=> Building biology/p5-BioPerl-Run Started : Friday, 20 JUL 2018 at 23:27:25 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.242.g757c0-DEVELOPMENT #30: Tue May 8 14:06:27 PDT 2018 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-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 -------------------------------------------------- ===> The following configuration options are available for p5-BioPerl-Run-1.007002: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- 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-BioPerl-Run XDG_CONFIG_HOME=/construction/biology/p5-BioPerl-Run HOME=/construction/biology/p5-BioPerl-Run TMPDIR="/tmp" PATH=/construction/biology/p5-BioPerl-Run/.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 -------------------------------------------------- --install_path lib="/usr/local/lib/perl5/site_perl" --install_path arch="/usr/local/lib/perl5/site_perl/mach/5.26" --install_path script="/usr/local/bin" --install_path bin="/usr/local/bin" --install_path libdoc="/usr/local/lib/perl5/site_perl/man/man3" --install_path bindoc="/usr/local/lib/perl5/site_perl/man/man1" --destdir /construction/biology/p5-BioPerl-Run/stage --perl="/usr/local/bin/perl" --create_packlist 1 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-BioPerl-Run XDG_CONFIG_HOME=/construction/biology/p5-BioPerl-Run HOME=/construction/biology/p5-BioPerl-Run TMPDIR="/tmp" PATH=/construction/biology/p5-BioPerl-Run/.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-BioPerl-Run/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.2 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/BioPerl-Run" EXAMPLESDIR="share/examples/BioPerl-Run" DATADIR="share/BioPerl-Run" WWWDIR="www/BioPerl-Run" ETCDIR="etc/BioPerl-Run" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/BioPerl-Run DOCSDIR=/usr/local/share/doc/BioPerl-Run EXAMPLESDIR=/usr/local/share/examples/BioPerl-Run WWWDIR=/usr/local/www/BioPerl-Run ETCDIR=/usr/local/etc/BioPerl-Run -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.2 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=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-Run-1.007002 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-BioPerl-Run-1.007002 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-BioPerl-Run-1.007002 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-Run-1.007002 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-Run-1.007002 for building => SHA256 Checksum OK for BioPerl-Run-1.007002.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-Run-1.007002 for building ===> Extracting for p5-BioPerl-Run-1.007002 => SHA256 Checksum OK for BioPerl-Run-1.007002.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for p5-BioPerl-Run-1.007002 ===> Applying ports patches for p5-BioPerl-Run-1.007002 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-Run-1.007002 depends on package: p5-Algorithm-Diff>=0 - not found ===> Installing existing package /packages/All/p5-Algorithm-Diff-1.1903.txz Installing p5-Algorithm-Diff-1.1903... `-- Installing perl5-5.26.2... `-- Extracting perl5-5.26.2: .......... done Extracting p5-Algorithm-Diff-1.1903: .......... 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-BioPerl-Run-1.007002 depends on package: p5-Algorithm-Diff>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007002 ===> p5-BioPerl-Run-1.007002 depends on package: p5-Bio-FeatureIO>=0 - not found ===> Installing existing package /packages/All/p5-Bio-FeatureIO-1.6.905.txz Installing p5-Bio-FeatureIO-1.6.905... `-- Installing p5-BioPerl-1.007002... | `-- Installing p5-Algorithm-Munkres-0.08_1... | `-- 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... | | | | `-- Installing p5-Params-Util-1.07_2... | | | | `-- Extracting p5-Params-Util-1.07_2: ........ done | | | | `-- Installing p5-Sub-Install-0.928_1... | | | | `-- Extracting p5-Sub-Install-0.928_1: ....... done | | | | `-- Extracting p5-Data-OptList-0.110: ....... done | | | `-- Extracting p5-Sub-Exporter-0.987_1: .......... done | | | `-- Extracting p5-Sub-Exporter-Progressive-0.001013: ....... done | | `-- Extracting p5-Devel-GlobalDestruction-0.14: ....... done | | `-- Installing p5-Module-Runtime-0.016... | | `-- Extracting p5-Module-Runtime-0.016: ....... done | | `-- Installing p5-Role-Tiny-2.000006... | | `-- Extracting p5-Role-Tiny-2.000006: ......... done | | `-- Installing p5-Sub-Quote-2.005001... | | `-- Extracting p5-Sub-Quote-2.005001: ......... done | | `-- Extracting p5-Moo-2.003004: .......... done | | `-- Installing p5-Type-Tiny-1.002002... | | `-- Installing p5-Devel-StackTrace-2.03... | | `-- Extracting p5-Devel-StackTrace-2.03: ........ done | | `-- Installing p5-Exporter-Tiny-1.000000... | | `-- Extracting p5-Exporter-Tiny-1.000000: .......... done | | `-- Installing p5-Ref-Util-XS-0.117... | | `-- Extracting p5-Ref-Util-XS-0.117: ....... done | | `-- Installing p5-Type-Tie-0.011... | | | `-- Installing p5-Hash-FieldHash-0.15... | | | `-- Extracting p5-Hash-FieldHash-0.15: ........ done | | `-- Extracting p5-Type-Tie-0.011: ......... done | | `-- Installing p5-Type-Tiny-XS-0.014... | | `-- Extracting p5-Type-Tiny-XS-0.014: .......... done | | `-- Extracting p5-Type-Tiny-1.002002: .......... done | `-- Extracting p5-Array-Compare-3.0.1: ....... done | `-- Installing p5-CGI-4.38... | | `-- Installing p5-HTML-Parser-3.72... | | `-- Installing p5-HTML-Tagset-3.20_1... | | `-- Extracting p5-HTML-Tagset-3.20_1: ....... done | | `-- Extracting p5-HTML-Parser-3.72: .......... done | `-- Extracting p5-CGI-4.38: .......... done | `-- Installing p5-Clone-0.39... | `-- Extracting p5-Clone-0.39: ......... done | `-- Installing p5-Convert-Binary-C-0.78... | `-- Extracting p5-Convert-Binary-C-0.78: .......... done | `-- Installing p5-DBD-mysql-4.046... | | `-- Installing mysql56-client-5.6.40... | | `-- Installing libedit-3.1.20170329_2,1... | | | `-- Installing ncurses-6.0.0s20171223_1... | | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting libedit-3.1.20170329_2,1: .......... done | | `-- Installing libevent-2.1.8_1... | | | `-- Installing libressl-2.7.4... | | | `-- Extracting libressl-2.7.4: .......... done | | `-- Extracting libevent-2.1.8_1: .......... done | | `-- Installing liblz4-1.8.2,1... | | `-- Extracting liblz4-1.8.2,1: .......... done | | `-- Extracting mysql56-client-5.6.40: .......... done | | `-- Installing p5-DBI-1.641... | | `-- Extracting p5-DBI-1.641: .......... done | `-- Extracting p5-DBD-mysql-4.046: .......... done | `-- Installing p5-Data-Stag-0.14_2... | | `-- Installing p5-IO-String-1.08_1... | | `-- Extracting p5-IO-String-1.08_1: ....... done | `-- Extracting p5-Data-Stag-0.14_2: .......... done | `-- Installing p5-Error-0.17026... | `-- Extracting p5-Error-0.17026: ......... done | `-- Installing p5-GD-2.68... | | `-- Installing libgd-2.2.4_1,1... | | `-- Installing fontconfig-2.12.6,1... | | | `-- Installing expat-2.2.5... | | | `-- Extracting expat-2.2.5: .......... done | | | `-- Installing freetype2-2.9.1... | | | `-- Extracting freetype2-2.9.1: .......... done | | `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | | `-- Installing jpeg-turbo-1.5.3... | | `-- Extracting jpeg-turbo-1.5.3: .......... done | | `-- Installing png-1.6.34... | | `-- Extracting png-1.6.34: .......... done | | `-- Installing tiff-4.0.9_1... | | | `-- Installing jbigkit-2.1_1... | | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Extracting tiff-4.0.9_1: .......... done | | `-- Installing webp-1.0.0... | | | `-- Installing giflib-5.1.4... | | | `-- Extracting giflib-5.1.4: .......... done | | `-- Extracting webp-1.0.0: .......... done | | `-- Extracting libgd-2.2.4_1,1: .......... done | | `-- Installing p5-ExtUtils-PkgConfig-1.16... | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Extracting p5-ExtUtils-PkgConfig-1.16: ...... done | `-- Extracting p5-GD-2.68: .......... done | `-- Installing p5-Graph-0.9704,1... | | `-- Installing p5-Heap-0.80_1... | | `-- Extracting p5-Heap-0.80_1: .......... done | `-- Extracting p5-Graph-0.9704,1: .......... done | `-- Installing p5-GraphViz-2.24... | | `-- Installing graphviz-2.40.1_5... | | `-- Installing cairo-1.14.8_1,2... | | | `-- Installing dri2proto-2.8... | | | `-- Extracting dri2proto-2.8: .... done | | | `-- Installing gettext-runtime-0.19.8.1_1... | | | `-- Installing indexinfo-0.3.1... | | | `-- Extracting indexinfo-0.3.1: .... done | | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | | `-- Installing glib-2.50.3_4,1... | | | `-- Installing libffi-3.2.1_2... | | | `-- Extracting libffi-3.2.1_2: .......... done | | | `-- Installing libiconv-1.14_11... | | | `-- Extracting libiconv-1.14_11: .......... done | | | `-- Installing pcre-8.42... | | | `-- Extracting pcre-8.42: .......... done | | | `-- Installing python27-2.7.15... | | | | `-- Installing readline-7.0.3_1... | | | | `-- Extracting readline-7.0.3_1: .......... done | | | `-- Extracting python27-2.7.15: .......... done | | | `-- Extracting glib-2.50.3_4,1: .......... done No schema files found: doing nothing. | | | `-- Installing glproto-1.4.17... | | | `-- Extracting glproto-1.4.17: ...... done | | | `-- Installing libX11-1.6.5,1... | | | `-- Installing kbproto-1.0.7... | | | `-- Extracting kbproto-1.0.7: .......... done | | | `-- Installing libXau-1.0.8_3... | | | | `-- Installing xproto-7.0.31... | | | | `-- Extracting xproto-7.0.31: .......... done | | | `-- Extracting libXau-1.0.8_3: .......... done | | | `-- Installing libXdmcp-1.1.2... | | | `-- Extracting libXdmcp-1.1.2: ......... done | | | `-- Installing libxcb-1.13... | | | | `-- Installing libpthread-stubs-0.4... | | | | `-- Extracting libpthread-stubs-0.4: .... done | | | | `-- Installing libxml2-2.9.7... | | | | `-- Extracting libxml2-2.9.7: .......... done | | | `-- Extracting libxcb-1.13: .......... done | | | `-- Extracting libX11-1.6.5,1: .......... done | | | `-- Installing libXext-1.3.3_1,1... | | | `-- Installing xextproto-7.3.0... | | | `-- Extracting xextproto-7.3.0: .......... done | | | `-- Extracting libXext-1.3.3_1,1: .......... done | | | `-- Installing libXrender-0.9.10... | | | `-- Installing renderproto-0.11.1... | | | `-- Extracting renderproto-0.11.1: .... done | | | `-- Extracting libXrender-0.9.10: .......... done | | | `-- Installing mesa-libs-18.1.2... | | | `-- Installing libXdamage-1.1.4_3... | | | | `-- Installing damageproto-1.2.1... | | | | `-- Extracting damageproto-1.2.1: .... done | | | | `-- Installing libXfixes-5.0.3... | | | | `-- Installing fixesproto-5.0... | | | | `-- Extracting fixesproto-5.0: .... done | | | | `-- Extracting libXfixes-5.0.3: .......... done | | | `-- Extracting libXdamage-1.1.4_3: ...... done | | | `-- Installing libXxf86vm-1.1.4_1... | | | | `-- Installing xf86vidmodeproto-2.3.1... | | | | `-- Extracting xf86vidmodeproto-2.3.1: .... done | | | `-- Extracting libXxf86vm-1.1.4_1: .......... done | | | `-- Installing libdrm-2.4.92,1... | | | | `-- Installing libpciaccess-0.13.5... | | | | `-- Installing pciids-20180428... | | | | `-- Extracting pciids-20180428: ..... done | | | | `-- Extracting libpciaccess-0.13.5: ......... done | | | `-- Extracting libdrm-2.4.92,1: .......... done | | | `-- Installing libelf-0.8.13_3... | | | `-- Extracting libelf-0.8.13_3: .......... done | | | `-- Installing libxshmfence-1.2_2... | | | `-- Extracting libxshmfence-1.2_2: ......... done | | | `-- Extracting mesa-libs-18.1.2: .......... done | | | `-- Installing pixman-0.34.0... | | | `-- Extracting pixman-0.34.0: .......... done | | | `-- Installing xcb-util-renderutil-0.3.9_1... | | | `-- Installing xcb-util-0.4.0_2,1... | | | `-- Extracting xcb-util-0.4.0_2,1: .......... done | | | `-- Extracting xcb-util-renderutil-0.3.9_1: ...... done | | `-- Extracting cairo-1.14.8_1,2: .......... done | | `-- Installing libICE-1.0.9_1,1... | | `-- Extracting libICE-1.0.9_1,1: .......... done | | `-- Installing libSM-1.2.2_3,1... | | `-- Extracting libSM-1.2.2_3,1: .......... done | | `-- Installing libXaw-1.0.13,2... | | | `-- Installing libXmu-1.1.2_3,1... | | | `-- Installing libXt-1.1.5,1... | | | `-- Extracting libXt-1.1.5,1: .......... done | | | `-- Extracting libXmu-1.1.2_3,1: .......... done | | | `-- Installing libXp-1.0.3,1... | | | `-- Installing printproto-1.0.5... | | | `-- Extracting 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| | `-- Installing mkfontdir-1.0.7... | | | | `-- Installing mkfontscale-1.1.3... | | | | | `-- Installing libfontenc-1.1.3_1... | | | | | `-- Extracting libfontenc-1.1.3_1: ......... done | | | | `-- Extracting mkfontscale-1.1.3: ..... done | | | | `-- Extracting mkfontdir-1.0.7: ..... done | | | `-- Extracting dejavu-2.37: .......... done | | | `-- Installing font-bh-ttf-1.0.3_3... | | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done | | | `-- Installing font-misc-ethiopic-1.0.3_3... | | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done | | | `-- Installing font-misc-meltho-1.0.3_3... | | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done | | `-- Extracting pango-1.42.0: .......... done | | `-- Extracting graphviz-2.40.1_5: .......... done | | `-- Installing p5-IPC-Run-0.99... | | `-- Installing p5-IO-Tty-1.12_2... | | `-- Extracting p5-IO-Tty-1.12_2: .......... done | | `-- Extracting p5-IPC-Run-0.99: .......... done | | `-- Installing p5-Parse-RecDescent-1.967.009_2... | | `-- Extracting p5-Parse-RecDescent-1.967.009_2: .......... done | | `-- Installing p5-XML-Twig-3.52... | | `-- Installing p5-HTML-Tree-5.07... | | | `-- Installing p5-libwww-6.33... | | | `-- Installing p5-Authen-NTLM-1.09_1... | | | | `-- Installing p5-Digest-HMAC-1.03_1... | | | | `-- Extracting p5-Digest-HMAC-1.03_1: .......... done | | | `-- Extracting p5-Authen-NTLM-1.09_1: ......... done | | | `-- Installing p5-Encode-Locale-1.05... | | | `-- Extracting p5-Encode-Locale-1.05: ....... done | | | `-- Installing p5-File-Listing-6.04_1... | | | | `-- Installing p5-HTTP-Date-6.02_1... | | | | `-- Extracting p5-HTTP-Date-6.02_1: ....... done | | | `-- Extracting p5-File-Listing-6.04_1: ....... done | | | `-- Installing p5-HTTP-Cookies-6.04... | | | | `-- Installing p5-HTTP-Message-6.18... | | | | `-- Installing p5-IO-HTML-1.001_1... | | | | `-- Extracting p5-IO-HTML-1.001_1: ....... done | | | | `-- Installing p5-LWP-MediaTypes-6.02_1... | | | | `-- Extracting p5-LWP-MediaTypes-6.02_1: ........ done | | | | `-- Installing p5-URI-1.74... | | | | `-- Extracting p5-URI-1.74: .......... done | | | | `-- Extracting p5-HTTP-Message-6.18: .......... done | | | `-- Extracting p5-HTTP-Cookies-6.04: .......... done | | | `-- Installing p5-HTTP-Daemon-6.01_1... | | | `-- Extracting p5-HTTP-Daemon-6.01_1: ....... done | | | `-- Installing p5-HTTP-Negotiate-6.01_1... | | | `-- Extracting p5-HTTP-Negotiate-6.01_1: ....... done | | | `-- Installing p5-Net-HTTP-6.18... | | | | `-- Installing p5-IO-Socket-SSL-2.056... | | | | `-- Installing p5-Mozilla-CA-20180117... | | | | `-- Extracting p5-Mozilla-CA-20180117: ........ done | | | | `-- Installing p5-Net-SSLeay-1.85... | | | | `-- Extracting p5-Net-SSLeay-1.85: .......... done | | | | `-- Extracting p5-IO-Socket-SSL-2.056: .......... done | | | `-- Extracting p5-Net-HTTP-6.18: .......... done | | | `-- Installing p5-Try-Tiny-0.28... | | | `-- Extracting p5-Try-Tiny-0.28: ...... done | | | `-- Installing p5-WWW-RobotRules-6.02_1... | | | `-- Extracting p5-WWW-RobotRules-6.02_1: ......... done | | | `-- Extracting p5-libwww-6.33: .......... done | | `-- Extracting p5-HTML-Tree-5.07: .......... done | | `-- Installing p5-Text-Iconv-1.7_3... | | `-- Extracting p5-Text-Iconv-1.7_3: ......... done | | `-- Installing p5-Tie-IxHash-1.23_1... | | `-- Extracting p5-Tie-IxHash-1.23_1: ....... done | | `-- Installing p5-XML-Parser-2.44... | | `-- Extracting p5-XML-Parser-2.44: .......... done | | `-- Installing p5-XML-XPath-1.42... | | `-- Extracting p5-XML-XPath-1.42: .......... done | | `-- Extracting p5-XML-Twig-3.52: .......... done | `-- Extracting p5-GraphViz-2.24: .......... done | `-- Installing p5-HTML-TableExtract-2.15... | | `-- Installing p5-HTML-Element-Extended-1.18_1... | | `-- Extracting p5-HTML-Element-Extended-1.18_1: ......... done | `-- Extracting p5-HTML-TableExtract-2.15: ....... done | `-- Installing p5-IO-stringy-2.111... | `-- Extracting p5-IO-stringy-2.111: .......... done | `-- Installing p5-Inline-C-0.78... | | `-- Installing p5-Inline-0.80... | | `-- Extracting p5-Inline-0.80: .......... done | | `-- Installing p5-Pegex-0.64... | | `-- Installing p5-JSON-XS-3.04... | | | `-- Installing p5-Types-Serialiser-1.0_1... | | | `-- Installing p5-common-sense-3.74... | | | `-- Extracting p5-common-sense-3.74: ........ done | | | `-- Extracting p5-Types-Serialiser-1.0_1: ......... done | | `-- Extracting p5-JSON-XS-3.04: .......... done | | `-- Installing p5-YAML-LibYAML-0.67... | | `-- Extracting p5-YAML-LibYAML-0.67: .......... done | | `-- Extracting p5-Pegex-0.64: .......... done | `-- Extracting p5-Inline-C-0.78: .......... done | `-- Installing p5-List-MoreUtils-0.428... | | `-- Installing p5-List-MoreUtils-XS-0.428... | | `-- Extracting p5-List-MoreUtils-XS-0.428: ....... done | `-- Extracting p5-List-MoreUtils-0.428: .......... done | `-- Installing p5-PostScript-0.06_2... | `-- Extracting p5-PostScript-0.06_2: ......... done | `-- Installing p5-SVG-2.84... | `-- Extracting p5-SVG-2.84: .......... done | `-- Installing p5-SVG-Graph-0.04_1... | | `-- Installing p5-Math-Spline-0.02_1... | | `-- Installing p5-Math-Derivative-1.01... | | `-- Extracting p5-Math-Derivative-1.01: ....... done | | `-- Extracting p5-Math-Spline-0.02_1: ....... done | | `-- Installing p5-Statistics-Descriptive-3.0609_1... | | `-- Extracting p5-Statistics-Descriptive-3.0609_1: ......... done | | `-- Installing p5-Tree-DAG_Node-1.31... | | `-- Installing p5-File-Slurp-Tiny-0.004... | | `-- Extracting p5-File-Slurp-Tiny-0.004: ....... done | | `-- Extracting p5-Tree-DAG_Node-1.31: ....... done | `-- Extracting p5-SVG-Graph-0.04_1: .......... done | `-- Installing p5-Set-Scalar-1.29... | `-- Extracting p5-Set-Scalar-1.29: .......... done | `-- Installing p5-Sort-Naturally-1.03_1... | `-- Extracting p5-Sort-Naturally-1.03_1: ....... done | `-- Installing p5-Spreadsheet-ParseExcel-0.65_2,1... | | `-- Installing p5-Crypt-RC4-2.02_1... | | `-- Extracting p5-Crypt-RC4-2.02_1: ... done | | `-- Installing p5-Digest-Perl-MD5-1.9_1... | | `-- Extracting p5-Digest-Perl-MD5-1.9_1: ... done | | `-- Installing p5-OLE-Storage_Lite-0.19_1... | | `-- Extracting p5-OLE-Storage_Lite-0.19_1: ... done | `-- Extracting p5-Spreadsheet-ParseExcel-0.65_2,1: .......... done | `-- Installing p5-XML-DOM-1.44_1... | | `-- Installing p5-XML-RegExp-0.04_1... | | `-- Extracting p5-XML-RegExp-0.04_1: ....... done | | `-- Installing p5-libxml-0.08_1... | | `-- Extracting p5-libxml-0.08_1: .......... done | `-- Extracting p5-XML-DOM-1.44_1: .......... done | `-- Installing p5-XML-DOM-XPath-0.14_1... | | `-- Installing p5-XML-XPathEngine-0.14_1... | | `-- Extracting p5-XML-XPathEngine-0.14_1: .......... done | `-- Extracting p5-XML-DOM-XPath-0.14_1: ....... done | `-- Installing p5-XML-LibXML-2.0132,1... | | `-- Installing p5-XML-NamespaceSupport-1.12... | | `-- Extracting p5-XML-NamespaceSupport-1.12: ....... done | | `-- Installing p5-XML-SAX-1.00... | | `-- Installing p5-XML-SAX-Base-1.09... | | `-- Extracting p5-XML-SAX-Base-1.09: .......... done | | `-- Extracting p5-XML-SAX-1.00: .......... done could not find ParserDetails.ini in /usr/local/lib/perl5/site_perl/XML/SAX | `-- Extracting p5-XML-LibXML-2.0132,1: .......... done | `-- Installing p5-XML-SAX-Writer-0.57... | | `-- Installing 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 Extracting p5-Bio-FeatureIO-1.6.905: .......... done 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-BioPerl-Run-1.007002 depends on package: p5-Bio-FeatureIO>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007002 ===> p5-BioPerl-Run-1.007002 depends on package: p5-BioPerl>=1.007000 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-Config-Any>=0 - not found ===> Installing existing package /packages/All/p5-Config-Any-0.32.txz Installing p5-Config-Any-0.32... `-- Installing p5-Config-General-2.63... `-- Extracting p5-Config-General-2.63: .......... done `-- Installing p5-Config-Tiny-2.23... `-- Extracting p5-Config-Tiny-2.23: ....... done `-- Installing p5-Cpanel-JSON-XS-4.04... `-- Extracting p5-Cpanel-JSON-XS-4.04: .......... done `-- Installing p5-Module-Pluggable-5.2... `-- Extracting p5-Module-Pluggable-5.2: .......... done Extracting p5-Config-Any-0.32: .......... done ===> p5-BioPerl-Run-1.007002 depends on package: p5-Config-Any>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007002 ===> p5-BioPerl-Run-1.007002 depends on package: p5-File-Sort>=0 - not found ===> Installing existing package /packages/All/p5-File-Sort-1.01_1.txz Installing p5-File-Sort-1.01_1... Extracting p5-File-Sort-1.01_1: ....... done ===> p5-BioPerl-Run-1.007002 depends on package: p5-File-Sort>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007002 ===> p5-BioPerl-Run-1.007002 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-IPC-Run>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-Module-Build>=0.4206 - not found ===> Installing existing package /packages/All/p5-Module-Build-0.4224.txz Installing p5-Module-Build-0.4224... Extracting p5-Module-Build-0.4224: .......... done ===> p5-BioPerl-Run-1.007002 depends on package: p5-Module-Build>=0.4206 - found ===> Returning to build of p5-BioPerl-Run-1.007002 ===> p5-BioPerl-Run-1.007002 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for p5-BioPerl-Run-1.007002 - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007002' -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for p5-BioPerl-Run-1.007002 Building BioPerl-Run (cd /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002 && /usr/local/bin/perl ./Build manifest) File 'MANIFEST.SKIP' does not exist: Creating a temporary 'MANIFEST.SKIP' Added to MANIFEST: Build.PL.orig -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-Run-1.007002 depends on package: p5-Algorithm-Diff>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-Bio-FeatureIO>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-BioPerl>=1.007000 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-Config-Any>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-File-Sort>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-IPC-Run>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-Run-1.007002 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for p5-BioPerl-Run-1.007002 ===> Generating temporary packing list Building BioPerl-Run Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Generic.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Muscle.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Probcons.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/SLR.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Hyphy.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/EMBOSS.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/TribeMCL.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/TigrAssembler.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Signalp.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneNCBIBlast.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/RepeatMasker.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneWUBlast.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Promoterwise.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Pseudowise.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Primate.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Simprot.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneBlast.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Tmhmm.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Vista.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Primer3.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Seg.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/WrapperBase.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/RNAMotif.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/tRNAscanSE.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Profile.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Prints.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Samtools.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/ERPIN.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/FootPrinter.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Analysis.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BEDTools.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Bowtie.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Newbler.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/AnalysisFactory.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Genewise.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Minimo.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Genemark.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Mdust.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Genscan.pm Installing 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/construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/WrapperBase/CommandExts.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BlastPlus/Config.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BEDTools/Config.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Bowtie/Config.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Analysis/soap.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/QuickTree.pm Installing 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Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::StandAloneBlast.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Gmap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Semphy.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Proda.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Samtools.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3 Installing 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Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::MAFFT.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Amap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Raxml.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Bowtie.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::StandAloneWUBlast.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::FastTree.3 Installing 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Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Installer::EMBOSS.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Installer::Muscle.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::TribeMCL.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Coil.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::DocSumAdaptor.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Mdust.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::StandAloneFasta.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::TigrAssembler.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Kalign.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Ensembl.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Maq.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Meme.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Pseudowise.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Cap3.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Samtools::Config.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Primate.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::Result.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Glimmer.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Seg.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Sim4.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Tmhmm.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Infernal.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::RepeatMasker.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Analysis::soap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Lagan.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Blat.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::AnalysisFactory.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::ESoap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::ESoap::WSDL.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities.3 install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/scripts/bioperl_application_installer.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_bioperl_application_installer install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/scripts/multi_hmmsearch.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_multi_hmmsearch install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/scripts/panalysis.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_panalysis install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/scripts/papplmaker.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_papplmaker install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/scripts/run_neighbor.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_run_neighbor install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/scripts/run_protdist.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_run_protdist install -m 0644 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/AUTHORS /construction/biology/p5-BioPerl-Run/stage/usr/local/share/doc/BioPerl-Run install -m 0644 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/Changes /construction/biology/p5-BioPerl-Run/stage/usr/local/share/doc/BioPerl-Run install -m 0644 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/INSTALL.PROGRAMS /construction/biology/p5-BioPerl-Run/stage/usr/local/share/doc/BioPerl-Run install -m 0644 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007002/README.md /construction/biology/p5-BioPerl-Run/stage/usr/local/share/doc/BioPerl-Run ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for p5-BioPerl-Run-1.007002 file sizes/checksums [260]: ... done packing files [260]: ... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 23:28:09 UTC Duration: 00:00:43