=> Building biology/p5-BioPerl build started at Sun Mar 12 21:38:16 PDT 2017 port directory: /usr/ports/biology/p5-BioPerl building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.1380.gb4315f-DEVELOPMENT #0: Fri Mar 3 17:20:21 PST 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: perl@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/Release48-default/ref/../09//usr/ports/biology/p5-BioPerl/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400713 Jail OSVERSION: 400713 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release48-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=p5-BioPerl-1.007001_1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release48-default/ref/.p/pool MASTERNAME=Release48-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for p5-BioPerl-1.007001_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples PGTEST=off: Test PostGreSQL SQLITETEST=off: Test SQLite ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --install_path lib="/usr/local/lib/perl5/site_perl" --install_path arch="/usr/local/lib/perl5/site_perl/mach/5.24" --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 /wrkdirs/biology/p5-BioPerl/stage --perl="/usr/local/bin/perl" --create_packlist 1 CC="cc" CCFLAGS="-pipe -O2 -fno-strict-aliasing" PREFIX="/usr/local" INSTALLPRIVLIB="/usr/local/lib" INSTALLARCHLIB="/usr/local/lib" --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/p5-BioPerl XDG_CONFIG_HOME=/wrkdirs/biology/p5-BioPerl HOME=/wrkdirs/biology/p5-BioPerl TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 PERL_EXTUTILS_AUTOINSTALL="--skipdeps" PERL_MM_USE_DEFAULT="YES" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/p5-BioPerl XDG_CONFIG_HOME=/wrkdirs/biology/p5-BioPerl HOME=/wrkdirs/biology/p5-BioPerl TMPDIR="/tmp" 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 LIBDIR="/usr/lib" 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 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.1 PERL_VER=5.24 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/5.24 PROFILE="@comment " DOCSDIR="share/doc/BioPerl" EXAMPLESDIR="share/examples/BioPerl" DATADIR="share/BioPerl" WWWDIR="www/BioPerl" ETCDIR="etc/BioPerl" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/BioPerl DOCSDIR=/usr/local/share/doc/BioPerl EXAMPLESDIR=/usr/local/share/examples/BioPerl WWWDIR=/usr/local/www/BioPerl ETCDIR=/usr/local/etc/BioPerl --End SUB_LIST-- ---Begin make.conf--- NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License ART10 GPLv1 accepted by the user =========================================================================== =================================================== ===> p5-BioPerl-1.007001_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz Installing pkg-1.9.4_1... Extracting pkg-1.9.4_1: .......... done ===> p5-BioPerl-1.007001_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-BioPerl-1.007001_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 GPLv1 accepted by the user ===> Fetching all distfiles required by p5-BioPerl-1.007001_1 for building =========================================================================== =================================================== ===> License ART10 GPLv1 accepted by the user ===> Fetching all distfiles required by p5-BioPerl-1.007001_1 for building => SHA256 Checksum OK for BioPerl-1.007001.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 GPLv1 accepted by the user ===> Fetching all distfiles required by p5-BioPerl-1.007001_1 for building ===> Extracting for p5-BioPerl-1.007001_1 => SHA256 Checksum OK for BioPerl-1.007001.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for p5-BioPerl-1.007001_1 ===> Applying ports patches for p5-BioPerl-1.007001_1 No such line 1151 in input file, ignoring =========================================================================== =================================================== ===> p5-BioPerl-1.007001_1 depends on package: p5-Algorithm-Munkres>=0 - not found ===> Installing existing package /packages/All/p5-Algorithm-Munkres-0.08_1.txz Installing p5-Algorithm-Munkres-0.08_1... `-- Installing perl5-5.24.1... `-- Extracting perl5-5.24.1: .......... done Extracting p5-Algorithm-Munkres-0.08_1: ... done Message from perl5-5.24.1: 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-1.007001_1 depends on package: p5-Algorithm-Munkres>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Array-Compare>=0 - not found ===> Installing existing package /packages/All/p5-Array-Compare-3.0.0.txz Installing p5-Array-Compare-3.0.0... `-- Installing p5-Moo-2.003000... | `-- Installing p5-Role-Tiny-2.000005... | | `-- Installing p5-Class-Method-Modifiers-2.12... | | `-- Extracting p5-Class-Method-Modifiers-2.12: ....... done | `-- Extracting p5-Role-Tiny-2.000005: ......... done | `-- Installing p5-Devel-GlobalDestruction-0.14... | | `-- Installing p5-Sub-Exporter-Progressive-0.001013... | | `-- Installing p5-Sub-Exporter-0.987_1... | | | `-- 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 | | | `-- Installing p5-Data-OptList-0.110... | | | `-- 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-0.014_1... | `-- Extracting p5-Module-Runtime-0.014_1: ....... done | `-- Installing p5-Sub-Quote-2.003001... | `-- Extracting p5-Sub-Quote-2.003001: ......... done `-- Extracting p5-Moo-2.003000: .......... done `-- Installing p5-Type-Tiny-1.000006... | `-- Installing p5-Exporter-Tiny-0.044... | `-- Extracting p5-Exporter-Tiny-0.044: .......... done | `-- Installing p5-Type-Tiny-XS-0.012_1... | `-- Extracting p5-Type-Tiny-XS-0.012_1: .......... done `-- Extracting p5-Type-Tiny-1.000006: .......... done Extracting p5-Array-Compare-3.0.0: ....... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Array-Compare>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Clone>=0 - not found ===> Installing existing package /packages/All/p5-Clone-0.38.txz Installing p5-Clone-0.38... Extracting p5-Clone-0.38: ..... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Clone>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Convert-Binary-C>=0 - not found ===> Installing existing package /packages/All/p5-Convert-Binary-C-0.78.txz Installing p5-Convert-Binary-C-0.78... Extracting p5-Convert-Binary-C-0.78: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Convert-Binary-C>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-DBD-mysql>=0 - not found ===> Installing existing package /packages/All/p5-DBD-mysql-4.041.txz Installing p5-DBD-mysql-4.041... `-- Installing mysql56-client-5.6.35_2... | `-- Installing liblz4-1.7.5,1... | `-- Extracting liblz4-1.7.5,1: .......... done | `-- Installing libressl-2.4.5... | `-- Extracting libressl-2.4.5: .......... done | `-- Installing libevent2-2.1.8... | `-- Extracting libevent2-2.1.8: .......... done | `-- Installing libedit-3.1.20150325_2,1... | | `-- Installing ncurses-6.0_3... | | `-- Extracting ncurses-6.0_3: .......... done | `-- Extracting libedit-3.1.20150325_2,1: .......... done `-- Extracting mysql56-client-5.6.35_2: .......... done `-- Installing p5-DBI-1.636_1... `-- Extracting p5-DBI-1.636_1: .......... done Extracting p5-DBD-mysql-4.041: .......... done Message from ncurses-6.0_3: ===> NOTICE: The ncurses 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from mysql56-client-5.6.35_2: * * * * * * * * * * * * * * * * * * * * * * * * 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. * * * * * * * * * * * * * * * * * * * * * * * * ===> p5-BioPerl-1.007001_1 depends on package: p5-DBD-mysql>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-DBI>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Data-Stag>=0.11 - not found ===> Installing existing package /packages/All/p5-Data-Stag-0.14_2.txz 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 ===> p5-BioPerl-1.007001_1 depends on package: p5-Data-Stag>=0.11 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Error>=0 - not found ===> Installing existing package /packages/All/p5-Error-0.17024.txz Installing p5-Error-0.17024... Extracting p5-Error-0.17024: ......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Error>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-GD>=0 - not found ===> Installing existing package /packages/All/p5-GD-2.56_4.txz Installing p5-GD-2.56_4... `-- Installing libgd-2.2.4,1... | `-- Installing fontconfig-2.12.1,1... | | `-- Installing expat-2.2.0_1... | | `-- Extracting expat-2.2.0_1: .......... done | | `-- Installing freetype2-2.6.3... | | `-- Extracting freetype2-2.6.3: .......... done | `-- Extracting fontconfig-2.12.1,1: .......... 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-1.5.1... | `-- Extracting jpeg-turbo-1.5.1: .......... done | `-- Installing png-1.6.27... | `-- Extracting png-1.6.27: .......... done | `-- Installing tiff-4.0.7_1... | | `-- Installing jbigkit-2.1_1... | | `-- Extracting jbigkit-2.1_1: .......... done | `-- Extracting tiff-4.0.7_1: .......... done | `-- Installing webp-0.5.2... | | `-- Installing giflib-5.1.4... | | `-- Extracting giflib-5.1.4: .......... done | `-- Extracting webp-0.5.2: .......... done `-- Extracting libgd-2.2.4,1: .......... done Extracting p5-GD-2.56_4: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-GD>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Graph>=0.50 - not found ===> Installing existing package /packages/All/p5-Graph-0.96_2,1.txz Installing p5-Graph-0.96_2,1... `-- Installing p5-Heap-0.80_1... `-- Extracting p5-Heap-0.80_1: .......... done Extracting p5-Graph-0.96_2,1: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Graph>=0.50 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-GraphViz>=0 - not found ===> Installing existing package /packages/All/p5-GraphViz-2.24.txz Installing p5-GraphViz-2.24... `-- Installing graphviz-2.40.1... | `-- Installing libXt-1.1.5,1... | | `-- Installing xproto-7.0.31... | | `-- Extracting xproto-7.0.31: .......... done | | `-- Installing libSM-1.2.2_3,1... | | `-- Installing libICE-1.0.9_1,1... | | `-- Extracting libICE-1.0.9_1,1: .......... done | | `-- Extracting libSM-1.2.2_3,1: .......... done | | `-- Installing libX11-1.6.4,1... | | `-- Installing kbproto-1.0.7... | | `-- Extracting kbproto-1.0.7: .......... done | | `-- Installing libXdmcp-1.1.2... | | `-- Extracting libXdmcp-1.1.2: ......... done | | `-- Installing libxcb-1.12... | | | `-- Installing libxml2-2.9.4... | | | `-- Extracting libxml2-2.9.4: .......... done | | | `-- Installing libpthread-stubs-0.3_6... | | | `-- Extracting libpthread-stubs-0.3_6: ..... done | | | `-- Installing libXau-1.0.8_3... | | | `-- Extracting libXau-1.0.8_3: .......... done | | `-- Extracting libxcb-1.12: .......... done | | `-- Extracting libX11-1.6.4,1: .......... done | `-- Extracting libXt-1.1.5,1: .......... done | `-- Installing pango-1.38.0_1... | | `-- Installing encodings-1.0.4_3,1... | | `-- Installing font-util-1.3.1... | | `-- Extracting font-util-1.3.1: .......... done | | `-- Extracting encodings-1.0.4_3,1: .......... done | | `-- Installing libXft-2.3.2_1... | | `-- Installing libXrender-0.9.10... | | | `-- Installing renderproto-0.11.1... | | | `-- Extracting renderproto-0.11.1: .... done | | `-- Extracting libXrender-0.9.10: .......... done | | `-- Extracting libXft-2.3.2_1: ......... done | | `-- Installing harfbuzz-1.4.1... | | `-- Installing cairo-1.14.6_1,2... | | | `-- Installing glproto-1.4.17... | | | `-- Extracting glproto-1.4.17: ...... done | | | `-- Installing libEGL-11.2.2... | | | `-- Installing libdevq-0.0.4... | | | `-- Extracting libdevq-0.0.4: .......... done | | | `-- Installing libXdamage-1.1.4_3... | | | | `-- Installing libXfixes-5.0.3... | | | | `-- Installing fixesproto-5.0... | | | | `-- Extracting fixesproto-5.0: .... done | | | | `-- Extracting libXfixes-5.0.3: .......... done | | | | `-- Installing damageproto-1.2.1... | | | | `-- Extracting damageproto-1.2.1: .... done | | | `-- Extracting libXdamage-1.1.4_3: ...... done | | | `-- Installing libxshmfence-1.2... | | | `-- Extracting libxshmfence-1.2: ......... 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 gbm-11.2.2... | | | | `-- Installing libglapi-11.2.2... | | | | `-- Installing libXvMC-1.0.10... | | | | | `-- Installing libXv-1.0.11,1... | | | | | `-- Installing videoproto-2.3.3... | | | | | `-- Extracting videoproto-2.3.3: ......... done | | | | | `-- Extracting libXv-1.0.11,1: .......... done | | | | `-- Extracting libXvMC-1.0.10: .......... done | | | | `-- Installing libdrm-2.4.74_1,1... | | | | | `-- Installing libpciaccess-0.13.4... | | | | | `-- Installing pciids-20170128... | | | | | `-- Extracting pciids-20170128: ..... done | | | | | `-- Extracting libpciaccess-0.13.4: ...... done | | | | `-- Extracting libdrm-2.4.74_1,1: .......... done | | | | `-- Installing libelf-0.8.13_2... | | | | | `-- Installing gettext-runtime-0.19.8.1_1... | | | | | `-- Installing indexinfo-0.2.6... | | | | | `-- Extracting indexinfo-0.2.6: .... done | | | | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | | | `-- Extracting libelf-0.8.13_2: .......... done | | | | `-- Extracting libglapi-11.2.2: ... done | | | `-- Extracting gbm-11.2.2: ..... done | | | `-- Installing llvm37-3.7.1_4... | | | | `-- Installing python27-2.7.13_1... | | | | `-- Installing readline-6.3.8... | | | | `-- Extracting readline-6.3.8: .......... done | | | | `-- Installing libffi-3.2.1... | | | | `-- Extracting libffi-3.2.1: .......... done | | | | `-- Extracting python27-2.7.13_1: .......... done | | | `-- Extracting llvm37-3.7.1_4: .......... done | | | `-- Extracting libEGL-11.2.2: .......... done | | | `-- Installing libGL-11.2.2... | | | `-- Installing dri2proto-2.8... | | | `-- Extracting dri2proto-2.8: .... 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 | | | `-- Extracting libGL-11.2.2: .......... 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 | | | `-- Installing pixman-0.34.0... | | | `-- Extracting pixman-0.34.0: .......... done | | | `-- Installing glib-2.46.2_4... | | | `-- Installing libiconv-1.14_10... | | | `-- Extracting libiconv-1.14_10: .......... done | | | `-- Installing pcre-8.40... | | | `-- Extracting pcre-8.40: .......... done | | | `-- Extracting glib-2.46.2_4: .......... done No schema files found: doing nothing. | | `-- Extracting cairo-1.14.6_1,2: .......... done | | `-- Installing icu-58.2,1... | | `-- Extracting icu-58.2,1: .......... done | | `-- Installing graphite2-1.3.9... | | `-- Extracting graphite2-1.3.9: .......... done | | `-- Extracting harfbuzz-1.4.1: .......... done | | `-- Installing xorg-fonts-truetype-7.7_1... | | `-- Installing font-misc-meltho-1.0.3_3... | | | `-- Installing mkfontdir-1.0.7... | | | `-- Installing mkfontscale-1.1.2... | | | | `-- Installing libfontenc-1.1.3_1... | | | | `-- Extracting libfontenc-1.1.3_1: ......... done | | | `-- Extracting mkfontscale-1.1.2: .. done | | | `-- Extracting mkfontdir-1.0.7: .. done | | `-- Extracting font-misc-meltho-1.0.3_3: .......... 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 dejavu-2.37... | | `-- Extracting dejavu-2.37: .......... done | `-- Extracting pango-1.38.0_1: .......... done | `-- Installing libXaw-1.0.13,2... | | `-- Installing libXpm-3.5.12... | | `-- Extracting libXpm-3.5.12: .......... done | | `-- Installing libXmu-1.1.2_3,1... | | `-- Extracting libXmu-1.1.2_3,1: .......... done | | `-- Installing printproto-1.0.5... | | `-- Extracting printproto-1.0.5: .... done | | `-- Installing libXp-1.0.3,1... | | `-- Extracting libXp-1.0.3,1: .......... done | `-- Extracting libXaw-1.0.13,2: .......... done | `-- Installing libltdl-2.4.6... | `-- Extracting libltdl-2.4.6: .......... done `-- Extracting graphviz-2.40.1: .......... done `-- Installing p5-IPC-Run-0.94... | `-- Installing p5-IO-Tty-1.12_2... | `-- Extracting p5-IO-Tty-1.12_2: .......... done `-- Extracting p5-IPC-Run-0.94: .......... 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-Tie-IxHash-1.23_1... | `-- Extracting p5-Tie-IxHash-1.23_1: ....... done | `-- Installing p5-Text-Iconv-1.7_3... | `-- Extracting p5-Text-Iconv-1.7_3: ..... done | `-- Installing p5-HTML-Tree-5.03_2... | | `-- 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-HTML-Tree-5.03_2: .......... done | `-- Installing p5-libwww-6.18... | | `-- Installing p5-Net-HTTP-6.12... | | `-- Installing p5-URI-1.71... | | `-- Extracting p5-URI-1.71: .......... done | | `-- Installing p5-IO-Socket-SSL-2.044... | | | `-- Installing p5-Net-SSLeay-1.80... | | | `-- Extracting p5-Net-SSLeay-1.80: .......... done | | | `-- Installing p5-IO-Socket-IP-0.38... | | | `-- Extracting p5-IO-Socket-IP-0.38: ....... done | | | `-- Installing p5-Mozilla-CA-20160104... | | | `-- Extracting p5-Mozilla-CA-20160104: ........ done | | | `-- Installing p5-Socket-2.024... | | | `-- Extracting p5-Socket-2.024: ........ done | | `-- Extracting p5-IO-Socket-SSL-2.044: .......... done | | `-- Extracting p5-Net-HTTP-6.12: .......... done | | `-- Installing p5-HTTP-Daemon-6.01_1... | | `-- Installing p5-HTTP-Message-6.11... | | | `-- Installing p5-Encode-Locale-1.05... | | | `-- Extracting p5-Encode-Locale-1.05: ... done | | | `-- Installing p5-IO-HTML-1.001_1... | | | `-- Extracting p5-IO-HTML-1.001_1: ....... done | | | `-- Installing p5-HTTP-Date-6.02_1... | | | `-- Extracting p5-HTTP-Date-6.02_1: ....... done | | | `-- Installing p5-LWP-MediaTypes-6.02_1... | | | `-- Extracting p5-LWP-MediaTypes-6.02_1: .... done | | `-- Extracting p5-HTTP-Message-6.11: .......... done | | `-- 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-WWW-RobotRules-6.02_1... | | `-- Extracting p5-WWW-RobotRules-6.02_1: ..... done | | `-- Installing p5-HTTP-Cookies-6.01_1... | | `-- Extracting p5-HTTP-Cookies-6.01_1: .......... done | | `-- Installing p5-Try-Tiny-0.24... | | `-- Extracting p5-Try-Tiny-0.24: ...... done | | `-- Installing p5-File-Listing-6.04_1... | | `-- Extracting p5-File-Listing-6.04_1: ....... done | | `-- 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 | `-- Extracting p5-libwww-6.18: .......... done | `-- Installing p5-XML-Parser-2.44... | `-- Extracting p5-XML-Parser-2.44: .......... done | `-- Installing p5-XML-XPath-1.40... | `-- Extracting p5-XML-XPath-1.40: .......... done `-- Extracting p5-XML-Twig-3.52: .......... done Extracting p5-GraphViz-2.24: .......... done Message from python27-2.7.13_1: =========================================================================== 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-1.007001_1 depends on package: p5-GraphViz>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-HTML-Parser>=3 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-HTML-TableExtract>=0 - not found ===> Installing existing package /packages/All/p5-HTML-TableExtract-2.13.txz Installing p5-HTML-TableExtract-2.13... `-- Installing p5-HTML-Element-Extended-1.18_1... `-- Extracting p5-HTML-Element-Extended-1.18_1: ......... done Extracting p5-HTML-TableExtract-2.13: ....... done ===> p5-BioPerl-1.007001_1 depends on package: p5-HTML-TableExtract>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-HTTP-Message>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-IO-stringy>=0 - not found ===> Installing existing package /packages/All/p5-IO-stringy-2.111.txz Installing p5-IO-stringy-2.111... Extracting p5-IO-stringy-2.111: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-IO-stringy>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Inline-C>=0.67 - not found ===> Installing existing package /packages/All/p5-Inline-C-0.76_1.txz Installing p5-Inline-C-0.76_1... `-- Installing p5-Inline-0.80... `-- Extracting p5-Inline-0.80: .......... done `-- Installing p5-Pegex-0.63... | `-- Installing p5-JSON-XS-3.03... | | `-- Installing p5-common-sense-3.74... | | `-- Extracting p5-common-sense-3.74: ........ done | | `-- Installing p5-Types-Serialiser-1.0_1... | | `-- Extracting p5-Types-Serialiser-1.0_1: ......... done | `-- Extracting p5-JSON-XS-3.03: .......... done | `-- Installing p5-YAML-LibYAML-0.59_1... | `-- Extracting p5-YAML-LibYAML-0.59_1: .......... done `-- Extracting p5-Pegex-0.63: .......... done Extracting p5-Inline-C-0.76_1: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Inline-C>=0.67 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-List-MoreUtils>=0 - not found ===> Installing existing package /packages/All/p5-List-MoreUtils-0.416.txz Installing p5-List-MoreUtils-0.416... Extracting p5-List-MoreUtils-0.416: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-List-MoreUtils>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-PostScript>=0 - not found ===> Installing existing package /packages/All/p5-PostScript-0.06_2.txz Installing p5-PostScript-0.06_2... Extracting p5-PostScript-0.06_2: ......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-PostScript>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-SVG>=2.26 - not found ===> Installing existing package /packages/All/p5-SVG-2.64.txz Installing p5-SVG-2.64... Extracting p5-SVG-2.64: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-SVG>=2.26 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-SVG-Graph>=0.01 - not found ===> Installing existing package /packages/All/p5-SVG-Graph-0.04_1.txz Installing p5-SVG-Graph-0.04_1... `-- Installing p5-Tree-DAG_Node-1.29... | `-- Installing p5-File-Slurp-Tiny-0.004... | `-- Extracting p5-File-Slurp-Tiny-0.004: ....... done `-- Extracting p5-Tree-DAG_Node-1.29: ...... done `-- Installing p5-Statistics-Descriptive-3.0609_1... `-- Extracting p5-Statistics-Descriptive-3.0609_1: ......... done `-- Installing p5-Math-Spline-0.02_1... | `-- Installing p5-Math-Derivative-0.04... | `-- Extracting p5-Math-Derivative-0.04: ....... done `-- Extracting p5-Math-Spline-0.02_1: ....... done Extracting p5-SVG-Graph-0.04_1: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-SVG-Graph>=0.01 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Set-Scalar>=0 - not found ===> Installing existing package /packages/All/p5-Set-Scalar-1.26_1.txz Installing p5-Set-Scalar-1.26_1... Extracting p5-Set-Scalar-1.26_1: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Set-Scalar>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Sort-Naturally>=0 - not found ===> Installing existing package /packages/All/p5-Sort-Naturally-1.03_1.txz Installing p5-Sort-Naturally-1.03_1... Extracting p5-Sort-Naturally-1.03_1: ....... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Sort-Naturally>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Spreadsheet-ParseExcel>=0 - not found ===> Installing existing package /packages/All/p5-Spreadsheet-ParseExcel-0.65_2,1.txz Installing p5-Spreadsheet-ParseExcel-0.65_2,1... `-- Installing p5-Digest-Perl-MD5-1.9_1... `-- Extracting p5-Digest-Perl-MD5-1.9_1: ... done `-- Installing p5-Crypt-RC4-2.02_1... `-- Extracting p5-Crypt-RC4-2.02_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 ===> p5-BioPerl-1.007001_1 depends on package: p5-Spreadsheet-ParseExcel>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-DOM>=0 - not found ===> Installing existing package /packages/All/p5-XML-DOM-1.44_1.txz Installing p5-XML-DOM-1.44_1... `-- Installing p5-libxml-0.08_1... `-- Extracting p5-libxml-0.08_1: .......... done `-- Installing p5-XML-RegExp-0.04_1... `-- Extracting p5-XML-RegExp-0.04_1: ... done Extracting p5-XML-DOM-1.44_1: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-DOM>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-DOM-XPath>=0 - not found ===> Installing existing package /packages/All/p5-XML-DOM-XPath-0.14_1.txz 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 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-DOM-XPath>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-LibXML>=0 - not found ===> Installing existing package /packages/All/p5-XML-LibXML-2.0128,1.txz Installing p5-XML-LibXML-2.0128,1... `-- Installing p5-XML-NamespaceSupport-1.11_1... `-- Extracting p5-XML-NamespaceSupport-1.11_1: ... done `-- Installing p5-XML-SAX-0.99_2... | `-- Installing p5-XML-SAX-Base-1.08_1... | `-- Extracting p5-XML-SAX-Base-1.08_1: .......... done `-- Extracting p5-XML-SAX-0.99_2: .......... done Extracting p5-XML-LibXML-2.0128,1: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-LibXML>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Parser>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-SAX>=0.15 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-SAX-Writer>=0 - not found ===> Installing existing package /packages/All/p5-XML-SAX-Writer-0.56.txz Installing p5-XML-SAX-Writer-0.56... `-- Installing p5-XML-Filter-BufferText-1.01_1... `-- Extracting p5-XML-Filter-BufferText-1.01_1: ... done Extracting p5-XML-SAX-Writer-0.56: ......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-SAX-Writer>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Simple>=0 - not found ===> Installing existing package /packages/All/p5-XML-Simple-2.22.txz Installing p5-XML-Simple-2.22... `-- Installing p5-XML-SAX-Expat-0.51_1... `-- Extracting p5-XML-SAX-Expat-0.51_1: ....... done Extracting p5-XML-Simple-2.22: ......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Simple>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Writer>=0.400 - not found ===> Installing existing package /packages/All/p5-XML-Writer-0.625_1.txz Installing p5-XML-Writer-0.625_1... Extracting p5-XML-Writer-0.625_1: ... done ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Writer>=0.400 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-YAML>=0 - not found ===> Installing existing package /packages/All/p5-YAML-1.14.txz Installing p5-YAML-1.14... Extracting p5-YAML-1.14: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-YAML>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-libwww>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-libxml>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-CGI>=0 - not found ===> Installing existing package /packages/All/p5-CGI-4.35.txz Installing p5-CGI-4.35... Extracting p5-CGI-4.35: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-CGI>=0 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: p5-Module-Build>=0.4206 - not found ===> Installing existing package /packages/All/p5-Module-Build-0.4220.txz Installing p5-Module-Build-0.4220... Extracting p5-Module-Build-0.4220: .......... done ===> p5-BioPerl-1.007001_1 depends on package: p5-Module-Build>=0.4206 - found ===> Returning to build of p5-BioPerl-1.007001_1 ===> p5-BioPerl-1.007001_1 depends on package: perl5>=5.24<5.25 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for p5-BioPerl-1.007001_1 Checking prerequisites... build_requires: ! Test::Most is not installed recommends: * Bio::Phylo is not installed Checking optional features... EntrezGene............disabled requires: ! Bio::ASN1::EntrezGene is not installed Pg Tests..............disabled requires: ! DBD::Pg is not installed SQLite Tests..........disabled requires: ! DBD::SQLite is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. - will not run the BioDBGFF or BioDBSeqFeature live database tests - willt install all scripts - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl' version '1.007001' =========================================================================== =================================================== ===> Building for p5-BioPerl-1.007001_1 Building BioPerl =========================================================================== =================================================== ===> p5-BioPerl-1.007001_1 depends on package: p5-Algorithm-Munkres>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Array-Compare>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Clone>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Convert-Binary-C>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-DBD-mysql>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-DBI>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Data-Stag>=0.11 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Error>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-GD>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Graph>=0.50 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-GraphViz>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-HTML-Parser>=3 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-HTML-TableExtract>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-HTTP-Message>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-IO-stringy>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Inline-C>=0.67 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-List-MoreUtils>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-PostScript>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-SVG>=2.26 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-SVG-Graph>=0.01 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Set-Scalar>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Sort-Naturally>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-Spreadsheet-ParseExcel>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-DOM>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-DOM-XPath>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-LibXML>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Parser>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-SAX>=0.15 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-SAX-Writer>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Simple>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-XML-Writer>=0.400 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-YAML>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-libwww>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-libxml>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: p5-CGI>=0 - found ===> p5-BioPerl-1.007001_1 depends on package: perl5>=5.24<5.25 - found =========================================================================== =================================================== ===> Staging for p5-BioPerl-1.007001_1 ===> Generating temporary packing list Building BioPerl Reading skip patterns from 'INSTALL.SKIP'. Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_nrdb.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2alnblocks.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqfeature_load.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqpart.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_remote_blast.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_oligo_count.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqcut.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_nexus2nh.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_taxonomy2tree.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_pairwise_kaks.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqret.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seqretsplit.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_unflatten_seq.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2tribe.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_split_seq.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_process_sgd.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_query_entrez_taxa.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_seq_length.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_hmmer_to_table.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_local_taxonomydb_query.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_parse_hmmsearch.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_translate_seq.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_mask_by_search.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_search2table.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_index.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_mutate.pl.1 Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/man/man1/bp_process_wormbase.pl.1 Installing 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/wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/PrimarySeqI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/DasI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/NexmlIO.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/MapIO.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/LocationI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Seq.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/WebAgent.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/UpdateableSeqI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Range.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/TreeIO.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/IdCollectionI.pm Installing 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Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SeqI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnnotationI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SeqUtils.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/AnnotationCollectionI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/PullParserI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/Perl.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/FeatureHolderI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/ParameterBaseI.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/LocatableSeq.pm Installing /wrkdirs/biology/p5-BioPerl/stage/usr/local/lib/perl5/site_perl/Bio/SimpleAlign.pm Installing 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/wrkdirs/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl install -m 0644 /wrkdirs/biology/p5-BioPerl/BioPerl-1.007001/DEPRECATED /wrkdirs/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl install -m 0644 /wrkdirs/biology/p5-BioPerl/BioPerl-1.007001/INSTALL.md /wrkdirs/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl install -m 0644 /wrkdirs/biology/p5-BioPerl/BioPerl-1.007001/MANIFEST /wrkdirs/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl install -m 0644 /wrkdirs/biology/p5-BioPerl/BioPerl-1.007001/README.md /wrkdirs/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl /bin/cp -R /wrkdirs/biology/p5-BioPerl/BioPerl-1.007001/deobfuscator /wrkdirs/biology/p5-BioPerl/stage/usr/local/share/doc/BioPerl /bin/cp -R /wrkdirs/biology/p5-BioPerl/BioPerl-1.007001/examples/* /wrkdirs/biology/p5-BioPerl/stage/usr/local/share/examples/BioPerl ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for p5-BioPerl-1.007001_1 file sizes/checksums [1893]: .......... done packing files [1893]: .......... done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for p5-BioPerl-1.007001_1 build of biology/p5-BioPerl ended at Sun Mar 12 21:40:35 PDT 2017 build time: 00:02:19