=> Building biology/p5-Bio-Coordinate Started : Thursday, 30 AUG 2018 at 10:55:00 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 -------------------------------------------------- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/p5-Bio-Coordinate XDG_CONFIG_HOME=/construction/biology/p5-Bio-Coordinate HOME=/construction/biology/p5-Bio-Coordinate TMPDIR="/tmp" PATH=/construction/biology/p5-Bio-Coordinate/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- INSTALLDIRS="site" CC="cc" CCFLAGS="-pipe -O2 -fno-strict-aliasing" LD="cc" PREFIX="/usr/local" INSTALLPRIVLIB="/usr/local/lib" INSTALLARCHLIB="/usr/local/lib" -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/p5-Bio-Coordinate XDG_CONFIG_HOME=/construction/biology/p5-Bio-Coordinate HOME=/construction/biology/p5-Bio-Coordinate TMPDIR="/tmp" PATH=/construction/biology/p5-Bio-Coordinate/.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=gcc50 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/p5-Bio-Coordinate/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.2 PERL_VER=5.26 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.26 PROFILE="@comment " DOCSDIR="share/doc/Bio-Coordinate" EXAMPLESDIR="share/examples/Bio-Coordinate" DATADIR="share/Bio-Coordinate" WWWDIR="www/Bio-Coordinate" ETCDIR="etc/Bio-Coordinate" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Bio-Coordinate DOCSDIR=/usr/local/share/doc/Bio-Coordinate EXAMPLESDIR=/usr/local/share/examples/Bio-Coordinate WWWDIR=/usr/local/www/Bio-Coordinate ETCDIR=/usr/local/etc/Bio-Coordinate -------------------------------------------------- -- /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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> p5-Bio-Coordinate-1.007001 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> p5-Bio-Coordinate-1.007001 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-Bio-Coordinate-1.007001 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-Bio-Coordinate-1.007001 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-Bio-Coordinate-1.007001 for building => SHA256 Checksum OK for Bio-Coordinate-1.007001.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-Bio-Coordinate-1.007001 for building ===> Extracting for p5-Bio-Coordinate-1.007001 => SHA256 Checksum OK for Bio-Coordinate-1.007001.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for p5-Bio-Coordinate-1.007001 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> p5-Bio-Coordinate-1.007001 depends on package: p5-BioPerl>=1.007000 - not found ===> Installing existing package /packages/All/p5-BioPerl-1.007002.txz Installing p5-BioPerl-1.007002... `-- Installing p5-Algorithm-Munkres-0.08_1... | `-- Installing perl5-5.26.2... | `-- Extracting perl5-5.26.2: .......... done `-- Extracting p5-Algorithm-Munkres-0.08_1: ... done `-- Installing p5-Array-Compare-3.0.1... | `-- Installing p5-Moo-2.003004... | | `-- Installing p5-Class-Method-Modifiers-2.12... | | `-- Extracting p5-Class-Method-Modifiers-2.12: ....... done | | `-- Installing p5-Devel-GlobalDestruction-0.14... | | `-- Installing p5-Sub-Exporter-Progressive-0.001013... | | | `-- Installing p5-Sub-Exporter-0.987_1... | | | `-- Installing p5-Data-OptList-0.110... | | 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p5-XML-Filter-BufferText-1.01_1... | `-- Extracting p5-XML-Filter-BufferText-1.01_1: ....... done `-- Extracting p5-XML-SAX-Writer-0.57: ......... done `-- Installing p5-XML-Simple-2.25... | `-- Installing p5-XML-SAX-Expat-0.51_1... | `-- Extracting p5-XML-SAX-Expat-0.51_1: ....... done `-- Extracting p5-XML-Simple-2.25: ......... done `-- Installing p5-XML-Writer-0.625_1... `-- Extracting p5-XML-Writer-0.625_1: ...... done `-- Installing p5-YAML-1.24... `-- Extracting p5-YAML-1.24: .......... done Extracting p5-BioPerl-1.007002: .......... done Message from perl5-5.26.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from mysql56-client-5.6.40: * * * * * * * * * * * * * * * * * * * * * * * * Please be aware the database client is vulnerable to CVE-2015-3152 - SSL Downgrade aka "BACKRONYM". You may find more information at the following URL: http://www.vuxml.org/freebsd/36bd352d-299b-11e5-86ff-14dae9d210b8.html Although this database client is not listed as "affected", it is vulnerable and will not be receiving a patch. Please take note of this when deploying this software. * * * * * * * * * * * * * * * * * * * * * * * * Message from freetype2-2.9.1: 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. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from dejavu-2.37: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===> p5-Bio-Coordinate-1.007001 depends on package: p5-BioPerl>=1.007000 - found ===> Returning to build of p5-Bio-Coordinate-1.007001 ===> p5-Bio-Coordinate-1.007001 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for p5-Bio-Coordinate-1.007001 Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Coordinate Writing MYMETA.yml and MYMETA.json -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for p5-Bio-Coordinate-1.007001 --- blib/lib/Bio/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/Bio/Coordinate/.exists --- --- blib/arch/auto/Bio/Coordinate/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- config --- --- subdirs --- --- dynamic --- --- pm_to_blib --- --- blibdirs --- --- config --- --- dynamic --- --- linkext --- --- pm_to_blib --- cp lib/Bio/Coordinate/Result/Gap.pm blib/lib/Bio/Coordinate/Result/Gap.pm cp lib/Bio/Coordinate/ResultI.pm blib/lib/Bio/Coordinate/ResultI.pm cp lib/Bio/Coordinate/MapperI.pm blib/lib/Bio/Coordinate/MapperI.pm cp lib/Bio/Coordinate/Pair.pm blib/lib/Bio/Coordinate/Pair.pm cp lib/Bio/Coordinate/GeneMapper.pm blib/lib/Bio/Coordinate/GeneMapper.pm cp lib/Bio/Coordinate/Graph.pm blib/lib/Bio/Coordinate/Graph.pm cp lib/Bio/Coordinate/Result.pm blib/lib/Bio/Coordinate/Result.pm cp lib/Bio/Coordinate/Utils.pm blib/lib/Bio/Coordinate/Utils.pm cp lib/Bio/Coordinate.pm blib/lib/Bio/Coordinate.pm cp lib/Bio/Coordinate/Collection.pm blib/lib/Bio/Coordinate/Collection.pm cp lib/Bio/Coordinate/Result/Match.pm blib/lib/Bio/Coordinate/Result/Match.pm cp lib/Bio/Coordinate/Chain.pm blib/lib/Bio/Coordinate/Chain.pm cp lib/Bio/Coordinate/ExtrapolatingPair.pm blib/lib/Bio/Coordinate/ExtrapolatingPair.pm --- pure_all --- --- manifypods --- Manifying 13 pod documents --- all --- -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> p5-Bio-Coordinate-1.007001 depends on package: p5-BioPerl>=1.007000 - found ===> p5-Bio-Coordinate-1.007001 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for p5-Bio-Coordinate-1.007001 ===> Generating temporary packing list Manifying 13 pod documents Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Result.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/MapperI.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Chain.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Graph.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Collection.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/GeneMapper.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/ExtrapolatingPair.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Utils.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/ResultI.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Pair.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Result/Gap.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/Bio/Coordinate/Result/Match.pm Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::MapperI.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Result::Gap.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Result::Match.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Result.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Utils.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::ResultI.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Pair.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Graph.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::GeneMapper.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Collection.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::Chain.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate.3 Installing /construction/biology/p5-Bio-Coordinate/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Coordinate::ExtrapolatingPair.3 ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for p5-Bio-Coordinate-1.007001 file sizes/checksums [31]: . done packing files [31]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 10:55:36 UTC Duration: 00:00:35