=> Building biology/p5-Bio-GFF3 Started : Thursday, 30 AUG 2018 at 13:04:22 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-GFF3 XDG_CONFIG_HOME=/construction/biology/p5-Bio-GFF3 HOME=/construction/biology/p5-Bio-GFF3 TMPDIR="/tmp" PATH=/construction/biology/p5-Bio-GFF3/.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-GFF3 XDG_CONFIG_HOME=/construction/biology/p5-Bio-GFF3 HOME=/construction/biology/p5-Bio-GFF3 TMPDIR="/tmp" PATH=/construction/biology/p5-Bio-GFF3/.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-GFF3/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-GFF3" EXAMPLESDIR="share/examples/Bio-GFF3" DATADIR="share/Bio-GFF3" WWWDIR="www/Bio-GFF3" ETCDIR="etc/Bio-GFF3" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Bio-GFF3 DOCSDIR=/usr/local/share/doc/Bio-GFF3 EXAMPLESDIR=/usr/local/share/examples/Bio-GFF3 WWWDIR=/usr/local/www/Bio-GFF3 ETCDIR=/usr/local/etc/Bio-GFF3 -------------------------------------------------- -- /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-GFF3-2.0_2 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-GFF3-2.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-Bio-GFF3-2.0_2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-Bio-GFF3-2.0_2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-Bio-GFF3-2.0_2 for building => SHA256 Checksum OK for Bio-GFF3-2.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-Bio-GFF3-2.0_2 for building ===> Extracting for p5-Bio-GFF3-2.0_2 => SHA256 Checksum OK for Bio-GFF3-2.0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for p5-Bio-GFF3-2.0_2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> p5-Bio-GFF3-2.0_2 depends on package: p5-File-ReadBackwards>=0 - not found ===> Installing existing package /packages/All/p5-File-ReadBackwards-1.05_1.txz Installing p5-File-ReadBackwards-1.05_1... `-- Installing perl5-5.26.2... `-- Extracting perl5-5.26.2: .......... done Extracting p5-File-ReadBackwards-1.05_1: ....... 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. ===> p5-Bio-GFF3-2.0_2 depends on package: p5-File-ReadBackwards>=0 - found ===> Returning to build of p5-Bio-GFF3-2.0_2 ===> p5-Bio-GFF3-2.0_2 depends on package: p5-List-MoreUtils>=0 - not found ===> Installing existing package /packages/All/p5-List-MoreUtils-0.428.txz Installing p5-List-MoreUtils-0.428... `-- Installing p5-Exporter-Tiny-1.000000... `-- Extracting p5-Exporter-Tiny-1.000000: .......... done `-- Installing p5-List-MoreUtils-XS-0.428... `-- Extracting p5-List-MoreUtils-XS-0.428: ....... done Extracting p5-List-MoreUtils-0.428: .......... done ===> p5-Bio-GFF3-2.0_2 depends on package: p5-List-MoreUtils>=0 - found ===> Returning to build of p5-Bio-GFF3-2.0_2 ===> p5-Bio-GFF3-2.0_2 depends on package: p5-URI>=0 - not found ===> Installing existing package /packages/All/p5-URI-1.74.txz Installing p5-URI-1.74... Extracting p5-URI-1.74: .......... done ===> p5-Bio-GFF3-2.0_2 depends on package: p5-URI>=0 - found ===> Returning to build of p5-Bio-GFF3-2.0_2 ===> p5-Bio-GFF3-2.0_2 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for p5-Bio-GFF3-2.0_2 Warning: prerequisite IO::String 0 not found. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::GFF3 Writing MYMETA.yml and MYMETA.json -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for p5-Bio-GFF3-2.0_2 --- blib/lib/Bio/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/Bio/GFF3/.exists --- --- blib/arch/auto/Bio/GFF3/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- config --- --- subdirs --- --- dynamic --- --- pm_to_blib --- --- blib/script/gff3_from_fasta --- cp bin/gff3_from_fasta blib/script/gff3_from_fasta "/usr/local/bin/perl5.26.2" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/gff3_from_fasta --- blibdirs --- --- config --- --- dynamic --- --- linkext --- --- pm_to_blib --- cp lib/Bio/GFF3/LowLevel/Parser.pm blib/lib/Bio/GFF3/LowLevel/Parser.pm cp lib/Bio/GFF3/LowLevel.pm blib/lib/Bio/GFF3/LowLevel.pm cp lib/Bio/GFF3/LowLevel/Parser/1_0_backcompat.pm blib/lib/Bio/GFF3/LowLevel/Parser/1_0_backcompat.pm cp lib/Bio/GFF3/Transform/FromFasta.pm blib/lib/Bio/GFF3/Transform/FromFasta.pm cp lib/Bio/GFF3/Transform/SyncDirectives.pm blib/lib/Bio/GFF3/Transform/SyncDirectives.pm --- pure_all --- --- pure_all --- --- manifypods --- Manifying 1 pod document Manifying 5 pod documents --- all --- -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> p5-Bio-GFF3-2.0_2 depends on package: p5-File-ReadBackwards>=0 - found ===> p5-Bio-GFF3-2.0_2 depends on package: p5-List-MoreUtils>=0 - found ===> p5-Bio-GFF3-2.0_2 depends on package: p5-URI>=0 - found ===> p5-Bio-GFF3-2.0_2 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for p5-Bio-GFF3-2.0_2 ===> Generating temporary packing list Manifying 1 pod document Manifying 5 pod documents Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/Bio/GFF3/LowLevel.pm Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/Bio/GFF3/Transform/FromFasta.pm Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/Bio/GFF3/Transform/SyncDirectives.pm Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/Bio/GFF3/LowLevel/Parser.pm Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/Bio/GFF3/LowLevel/Parser/1_0_backcompat.pm Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/man/man1/gff3_from_fasta.1 Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::GFF3::LowLevel.3 Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::GFF3::LowLevel::Parser::1_0_backcompat.3 Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::GFF3::Transform::FromFasta.3 Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::GFF3::LowLevel::Parser.3 Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::GFF3::Transform::SyncDirectives.3 Installing /construction/biology/p5-Bio-GFF3/stage/usr/local/bin/gff3_from_fasta ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for p5-Bio-GFF3-2.0_2 file sizes/checksums [17]: . done packing files [17]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:04:35 UTC Duration: 00:00:12