqlite3-3.9.17_7.pkg Installing /packages/All/py39-tzdata-2023.3_1.pkg Installing /packages/All/py39-bottleneck-1.3.7_1.pkg Installing /packages/All/py39-numexpr-2.8.4_1.pkg Installing /packages/All/py39-pandas-2.0.2,1.pkg ===== Message from py39-pandas-2.0.2,1: -- Install math/py-statsmodels to enable parts of pandas.stats. Install devel/py-xarray to enable the to_xarray() function. Installing /packages/All/brotli-1.0.9,1.pkg Installing /packages/All/png-1.6.39.pkg Installing /packages/All/freetype2-2.12.1_2.pkg ===== Message from freetype2-2.12.1_2: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). Installing /packages/All/qhull-8.0.2_1,1.pkg Installing /packages/All/fontconfig-2.14.2,1.pkg Running fc-cache to build fontconfig cache... Installing /packages/All/py39-contourpy-1.0.7_1.pkg Installing /packages/All/py39-cycler-0.11.0.pkg Installing /packages/All/py39-zipp-3.15.0.pkg Installing /packages/All/py39-importlib-resources-5.4.0_1.pkg Installing /packages/All/py39-pyparsing-3.0.9_2.pkg Installing /packages/All/py39-tornado-6.3.2.pkg Installing /packages/All/py39-pluggy-1.0.0_1.pkg Installing /packages/All/libimagequant-4.2.0_1.pkg Installing /packages/All/libdeflate-1.18.pkg Installing /packages/All/jbigkit-2.1_1.pkg Installing /packages/All/jpeg-turbo-2.1.5.1.pkg Installing /packages/All/tiff-4.4.0_1.pkg Installing /packages/All/lcms2-2.15_1.pkg Installing /packages/All/openjpeg-2.5.0.pkg Installing /packages/All/fribidi-1.0.13.pkg Installing /packages/All/graphite2-1.3.14.pkg Installing /packages/All/pcre2-10.42.pkg Installing /packages/All/libxml2-2.10.4.pkg Installing /packages/All/libiconv-1.17.pkg Installing /packages/All/glib-2.76.4,2.pkg Generating GIO modules cache Compiling glib schemas No schema files found: doing nothing. Installing /packages/All/harfbuzz-7.3.0.pkg Installing /packages/All/libraqm-0.10.1.pkg Installing /packages/All/giflib-5.2.1.pkg Installing /packages/All/webp-1.3.0_1.pkg Installing /packages/All/tcl86-8.6.13.pkg Installing /packages/All/libXau-1.0.9.pkg Installing /packages/All/xorgproto-2022.1_1.pkg Installing /packages/All/libXdmcp-1.1.3.pkg Installing /packages/All/libxcb-1.15_1.pkg Installing /packages/All/libX11-1.8.6,1.pkg Installing /packages/All/libXext-1.3.4,1.pkg Installing /packages/All/libXrender-0.9.10_2.pkg Installing /packages/All/libXft-2.3.7.pkg Installing /packages/All/libXScrnSaver-1.2.4.pkg Installing /packages/All/tk86-8.6.13.pkg Installing /packages/All/py39-olefile-0.46.pkg Installing /packages/All/py39-tkinter-3.9.17_6.pkg Installing /packages/All/py39-pillow-9.5.0.pkg Installing /packages/All/py39-certifi-2023.5.7.pkg Installing /packages/All/py39-kiwisolver-1.4.4_1,1.pkg Installing /packages/All/libgpg-error-1.47.pkg Installing /packages/All/libgcrypt-1.10.2.pkg Installing /packages/All/libxslt-1.1.37.pkg Installing /packages/All/py39-lxml-4.9.2.pkg Installing /packages/All/py39-appdirs-1.4.4.pkg Installing /packages/All/py39-fs2-2.4.16.pkg Installing /packages/All/py39-unicodedata2-15.0.0.pkg Installing /packages/All/py39-fonttools-4.39.4_1.pkg Installing /packages/All/py39-packaging-23.1.pkg Installing /packages/All/py39-matplotlib-3.7.1_3.pkg Installing /packages/All/py39-greenlet-2.0.2_1.pkg Installing /packages/All/py39-sqlalchemy14-1.4.48.pkg UNFLAVORED devel/binutils -> use devel/binutils@native UNFLAVORED databases/sqlite3 -> use databases/sqlite3@default SUCCEEDED 00:00:19 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on file: /usr/local/sbin/pkg - found => pyteomics-4.6.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://files.pythonhosted.org/packages/source/p/pyteomics/pyteomics-4.6.tar.gz pyteomics-4.6.tar.gz 0% of 203 kB 0 Bps pyteomics-4.6.tar.gz 203 kB 29 MBps 00s ===> Fetching all distfiles required by py39-pyteomics-4.6 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pyteomics-4.6 for building => SHA256 Checksum OK for pyteomics-4.6.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pyteomics-4.6 for building ===> Extracting for py39-pyteomics-4.6 => SHA256 Checksum OK for pyteomics-4.6.tar.gz. Extracted Memory Use: 0.99M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-pyteomics-4.6 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pyteomics-4.6 depends on file: /usr/local/bin/python3.9 - found ===> py39-pyteomics-4.6 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pyteomics-4.6 depends on file: /usr/local/bin/python3.9 - found ===> py39-pyteomics-4.6 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-pyteomics-4.6 /usr/local/lib/python3.9/site-packages/setuptools/dist.py:286: SetuptoolsDeprecationWarning: The namespace_packages parameter is deprecated, consider using implicit namespaces instead (PEP 420). warnings.warn(msg, SetuptoolsDeprecationWarning) running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-pyteomics-4.6 /usr/local/lib/python3.9/site-packages/setuptools/dist.py:286: SetuptoolsDeprecationWarning: The namespace_packages parameter is deprecated, consider using implicit namespaces instead (PEP 420). warnings.warn(msg, SetuptoolsDeprecationWarning) running build running build_py creating build creating build/lib creating build/lib/pyteomics copying pyteomics/__init__.py -> build/lib/pyteomics copying pyteomics/_schema_defaults.py -> build/lib/pyteomics copying pyteomics/achrom.py -> build/lib/pyteomics copying pyteomics/electrochem.py -> build/lib/pyteomics copying pyteomics/fasta.py -> build/lib/pyteomics copying pyteomics/mgf.py -> build/lib/pyteomics copying pyteomics/ms1.py -> build/lib/pyteomics copying pyteomics/ms2.py -> build/lib/pyteomics copying pyteomics/mzid.py -> build/lib/pyteomics copying pyteomics/mzml.py -> build/lib/pyteomics copying pyteomics/mzmlb.py -> build/lib/pyteomics copying pyteomics/mztab.py -> build/lib/pyteomics copying pyteomics/mzxml.py -> build/lib/pyteomics copying pyteomics/parser.py -> build/lib/pyteomics copying pyteomics/peff.py -> build/lib/pyteomics copying pyteomics/pepxml.py -> build/lib/pyteomics copying pyteomics/proforma.py -> build/lib/pyteomics copying pyteomics/protxml.py -> build/lib/pyteomics copying pyteomics/pylab_aux.py -> build/lib/pyteomics copying pyteomics/tandem.py -> build/lib/pyteomics copying pyteomics/traml.py -> build/lib/pyteomics copying pyteomics/usi.py -> build/lib/pyteomics copying pyteomics/version.py -> build/lib/pyteomics copying pyteomics/xml.py -> build/lib/pyteomics creating build/lib/pyteomics/mass copying pyteomics/mass/__init__.py -> build/lib/pyteomics/mass copying pyteomics/mass/mass.py -> build/lib/pyteomics/mass copying pyteomics/mass/unimod.py -> build/lib/pyteomics/mass creating build/lib/pyteomics/openms copying pyteomics/openms/__init__.py -> build/lib/pyteomics/openms copying pyteomics/openms/featurexml.py -> build/lib/pyteomics/openms copying pyteomics/openms/idxml.py -> build/lib/pyteomics/openms copying pyteomics/openms/trafoxml.py -> build/lib/pyteomics/openms creating build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/__init__.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/constants.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/file_helpers.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/math.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/patch.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/structures.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/target_decoy.py -> build/lib/pyteomics/auxiliary copying pyteomics/auxiliary/utils.py -> build/lib/pyteomics/auxiliary SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-pyteomics-4.6 depends on package: py39-pandas>=0,1 - found ===> py39-pyteomics-4.6 depends on package: py39-matplotlib>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-numpy>=0,1 - found ===> py39-pyteomics-4.6 depends on package: py39-lxml>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-sqlalchemy14>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-lxml>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-numpy>=0,1 - found ===> py39-pyteomics-4.6 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pyteomics-4.6 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-pyteomics-4.6 ===> py39-pyteomics-4.6 depends on package: py39-pandas>=0,1 - found ===> py39-pyteomics-4.6 depends on package: py39-matplotlib>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-numpy>=0,1 - found ===> py39-pyteomics-4.6 depends on package: py39-lxml>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-sqlalchemy14>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-lxml>=0 - found ===> py39-pyteomics-4.6 depends on package: py39-numpy>=0,1 - found ===> py39-pyteomics-4.6 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pyteomics-4.6 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list /usr/local/lib/python3.9/site-packages/setuptools/dist.py:286: SetuptoolsDeprecationWarning: The namespace_packages parameter is deprecated, consider using implicit namespaces instead (PEP 420). warnings.warn(msg, SetuptoolsDeprecationWarning) 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 install_lib Skipping installation of /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/__init__.py (namespace package) copying pyteomics/_schema_defaults.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/achrom.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/electrochem.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/fasta.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mgf.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/ms1.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/ms2.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mzid.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mzml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mzmlb.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mztab.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mzxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/parser.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/peff.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/pepxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/proforma.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/protxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/pylab_aux.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/tandem.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/traml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/usi.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/version.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/xml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics copying pyteomics/mass/__init__.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mass copying pyteomics/mass/mass.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mass copying pyteomics/mass/unimod.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mass copying pyteomics/openms/__init__.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms copying pyteomics/openms/featurexml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms copying pyteomics/openms/idxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms copying pyteomics/openms/trafoxml.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms copying pyteomics/auxiliary/__init__.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/constants.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/file_helpers.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/math.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/patch.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/structures.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/target_decoy.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary copying pyteomics/auxiliary/utils.py -> /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/_schema_defaults.py to _schema_defaults.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/achrom.py to achrom.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/electrochem.py to electrochem.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/fasta.py to fasta.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mgf.py to mgf.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/ms1.py to ms1.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/ms2.py to ms2.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mzid.py to mzid.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mzml.py to mzml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mzmlb.py to mzmlb.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mztab.py to mztab.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mzxml.py to mzxml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/parser.py to parser.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/peff.py to peff.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/pepxml.py to pepxml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/proforma.py to proforma.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/protxml.py to protxml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/pylab_aux.py to pylab_aux.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/tandem.py to tandem.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/traml.py to traml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/usi.py to usi.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/version.py to version.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/xml.py to xml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mass/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mass/mass.py to mass.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/mass/unimod.py to unimod.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms/featurexml.py to featurexml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms/idxml.py to idxml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/openms/trafoxml.py to trafoxml.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/constants.py to constants.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/file_helpers.py to file_helpers.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/math.py to math.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/patch.py to patch.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/structures.py to structures.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/target_decoy.py to target_decoy.cpython-39.pyc byte-compiling /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics/auxiliary/utils.py to utils.cpython-39.pyc writing byte-compilation script '/tmp/tmpojatysmh.py' /usr/local/bin/python3.9 /tmp/tmpojatysmh.py removing /tmp/tmpojatysmh.py running install_egg_info running egg_info writing pyteomics.egg-info/PKG-INFO writing dependency_links to pyteomics.egg-info/dependency_links.txt writing namespace_packages to pyteomics.egg-info/namespace_packages.txt writing requirements to pyteomics.egg-info/requires.txt writing top-level names to pyteomics.egg-info/top_level.txt reading manifest file 'pyteomics.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' adding license file 'NOTICE' adding license file 'AUTHORS' writing manifest file 'pyteomics.egg-info/SOURCES.txt' Copying pyteomics.egg-info to /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics-4.6-py3.9.egg-info Installing /construction/science/py-pyteomics/stage/usr/local/lib/python3.9/site-packages/pyteomics-4.6-py3.9-nspkg.pth running install_scripts writing list of installed files to '/construction/science/py-pyteomics/.PLIST.pymodtmp' ===> Creating unique files: Move MAN files needing SUFFIX ===> Creating unique files: Move files needing SUFFIX ====> 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 00:00:03 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-pyteomics-4.6 file sizes/checksums [122]: 0% file sizes/checksums [122]: 81% file sizes/checksums [122]: 100% Service unavailablepacking files [122]: 0% packing files [122]: 81% packing files [122]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:26