=> Building biology/p5-bioperl-run build started at Sat Oct 8 13:11:17 PDT 2016 port directory: /usr/ports/biology/p5-bioperl-run building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 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/Release46-default/ref/../02//usr/ports/biology/p5-bioperl-run/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400600 ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/Release46-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-run-1.6.901_1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/Release46-default/ref/.p/pool MASTERNAME=Release46-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-run-1.6.901_1: DOCS=on: Build and/or install documentation ===> 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/5.20" --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-run/stage --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-run XDG_CONFIG_HOME=/wrkdirs/biology/p5-bioperl-run HOME=/wrkdirs/biology/p5-bioperl-run 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-run XDG_CONFIG_HOME=/wrkdirs/biology/p5-bioperl-run HOME=/wrkdirs/biology/p5-bioperl-run 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=4.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 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/5.20 PROFILE="@comment " DOCSDIR="share/doc/bioperl-run" EXAMPLESDIR="share/examples/bioperl-run" DATADIR="share/bioperl-run" WWWDIR="www/bioperl-run" ETCDIR="etc/bioperl-run" --End PLIST_SUB-- --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 --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 GPLv3 accepted by the user =========================================================================== =================================================== ===> p5-bioperl-run-1.6.901_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> p5-bioperl-run-1.6.901_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-bioperl-run-1.6.901_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 GPLv3 accepted by the user ===> Fetching all distfiles required by p5-bioperl-run-1.6.901_1 for building =========================================================================== =================================================== ===> License ART10 GPLv3 accepted by the user ===> Fetching all distfiles required by p5-bioperl-run-1.6.901_1 for building => SHA256 Checksum OK for bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 GPLv3 accepted by the user ===> Fetching all distfiles required by p5-bioperl-run-1.6.901_1 for building ===> Extracting for p5-bioperl-run-1.6.901_1 => SHA256 Checksum OK for bioperl-bioperl-run-1.6.901-96ccd93_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for p5-bioperl-run-1.6.901_1 ===> Applying ports patches for p5-bioperl-run-1.6.901_1 =========================================================================== =================================================== ===> p5-bioperl-run-1.6.901_1 depends on package: p5-bioperl>=1.6.0 - not found ===> Installing existing package /packages/All/p5-bioperl-1.6.924_4.txz Installing p5-bioperl-1.6.924_4... `-- Installing p5-Set-Scalar-1.26_1... | `-- Installing perl5-5.20.3_15... | `-- Extracting perl5-5.20.3_15: .......... done `-- Extracting p5-Set-Scalar-1.26_1: .......... 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-URI-1.71... `-- Extracting p5-URI-1.71: .......... done `-- Installing p5-XML-DOM-1.44_1... | `-- Installing p5-libwww-6.15... | | `-- Installing p5-Net-HTTP-6.09... | | `-- Installing p5-IO-Socket-SSL-2.038... | | | `-- Installing p5-Net-SSLeay-1.78... | | | `-- Extracting p5-Net-SSLeay-1.78: .......... done | | | `-- Installing p5-IO-Socket-IP-0.37_1... | | | `-- Extracting p5-IO-Socket-IP-0.37_1: ....... done | | | `-- Installing p5-Mozilla-CA-20160104... | | | `-- Extracting p5-Mozilla-CA-20160104: ........ done | | | `-- Installing 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Extracting p5-XML-DOM-1.44_1: .......... done `-- Installing p5-SOAP-Lite-1.20... | `-- Installing p5-IO-SessionData-1.03_1... | `-- Extracting p5-IO-SessionData-1.03_1: ....... done | `-- Installing p5-Task-Weaken-1.04_1... | `-- Extracting p5-Task-Weaken-1.04_1: ... done | `-- Installing p5-LWP-Protocol-https-6.06_1... | `-- Extracting p5-LWP-Protocol-https-6.06_1: ....... done | `-- Installing p5-Class-Inspector-1.28_1... | `-- Extracting p5-Class-Inspector-1.28_1: ......... done | `-- Installing p5-MIME-Tools-5.508,2... | | `-- Installing p5-Mail-Tools-2.14... | | `-- Installing p5-TimeDate-2.30_2,1... | | `-- Extracting p5-TimeDate-2.30_2,1: .......... done | | `-- Extracting p5-Mail-Tools-2.14: .......... done | | `-- Installing p5-Convert-BinHex-1.125... | | `-- Extracting p5-Convert-BinHex-1.125: .......... done | `-- Extracting p5-MIME-Tools-5.508,2: .......... done | `-- Installing p5-XML-Parser-Lite-0.721... | `-- Extracting p5-XML-Parser-Lite-0.721: ....... done `-- Extracting p5-SOAP-Lite-1.20: .......... done `-- Installing p5-HTML-TableExtract-2.13... | `-- Installing p5-HTML-Element-Extended-1.18_1... | | `-- Installing p5-HTML-Tree-5.03_1... | | `-- Extracting p5-HTML-Tree-5.03_1: .......... done | `-- Extracting p5-HTML-Element-Extended-1.18_1: ......... done `-- Extracting p5-HTML-TableExtract-2.13: ....... done `-- Installing p5-Sort-Naturally-1.03_1... `-- Extracting p5-Sort-Naturally-1.03_1: ....... done `-- Installing p5-XML-LibXML-2.0126,1... | `-- Installing libxml2-2.9.4... | `-- Extracting libxml2-2.9.4: .......... done | `-- 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-2.0126,1: .......... done `-- Installing p5-Text-Shellwords-1.08_1... `-- Extracting p5-Text-Shellwords-1.08_1: ....... done `-- Installing p5-DBD-mysql-4.036... | `-- Installing mysql56-client-5.6.33... | | `-- Installing libedit-3.1.20150325_2,1... | | `-- Installing ncurses-6.0_5... | | `-- Extracting ncurses-6.0_5: .......... done | | `-- Extracting libedit-3.1.20150325_2,1: .......... done | `-- Extracting mysql56-client-5.6.33: .......... done | `-- Installing p5-DBI-1.636... | `-- Extracting p5-DBI-1.636: .......... done `-- Extracting p5-DBD-mysql-4.036: .......... 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-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 `-- Installing p5-Test-Most-0.34_1... | `-- Installing p5-Test-Warn-0.30_2... | | `-- Installing 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done | `-- Extracting p5-Test-Deep-1.123: .......... done `-- Extracting p5-Test-Most-0.34_1: ..... done `-- Installing p5-Convert-Binary-C-0.78... `-- Extracting p5-Convert-Binary-C-0.78: .......... done `-- Installing p5-GD-SVG-0.33_6... | `-- Installing p5-SVG-2.64... | `-- Extracting p5-SVG-2.64: .......... done | `-- Installing p5-GD-2.56_3... | | `-- Installing libgd-2.2.3,1... | | `-- Installing fontconfig-2.12.1,1... | | | `-- 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-1.4.2... | | `-- Extracting jpeg-turbo-1.4.2: .......... done | | `-- Installing tiff-4.0.6_2... | | | `-- Installing jbigkit-2.1_1... | | | `-- Extracting jbigkit-2.1_1: .......... done | | `-- Extracting tiff-4.0.6_2: .......... done | | `-- Installing png-1.6.23... | | `-- Extracting png-1.6.23: .......... done | | `-- Extracting libgd-2.2.3,1: .......... done | `-- Extracting p5-GD-2.56_3: .......... done `-- Extracting p5-GD-SVG-0.33_6: ....... done `-- 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... | `-- Extracting p5-Statistics-Descriptive-3.0609: ......... 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 `-- Installing p5-XML-Twig-3.49... | `-- Installing p5-Tie-IxHash-1.23_1... | `-- Extracting p5-Tie-IxHash-1.23_1: ... done | `-- Installing p5-Text-Iconv-1.7_3... | | `-- Installing libiconv-1.14_9... | | `-- Extracting libiconv-1.14_9: .......... done | `-- Extracting p5-Text-Iconv-1.7_3: ..... done | `-- Installing p5-XML-XPath-1.37... | `-- Extracting p5-XML-XPath-1.37: .......... done `-- Extracting p5-XML-Twig-3.49: .......... done `-- Installing p5-Error-0.17024... `-- Extracting p5-Error-0.17024: ......... done `-- Installing p5-Math-Random-0.72... `-- Extracting p5-Math-Random-0.72: ........ done `-- Installing p5-GraphViz-2.21... | `-- Installing graphviz-2.38.0_13... | | `-- Installing libXt-1.1.5,1... | | `-- Installing xproto-7.0.28... | | `-- Extracting xproto-7.0.28: .......... 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 libX11-1.6.3,1... | | | `-- Installing kbproto-1.0.7... | | | `-- Extracting 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......... done | | `-- Installing harfbuzz-1.3.2... | | | `-- 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-0.0.2_1... | | | | `-- Extracting libdevq-0.0.2_1: ....... done | | | | `-- Installing libXdamage-1.1.4_3... | | | | `-- Installing libXfixes-5.0.1_3... | | | | | `-- Installing fixesproto-5.0... | | | | | `-- Extracting fixesproto-5.0: .... done | | | | `-- Extracting libXfixes-5.0.1_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: .......... 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p5-Text-Tabs+Wrap-2013.0523_1: ..... done Extracting p5-bioperl-1.6.924_4: .......... done Message from perl5-5.20.3_15: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from ncurses-6.0_5: ===> 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-5.6.33: * * * * * * * * * * * * * * * * * * * * * * * * Please be aware the database client is vulnerable to CVE-2015-3152 - SSL Downgrade aka "BACKRONYM". You may find more information at the following URL: http://www.vuxml.org/freebsd/36bd352d-299b-11e5-86ff-14dae9d210b8.html Although this database client is not listed as "affected", it is vulnerable and will not be receiving a patch. Please take note of this when deploying this software. * * * * * * * * * * * * * * * * * * * * * * * * Message from python27-2.7.12: =========================================================================== 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-2.35: Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===> p5-bioperl-run-1.6.901_1 depends on package: p5-bioperl>=1.6.0 - found ===> Returning to build of p5-bioperl-run-1.6.901_1 ===> p5-bioperl-run-1.6.901_1 depends on package: p5-IPC-Run>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-Algorithm-Diff>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-XML-Twig>=0 - found ===> p5-bioperl-run-1.6.901_1 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-1.6.901_1 depends on package: p5-File-Sort>=0 - found ===> Returning to build of p5-bioperl-run-1.6.901_1 ===> p5-bioperl-run-1.6.901_1 depends on package: p5-Config-Any>=0 - not found ===> Installing existing package /packages/All/p5-Config-Any-0.27.txz Installing p5-Config-Any-0.27... `-- Installing p5-Config-Tiny-2.23... `-- Extracting p5-Config-Tiny-2.23: ....... done `-- Installing p5-Config-General-2.63... `-- Extracting p5-Config-General-2.63: .......... done `-- Installing p5-JSON-XS-3.02... | `-- 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-3.02: .......... done `-- Installing p5-Module-Pluggable-5.2... `-- Extracting p5-Module-Pluggable-5.2: .......... done `-- Installing p5-YAML-LibYAML-0.59_1... `-- Extracting p5-YAML-LibYAML-0.59_1: .......... done Extracting p5-Config-Any-0.27: .......... done ===> p5-bioperl-run-1.6.901_1 depends on package: p5-Config-Any>=0 - found ===> Returning to build of p5-bioperl-run-1.6.901_1 ===> p5-bioperl-run-1.6.901_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... `-- Installing p5-CPAN-Meta-2.150005... `-- Extracting p5-CPAN-Meta-2.150005: .......... done Extracting p5-Module-Build-0.4220: .......... done ===> p5-bioperl-run-1.6.901_1 depends on package: p5-Module-Build>=0.4206 - found ===> Returning to build of p5-bioperl-run-1.6.901_1 ===> p5-bioperl-run-1.6.901_1 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for p5-bioperl-run-1.6.901_1 Can't find dist packages without a MANIFEST file Run 'Build manifest' to generate one WARNING: Possible missing or corrupt 'MANIFEST' file. Nothing to enter for 'provides' field in metafile. - will not run internet-requiring tests Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'BioPerl-Run' version '1.006900' =========================================================================== =================================================== ===> Building for p5-bioperl-run-1.6.901_1 Building BioPerl-Run (cd /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93 && /usr/local/bin/perl ./Build manifest) File 'MANIFEST.SKIP' does not exist: Creating a temporary 'MANIFEST.SKIP' Added to MANIFEST: AUTHORS Added to MANIFEST: Build.PL Added to MANIFEST: Build.PL.orig Added to MANIFEST: Changes Added to MANIFEST: DEPENDENCIES Added to MANIFEST: INSTALL Added to MANIFEST: INSTALL.PROGRAMS Added to MANIFEST: INSTALL.SKIP Added to MANIFEST: lib/Bio/DB/ESoap.pm Added to MANIFEST: lib/Bio/DB/ESoap/WSDL.pm Added to MANIFEST: lib/Bio/DB/SoapEUtilities.pm Added to MANIFEST: lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Added to 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MANIFEST: lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/LVB.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Njtree/Best.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/Base.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/PhyloBase.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Phyml.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/QuickTree.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Raxml.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/Semphy.pm Added to MANIFEST: lib/Bio/Tools/Run/Phylo/SLR.pm Added to MANIFEST: lib/Bio/Tools/Run/Primate.pm Added to MANIFEST: lib/Bio/Tools/Run/Primer3.pm Added to MANIFEST: lib/Bio/Tools/Run/Prints.pm Added to MANIFEST: lib/Bio/Tools/Run/Profile.pm Added to MANIFEST: lib/Bio/Tools/Run/Promoterwise.pm Added to MANIFEST: lib/Bio/Tools/Run/Pseudowise.pm Added to MANIFEST: lib/Bio/Tools/Run/RepeatMasker.pm Added to MANIFEST: lib/Bio/Tools/Run/RNAMotif.pm Added to MANIFEST: lib/Bio/Tools/Run/Samtools.pm Added to MANIFEST: lib/Bio/Tools/Run/Samtools/Config.pm Added to MANIFEST: lib/Bio/Tools/Run/Seg.pm Added to MANIFEST: lib/Bio/Tools/Run/Signalp.pm Added to MANIFEST: lib/Bio/Tools/Run/Simprot.pm Added to MANIFEST: lib/Bio/Tools/Run/StandAloneBlastPlus.pm Added to MANIFEST: lib/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Added to MANIFEST: lib/Bio/Tools/Run/TigrAssembler.pm Added to MANIFEST: lib/Bio/Tools/Run/Tmhmm.pm Added to MANIFEST: lib/Bio/Tools/Run/TribeMCL.pm Added to MANIFEST: lib/Bio/Tools/Run/tRNAscanSE.pm Added to MANIFEST: lib/Bio/Tools/Run/Vista.pm Added to MANIFEST: LICENSE Added to MANIFEST: MANIFEST Added to MANIFEST: README Added to MANIFEST: scripts/bioperl_application_installer.PLS Added to MANIFEST: scripts/multi_hmmsearch.PLS Added to MANIFEST: scripts/panalysis.PLS Added to MANIFEST: scripts/papplmaker.PLS Added to MANIFEST: scripts/run_neighbor.PLS Added to MANIFEST: scripts/run_protdist.PLS Added to MANIFEST: t/Amap.t Added to MANIFEST: t/Analysis_soap.t Added to MANIFEST: t/AnalysisFactory_soap.t Added to MANIFEST: t/BEDTools.t Added to MANIFEST: t/Blat.t Added to MANIFEST: t/Bowtie.t Added to MANIFEST: t/BWA.t Added to MANIFEST: t/Cap3.t Added to MANIFEST: t/Clustalw.t Added to MANIFEST: t/Coil.t Added to MANIFEST: t/Consense.t Added to MANIFEST: t/data/1.bg Added to MANIFEST: t/data/2.bg Added to MANIFEST: t/data/219877.cdna.fasta Added to MANIFEST: t/data/219877.tree Added to MANIFEST: t/data/277523.cdna.fasta Added to MANIFEST: t/data/277523.tree Added to MANIFEST: t/data/3.bg Added to MANIFEST: t/data/amino.fa Added to MANIFEST: t/data/apes.multi_fasta Added to MANIFEST: t/data/apes.newick Added to MANIFEST: t/data/blat_dna.fa Added to MANIFEST: t/data/bowtie/indexes/e_coli.1.ebwt Added to MANIFEST: t/data/bowtie/indexes/e_coli.2.ebwt Added to MANIFEST: t/data/bowtie/indexes/e_coli.3.ebwt Added to MANIFEST: t/data/bowtie/indexes/e_coli.4.ebwt Added to MANIFEST: 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t/data/cysprot.raxml.tre Added to MANIFEST: t/data/cysprot.stockholm Added to MANIFEST: t/data/cysprot1a.fa Added to MANIFEST: t/data/cysprot1a.msf Added to MANIFEST: t/data/cysprot1b.fa Added to MANIFEST: t/data/cysprot1b.msf Added to MANIFEST: t/data/dba1a.fa Added to MANIFEST: t/data/dba1b.fa Added to MANIFEST: t/data/dba2.fa Added to MANIFEST: t/data/dna1.fa Added to MANIFEST: t/data/dna2.fa Added to MANIFEST: t/data/dna_seqs1.phy Added to MANIFEST: t/data/e_coli.bed3 Added to MANIFEST: t/data/e_coli_1.bedpe Added to MANIFEST: t/data/e_coli_2.bedpe Added to MANIFEST: t/data/ecolitst.fa Added to MANIFEST: t/data/efetch_seq.wsdl Added to MANIFEST: t/data/elink_result.xml Added to MANIFEST: t/data/eponine.fa Added to MANIFEST: t/data/esearch_result.xml Added to MANIFEST: t/data/esum_result.xml Added to MANIFEST: t/data/eutils.wsdl Added to MANIFEST: t/data/exonerate_cdna.fa Added to MANIFEST: t/data/exonerate_cdna_rev.fa Added to MANIFEST: t/data/exonerate_genomic.fa Added to 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to MANIFEST: t/data/human.genomic Added to MANIFEST: t/data/hyphy1.fasta Added to MANIFEST: t/data/hyphy1.tree Added to MANIFEST: t/data/lagan_dna.fa Added to MANIFEST: t/data/longnames.aln Added to MANIFEST: t/data/lvb.fa Added to MANIFEST: t/data/lvb_sequential.phy Added to MANIFEST: t/data/neighbor.dist Added to MANIFEST: t/data/new_dna.fa Added to MANIFEST: t/data/new_pep.fa Added to MANIFEST: t/data/njtree_aln2.nucl.mfa Added to MANIFEST: t/data/NM_002254.gb Added to MANIFEST: t/data/NM_002254.tfa Added to MANIFEST: t/data/pal2nal.aln Added to MANIFEST: t/data/pal2nal.nuc Added to MANIFEST: t/data/pfam_sample_R11 Added to MANIFEST: t/data/Phrap.fa Added to MANIFEST: t/data/primate_query.fa Added to MANIFEST: t/data/primate_target.fa Added to MANIFEST: t/data/Primer3.fa Added to MANIFEST: t/data/prints.dat Added to MANIFEST: t/data/Prints_prot.FastA Added to MANIFEST: t/data/profile_prot.FastA Added to MANIFEST: t/data/prosite.dat Added to MANIFEST: t/data/protpars.phy Added to 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t/data/taxdump/names.dmp Added to MANIFEST: t/data/taxdump/nodes.dmp Added to MANIFEST: t/data/test-aln.msf Added to MANIFEST: t/data/test-query.fas Added to MANIFEST: t/data/test-spa-p.fas Added to MANIFEST: t/data/test-spa.fas Added to MANIFEST: t/data/test.txt Added to MANIFEST: t/data/test_prot.FastA Added to MANIFEST: t/data/testaln.phylip Added to MANIFEST: t/data/transfac.dat Added to MANIFEST: t/data/tree_of_life Added to MANIFEST: t/data/treefile.example Added to MANIFEST: t/data/TribeMCL.bls Added to MANIFEST: t/data/TribeMCL.desc Added to MANIFEST: t/data/vista.cls Added to MANIFEST: t/data/vista.gff Added to MANIFEST: t/data/xprt.gb Added to MANIFEST: t/DBA.t Added to MANIFEST: t/DrawGram.t Added to MANIFEST: t/DrawTree.t Added to MANIFEST: t/EMBOSS.t Added to MANIFEST: t/Ensembl.t Added to MANIFEST: t/Eponine.t Added to MANIFEST: t/Exonerate.t Added to MANIFEST: t/FastTree.t Added to MANIFEST: t/FootPrinter.t Added to MANIFEST: t/Genemark.hmm.prokaryotic.t Added to MANIFEST: t/Genewise.t Added to MANIFEST: t/Genscan.t Added to MANIFEST: t/Gerp.t Added to MANIFEST: t/Glimmer2.t Added to MANIFEST: t/Glimmer3.t Added to MANIFEST: t/gmap-run.t Added to MANIFEST: t/Gumby.t Added to MANIFEST: t/Hmmer.t Added to MANIFEST: t/Hyphy.t Added to MANIFEST: t/Infernal.t Added to MANIFEST: t/Kalign.t Added to MANIFEST: t/Lagan.t Added to MANIFEST: t/lib/Sub/Uplevel.pm Added to MANIFEST: t/lib/Test/Builder.pm Added to MANIFEST: t/lib/Test/Builder/Module.pm Added to MANIFEST: t/lib/Test/Builder/Tester.pm Added to MANIFEST: t/lib/Test/Exception.pm Added to MANIFEST: t/lib/Test/Harness.pm Added to MANIFEST: t/lib/Test/Harness/Assert.pm Added to MANIFEST: t/lib/Test/Harness/Iterator.pm Added to MANIFEST: t/lib/Test/Harness/Point.pm Added to MANIFEST: t/lib/Test/Harness/Results.pm Added to MANIFEST: t/lib/Test/Harness/Straps.pm Added to MANIFEST: t/lib/Test/Harness/TAP.pod Added to MANIFEST: t/lib/Test/Harness/Util.pm Added to MANIFEST: t/lib/Test/More.pm Added to MANIFEST: t/lib/Test/Simple.pm Added to MANIFEST: t/lib/Test/Tutorial.pod Added to MANIFEST: t/lib/Test/Warn.pm Added to MANIFEST: t/LVB.t Added to MANIFEST: t/MAFFT.t Added to MANIFEST: t/Maq.t Added to MANIFEST: t/Match.t Added to MANIFEST: t/MCS.t Added to MANIFEST: t/Mdust.t Added to MANIFEST: t/Meme.t Added to MANIFEST: t/Minimo.t Added to MANIFEST: t/Molphy.t Added to MANIFEST: t/MSAProbs.t Added to MANIFEST: t/Muscle.t Added to MANIFEST: t/Neighbor.t Added to MANIFEST: t/Newbler.t Added to MANIFEST: t/Njtree.t Added to MANIFEST: t/Pal2Nal.t Added to MANIFEST: t/PAML.t Added to MANIFEST: t/PhastCons.t Added to MANIFEST: t/Phrap.t Added to MANIFEST: t/Phyml.t Added to MANIFEST: t/Primate.t Added to MANIFEST: t/Primer3.t Added to MANIFEST: t/Prints.t Added to MANIFEST: t/Probalign.t Added to MANIFEST: t/Probcons.t Added to MANIFEST: t/Profile.t Added to MANIFEST: t/Promoterwise.t Added to MANIFEST: t/ProtDist.t Added to MANIFEST: t/ProtPars.t Added to MANIFEST: t/Pseudowise.t Added to MANIFEST: t/QuickTree.t Added to MANIFEST: t/Raxml.t Added to MANIFEST: t/RepeatMasker.t Added to MANIFEST: t/SABlastPlus.t Added to MANIFEST: t/Samtools.t Added to MANIFEST: t/Seg.t Added to MANIFEST: t/Semphy.t Added to MANIFEST: t/SeqBoot.t Added to MANIFEST: t/Signalp.t Added to MANIFEST: t/Sim4.t Added to MANIFEST: t/Simprot.t Added to MANIFEST: t/SLR.t Added to MANIFEST: t/SoapEU-function.t Added to MANIFEST: t/SoapEU-unit.t Added to MANIFEST: t/StandAloneFasta.t Added to MANIFEST: t/TCoffee.t Added to MANIFEST: t/TigrAssembler.t Added to MANIFEST: t/Tmhmm.t Added to MANIFEST: t/TribeMCL.t Added to MANIFEST: t/tRNAscanSE.t Added to MANIFEST: t/Vista.t =========================================================================== =================================================== ===> p5-bioperl-run-1.6.901_1 depends on package: p5-bioperl>=1.6.0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-IPC-Run>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-Algorithm-Diff>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-XML-Twig>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-File-Sort>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: p5-Config-Any>=0 - found ===> p5-bioperl-run-1.6.901_1 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== ===> Staging for p5-bioperl-run-1.6.901_1 ===> Generating temporary packing list Building BioPerl-Run Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/EMBOSS.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Generic.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/SLR.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Muscle.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Hyphy.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/TCoffee.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Clustalw.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/PAML.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Installer/Probcons.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/ESoap.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/Result.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/GQueryAdaptor.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/DocSumAdaptor.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/LinkAdaptor.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/FetchAdaptor.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/FetchAdaptor/seq.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/SoapEUtilities/FetchAdaptor/species.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/DB/ESoap/WSDL.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Factory/EMBOSS.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/EMBOSSApplication.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/AssemblerBase.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/RNAMotif.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Hmmer.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Prints.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Tmhmm.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Coil.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Profile.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Infernal.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Newbler.pm Installing 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/wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Analysis.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BEDTools.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/EMBOSSacd.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Genscan.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Primate.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneBlastPlus.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BWA.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Pseudowise.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Bowtie.pm Installing 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/wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Primer3.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BEDTools/Config.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Samtools/Config.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BWA/Config.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Exonerate.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/MSAProbs.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/StandAloneFasta.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/DBA.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Blat.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Probalign.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Gmap.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Pal2Nal.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Lagan.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Kalign.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/MAFFT.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Sim4.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Muscle.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Clustalw.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Proda.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Probcons.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/Amap.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Alignment/TCoffee.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Maq/Config.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Analysis/soap.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/AnalysisFactory/soap.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/PhyloBase.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Gumby.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/LVB.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/SLR.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phyml.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Raxml.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Gerp.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/QuickTree.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Semphy.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/FastTree.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phast/PhastCons.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/PAML/Evolver.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/PAML/Yn00.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/PAML/Codeml.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/Base.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/Consense.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/Base.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/FEL.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/REL.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Njtree/Best.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Phylo/Molphy/ProtML.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/BlastPlus/Config.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/Bowtie/Config.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/Bio/Tools/Run/StandAloneBlastPlus/BlastMethods.pm Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Glimmer.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::EMBOSSacd.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Analysis.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::ESoap.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::AssemblerBase.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Maq::Config.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::BWA.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Maq.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Lagan.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::GQueryAdaptor.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::FetchAdaptor::seq.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Installer::Probcons.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Proda.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::AnalysisFactory::soap.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::ESoap::WSDL.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Probcons.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::BlastPlus.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Meme.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::TCoffee.3 Installing 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/wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::BEDTools.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Clustalw.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::ERPIN.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Exonerate.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Pal2Nal.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::LinkAdaptor.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::DB::SoapEUtilities::Result.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::DBA.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Sim4.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Coil.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Gmap.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Bowtie.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Bowtie::Config.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Eponine.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Installer::PAML.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Alignment::Amap.3 Installing 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/wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Factory::EMBOSS.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::FootPrinter.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Genemark.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::Neighbor.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Profile.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::QuickTree.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Seg.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Vista.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Simprot.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Raxml.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::Consense.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Prints.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Samtools.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::SeqBoot.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::SLR.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawGram.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::DrawTree.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::StandAloneBlastPlus.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Pseudowise.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::StandAloneBlastPlus::BlastMethods.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Primer3.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PhyloBase.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Signalp.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtPars.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::PhylipConf.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::tRNAscanSE.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Tmhmm.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Samtools::Config.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Semphy.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Promoterwise.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::TigrAssembler.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phyml.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::Base.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phylip::ProtDist.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::RNAMotif.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::RepeatMasker.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Primate.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::TribeMCL.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Gerp.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::Modeltest.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::LVB.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::FEL.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::Base.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::BatchFile.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PAML::Baseml.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Gumby.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Molphy::ProtML.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phrap.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::REL.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::FastTree.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phast::PhyloFit.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Phast::PhastCons.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Njtree::Best.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::Hyphy::SLAC.3 Installing /wrkdirs/biology/p5-bioperl-run/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3 /bin/cp /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/scripts/bioperl_application_installer.PLS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/bin/bp_bioperl_application_installer /bin/cp /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/scripts/multi_hmmsearch.PLS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/bin/bp_multi_hmmsearch /bin/cp /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/scripts/panalysis.PLS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/bin/bp_panalysis /bin/cp /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/scripts/papplmaker.PLS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/bin/bp_papplmaker /bin/cp /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/scripts/run_neighbor.PLS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/bin/bp_run_neighbor /bin/cp /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/scripts/run_protdist.PLS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/bin/bp_run_protdist install -m 0644 /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/AUTHORS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/share/doc/bioperl-run install -m 0644 /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/Changes /wrkdirs/biology/p5-bioperl-run/stage/usr/local/share/doc/bioperl-run install -m 0644 /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/INSTALL.PROGRAMS /wrkdirs/biology/p5-bioperl-run/stage/usr/local/share/doc/bioperl-run install -m 0644 /wrkdirs/biology/p5-bioperl-run/bioperl-run-96ccd93/README /wrkdirs/biology/p5-bioperl-run/stage/usr/local/share/doc/bioperl-run ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for p5-bioperl-run-1.6.901_1 file sizes/checksums [268]: ... done packing files [268]: ... done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for p5-bioperl-run-1.6.901_1 build of biology/p5-bioperl-run ended at Sat Oct 8 13:12:45 PDT 2016 build time: 00:01:28