=> Building biology/p5-BioPerl-Run Started : Sunday, 7 JUL 2019 at 04:28:40 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-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-1.007003: 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=gcc80 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/5.28" --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=gcc80 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="" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 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/5.28 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-5.4 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 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-Run-1.007003 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> p5-BioPerl-Run-1.007003 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-BioPerl-Run-1.007003 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-Run-1.007003 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-Run-1.007003 for building => SHA256 Checksum OK for BioPerl-Run-1.007003.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 GPLv1+ accepted by the user ===> Fetching all distfiles required by p5-BioPerl-Run-1.007003 for building ===> Extracting for p5-BioPerl-Run-1.007003 => SHA256 Checksum OK for BioPerl-Run-1.007003.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for p5-BioPerl-Run-1.007003 ===> Applying ports patches for p5-BioPerl-Run-1.007003 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-Run-1.007003 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 perl5-5.28.2... `-- Extracting perl5-5.28.2: .......... done Extracting p5-Algorithm-Diff-1.1903: .......... done Message from perl5-5.28.2: 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-1.007003 depends on package: p5-Algorithm-Diff>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007003 ===> p5-BioPerl-Run-1.007003 depends on package: p5-Bio-Cluster>=0 - not found ===> Installing existing package /packages/All/p5-Bio-Cluster-1.7.3.txz Installing p5-Bio-Cluster-1.7.3... `-- Installing p5-BioPerl-1.007005... | `-- Installing p5-DBI-1.642... | `-- Extracting p5-DBI-1.642: .......... 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-0.17027... | `-- Extracting p5-Error-0.17027: ......... done | `-- Installing p5-GD-2.71... | | `-- Installing libgd-2.2.5_1,1... | | `-- Installing fontconfig-2.12.6,1... | | | `-- Installing expat-2.2.6_1... | | | `-- Extracting expat-2.2.6_1: .......... done | | | `-- Installing freetype2-2.10.0... | | | `-- Extracting freetype2-2.10.0: .......... 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-2.0.2... | | `-- Extracting jpeg-turbo-2.0.2: .......... done | | `-- Installing png-1.6.37... | | `-- Extracting png-1.6.37: .......... done | | `-- Installing tiff-4.0.10_1... | | | `-- Installing jbigkit-2.1_1... | | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Extracting tiff-4.0.10_1: .......... done | | `-- Installing webp-1.0.2... | | | `-- Installing giflib-5.1.9... | | | `-- Extracting giflib-5.1.9: .......... done | | `-- Extracting webp-1.0.2: .......... done | | `-- Extracting libgd-2.2.5_1,1: .......... done | `-- Extracting p5-GD-2.71: .......... 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-HTTP-Message-6.18... | | `-- Installing p5-Encode-Locale-1.05... | | `-- Extracting p5-Encode-Locale-1.05: ....... done | | `-- Installing p5-HTTP-Date-6.02_1... | | `-- Extracting p5-HTTP-Date-6.02_1: ....... done | | `-- Installing p5-IO-HTML-1.001_1... | | `-- Extracting p5-IO-HTML-1.001_1: ....... done | | `-- Installing p5-LWP-MediaTypes-6.04... | | `-- Extracting p5-LWP-MediaTypes-6.04: ........ done | | `-- Installing p5-URI-1.76... | | `-- Extracting p5-URI-1.76: .......... done | `-- Extracting p5-HTTP-Message-6.18: .......... done | `-- Installing p5-IO-stringy-2.111... | `-- Extracting p5-IO-stringy-2.111: .......... 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-List-MoreUtils-0.428... | | `-- Installing p5-Exporter-Tiny-1.002001... | | `-- Extracting p5-Exporter-Tiny-1.002001: .......... done | | `-- Installing p5-List-MoreUtils-XS-0.428... | | `-- Extracting p5-List-MoreUtils-XS-0.428: ....... done | `-- Extracting p5-List-MoreUtils-0.428: .......... done | `-- Installing p5-Module-Build-0.4229... | `-- Extracting p5-Module-Build-0.4229: .......... done | `-- Installing p5-Set-Scalar-1.29... | `-- Extracting p5-Set-Scalar-1.29: .......... done | `-- Installing p5-Test-Most-0.35... | | `-- Installing p5-Exception-Class-1.44... | | `-- Installing p5-Class-Data-Inheritable-0.08_1... | | `-- Extracting p5-Class-Data-Inheritable-0.08_1: ....... done | | `-- Installing p5-Devel-StackTrace-2.04... | | `-- Extracting p5-Devel-StackTrace-2.04: ........ done | | `-- Extracting p5-Exception-Class-1.44: ......... done | | `-- Installing p5-Test-Deep-1.128... | | `-- Extracting p5-Test-Deep-1.128: .......... done | | `-- Installing p5-Test-Differences-0.650,1... | | `-- Installing p5-Text-Diff-1.45... | | `-- Extracting p5-Text-Diff-1.45: .......... done | | `-- Extracting p5-Test-Differences-0.650,1: ....... done | | `-- Installing p5-Test-Exception-0.43... | | `-- Installing p5-Sub-Uplevel-0.2800... | | `-- Extracting p5-Sub-Uplevel-0.2800: ....... done | | `-- Extracting p5-Test-Exception-0.43: ....... done | | `-- Installing p5-Test-Warn-0.36... | | `-- Extracting p5-Test-Warn-0.36: ....... done | `-- Extracting p5-Test-Most-0.35: ......... done | `-- Installing p5-Test-RequiresInternet-0.05... | `-- Extracting p5-Test-RequiresInternet-0.05: ....... done | `-- Installing p5-XML-DOM-1.44_1... | | `-- Installing p5-XML-Parser-2.44... | | `-- Extracting p5-XML-Parser-2.44: .......... done | | `-- Installing p5-XML-RegExp-0.04_1... | | `-- Extracting p5-XML-RegExp-0.04_1: ....... done | | `-- Installing p5-libwww-6.39... | | `-- 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-File-Listing-6.04_1... | | `-- Extracting p5-File-Listing-6.04_1: ....... done | | `-- 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 | | `-- Installing p5-HTTP-Cookies-6.04... | | `-- Extracting p5-HTTP-Cookies-6.04: .......... done | | `-- Installing p5-HTTP-Daemon-6.04... | | `-- Extracting p5-HTTP-Daemon-6.04: ....... done | | `-- Installing p5-HTTP-Negotiate-6.01_1... | | `-- Extracting p5-HTTP-Negotiate-6.01_1: ....... done | | `-- Installing p5-Net-HTTP-6.19... | | | `-- Installing p5-IO-Socket-SSL-2.066... | | | `-- Installing p5-IO-Socket-INET6-2.72_1... | | | | `-- Installing p5-Socket6-0.29... | | | | `-- Extracting p5-Socket6-0.29: ....... done | | | `-- Extracting p5-IO-Socket-INET6-2.72_1: ....... done | | | `-- Installing p5-Mozilla-CA-20180117... | | | `-- Extracting p5-Mozilla-CA-20180117: ........ done | | | `-- Installing p5-Net-SSLeay-1.85... | | | | `-- Installing libressl-2.9.2... | | | | `-- Extracting libressl-2.9.2: .......... done | | | `-- Extracting p5-Net-SSLeay-1.85: .......... done | | | `-- Extracting p5-IO-Socket-SSL-2.066: .......... done | | `-- Extracting p5-Net-HTTP-6.19: .......... done | | `-- Installing p5-Try-Tiny-0.30... | | `-- Extracting p5-Try-Tiny-0.30: ...... done | | `-- Installing p5-WWW-RobotRules-6.02_1... | | `-- Extracting p5-WWW-RobotRules-6.02_1: ......... done | | `-- Extracting p5-libwww-6.39: .......... 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-2.0134,1... | | `-- Installing libxml2-2.9.9... | | `-- Extracting libxml2-2.9.9: .......... done | | `-- Installing p5-XML-NamespaceSupport-1.12... | | `-- Extracting p5-XML-NamespaceSupport-1.12: ....... done | | `-- Installing p5-XML-SAX-1.02... | | `-- Installing p5-XML-SAX-Base-1.09... | | `-- Extracting p5-XML-SAX-Base-1.09: .......... done | | `-- Extracting p5-XML-SAX-1.02: .......... done could not find ParserDetails.ini in /usr/local/lib/perl5/site_perl/XML/SAX | `-- Extracting p5-XML-LibXML-2.0134,1: .......... 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-Twig-3.52... | | `-- Installing p5-HTML-Tree-5.07... | | `-- Extracting p5-HTML-Tree-5.07: .......... done | | `-- Installing p5-Text-Iconv-1.7_3... | | `-- Installing libiconv-1.14_11... | | `-- Extracting libiconv-1.14_11: .......... done | | `-- 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-XPath-1.44... | | `-- Extracting p5-XML-XPath-1.44: .......... done | `-- Extracting p5-XML-Twig-3.52: .......... done | `-- Installing p5-XML-Writer-0.625_1... | `-- Extracting p5-XML-Writer-0.625_1: ...... done | `-- Installing p5-YAML-1.29... | `-- Extracting p5-YAML-1.29: .......... done `-- Extracting p5-BioPerl-1.007005: .......... done Extracting p5-Bio-Cluster-1.7.3: .......... done Message from freetype2-2.10.0: 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/site/index.html, if documentation was installed). ===> p5-BioPerl-Run-1.007003 depends on package: p5-Bio-Cluster>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007003 ===> p5-BioPerl-Run-1.007003 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-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-Bio-FeatureIO-1.6.905: .......... done ===> p5-BioPerl-Run-1.007003 depends on package: p5-Bio-FeatureIO>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007003 ===> p5-BioPerl-Run-1.007003 depends on package: p5-BioPerl>=1.007000 - found ===> p5-BioPerl-Run-1.007003 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-2.24... `-- Extracting p5-Config-Tiny-2.24: ....... done `-- Installing p5-Cpanel-JSON-XS-4.12... `-- Extracting p5-Cpanel-JSON-XS-4.12: .......... done `-- Installing p5-Module-Pluggable-5.2... `-- Extracting p5-Module-Pluggable-5.2: .......... 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-YAML-LibYAML-0.79... `-- Extracting p5-YAML-LibYAML-0.79: .......... done Extracting p5-Config-Any-0.32: .......... done ===> p5-BioPerl-Run-1.007003 depends on package: p5-Config-Any>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007003 ===> p5-BioPerl-Run-1.007003 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-1.007003 depends on package: p5-File-Sort>=0 - found ===> Returning to build of p5-BioPerl-Run-1.007003 ===> p5-BioPerl-Run-1.007003 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-IPC-Run>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: perl5>=5.28.r1<5.29 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-Module-Build>=0.4206 - found ===> p5-BioPerl-Run-1.007003 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for p5-BioPerl-Run-1.007003 - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.007003' -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for p5-BioPerl-Run-1.007003 Building BioPerl-Run -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> p5-BioPerl-Run-1.007003 depends on package: p5-Algorithm-Diff>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-Bio-Cluster>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-Bio-FeatureIO>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-BioPerl>=1.007000 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-Config-Any>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-File-Sort>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-IO-String>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-IPC-Run>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: p5-XML-Twig>=0 - found ===> p5-BioPerl-Run-1.007003 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for p5-BioPerl-Run-1.007003 ===> Generating temporary packing list Building BioPerl-Run Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/ESoap.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/ESoap/WSDL.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/Result.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Glimmer.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/EMBOSSacd.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/RNAMotif.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/Vista.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Infernal.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/BEDTools.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/Match.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/BlastPlus.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/Profile.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/Primer3.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/Eponine.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Ensembl.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/Pseudowise.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/StandAloneBlastPlus.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/Coil.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/FootPrinter.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/Seg.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/EMBOSSApplication.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/Prints.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/MCS.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Hmmer.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/Genscan.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/QuickTree.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/SLR.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Raxml.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/FastTree.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Gerp.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Semphy.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phyml.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/LVB.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Samtools/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/BEDTools/Config.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/Analysis/soap.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Probalign.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/DBA.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Muscle.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Exonerate.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Kalign.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Blat.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Sim4.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Gmap.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Lagan.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Amap.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Probcons.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Proda.pm Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/MAFFT.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/Factory/EMBOSS.pm 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::Tools::Run::Tmhmm.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::StandAloneBlastPlus.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::Samtools::Config.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Signalp.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::Tools::Run::Promoterwise.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::TribeMCL.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::Prints.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::species.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Simprot.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::Primer3.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::QuickTree.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::RNAMotif.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::EMBOSS.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::Phylo::Semphy.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::Tools::Run::RepeatMasker.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::StandAloneBlastPlus::BlastMethods.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::tRNAscanSE.3 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::Samtools.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::Alignment::Gmap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::SLR.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Vista.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Profile.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Exonerate.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::DB::SoapEUtilities::Result.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::DBA.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::StandAloneNCBIBlast.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities.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::DB::SoapEUtilities::FetchAdaptor::seq.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::LVB.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::EMBOSSacd.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::Phylo::Phast::PhastCons.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.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::Glimmer.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Genemark.3 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::Pal2Nal.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Muscle.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Genewise.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::Phylo::Phylip::Consense.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::BEDTools.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.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::Phylo::Phylip::SeqBoot.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Genscan.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::ERPIN.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::Tools::Run::Analysis::soap.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::BEDTools::Config.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::Phylo::Hyphy::Modeltest.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::Alignment::Proda.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Gerp.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::Alignment::MSAProbs.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::FootPrinter.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::FastTree.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::Njtree::Best.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Probcons.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phyml.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Probalign.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::MCS.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::Phylo::Phylip::ProtPars.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::EMBOSSApplication.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Eponine.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Match.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Hmmer.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::Infernal.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::BlastPlus.3 Installing /construction/biology/p5-BioPerl-Run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3 install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/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-1.007003/scripts/panalysis.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_panalysis install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/scripts/papplmaker.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_papplmaker install -m 555 /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/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-1.007003/scripts/run_protdist.PLS /construction/biology/p5-BioPerl-Run/stage/usr/local/bin/bp_run_protdist cd /construction/biology/p5-BioPerl-Run/BioPerl-Run-1.007003 && install -m 0644 AUTHORS Changes INSTALL.PROGRAMS 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-1.007003 file sizes/checksums [209]: ... done packing files [209]: ... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:29:08 UTC Duration: 00:00:27