=> Building biology/p5-Bio-Phylo build started at Tue Oct 4 19:29:49 PDT 2016 port directory: /usr/ports/biology/p5-Bio-Phylo 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/bleeding-edge-default/ref/../08//usr/ports/biology/p5-Bio-Phylo/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-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-Bio-Phylo-0.58 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- INSTALLDIRS="site" 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-Bio-Phylo XDG_CONFIG_HOME=/wrkdirs/biology/p5-Bio-Phylo HOME=/wrkdirs/biology/p5-Bio-Phylo 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-Bio-Phylo XDG_CONFIG_HOME=/wrkdirs/biology/p5-Bio-Phylo HOME=/wrkdirs/biology/p5-Bio-Phylo TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 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/Bio-Phylo" EXAMPLESDIR="share/examples/Bio-Phylo" DATADIR="share/Bio-Phylo" WWWDIR="www/Bio-Phylo" ETCDIR="etc/Bio-Phylo" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/Bio-Phylo DOCSDIR=/usr/local/share/doc/Bio-Phylo EXAMPLESDIR=/usr/local/share/examples/Bio-Phylo WWWDIR=/usr/local/www/Bio-Phylo ETCDIR=/usr/local/etc/Bio-Phylo --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License ART10 GPLv1 accepted by the user =========================================================================== =================================================== ===> p5-Bio-Phylo-0.58 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-Bio-Phylo-0.58 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of p5-Bio-Phylo-0.58 =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 GPLv1 accepted by the user ===> Fetching all distfiles required by p5-Bio-Phylo-0.58 for building =========================================================================== =================================================== ===> License ART10 GPLv1 accepted by the user ===> Fetching all distfiles required by p5-Bio-Phylo-0.58 for building => SHA256 Checksum OK for Bio-Phylo-0.58.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART10 GPLv1 accepted by the user ===> Fetching all distfiles required by p5-Bio-Phylo-0.58 for building ===> Extracting for p5-Bio-Phylo-0.58 => SHA256 Checksum OK for Bio-Phylo-0.58.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for p5-Bio-Phylo-0.58 =========================================================================== =================================================== ===> p5-Bio-Phylo-0.58 depends on package: p5-GD>=0 - not found ===> Installing existing package /packages/All/p5-GD-2.56_3.txz Installing p5-GD-2.56_3... `-- Installing libgd-2.2.3,1... | `-- Installing fontconfig-2.12.1,1... | | `-- Installing expat-2.2.0... | | `-- Extracting expat-2.2.0: .......... done | | `-- Installing freetype2-2.6.3... | | `-- Extracting freetype2-2.6.3: .......... done | `-- Extracting fontconfig-2.12.1,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded | `-- Installing jpeg-turbo-1.4.2... | `-- 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 `-- Installing perl5-5.20.3_15... `-- Extracting perl5-5.20.3_15: .......... done Extracting p5-GD-2.56_3: .......... 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. ===> p5-Bio-Phylo-0.58 depends on package: p5-GD>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-Math-CDF>=0 - not found ===> Installing existing package /packages/All/p5-Math-CDF-0.1_2.txz Installing p5-Math-CDF-0.1_2... Extracting p5-Math-CDF-0.1_2: ..... done ===> p5-Bio-Phylo-0.58 depends on package: p5-Math-CDF>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-Math-Random>=0 - not found ===> Installing existing package /packages/All/p5-Math-Random-0.72.txz Installing p5-Math-Random-0.72... Extracting p5-Math-Random-0.72: ........ done ===> p5-Bio-Phylo-0.58 depends on package: p5-Math-Random>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-PDF-API2>=0 - not found ===> Installing existing package /packages/All/p5-PDF-API2-2.028.txz Installing p5-PDF-API2-2.028... `-- Installing p5-Font-TTF-1.05... | `-- Installing p5-IO-String-1.08_1... | `-- Extracting p5-IO-String-1.08_1: ... done `-- Extracting p5-Font-TTF-1.05: .......... done Extracting p5-PDF-API2-2.028: .......... done ===> p5-Bio-Phylo-0.58 depends on package: p5-PDF-API2>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-SVG>=0 - not found ===> Installing existing package /packages/All/p5-SVG-2.64.txz Installing p5-SVG-2.64... Extracting p5-SVG-2.64: .......... done ===> p5-Bio-Phylo-0.58 depends on package: p5-SVG>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-SWF-Builder>=0 - not found ===> Installing existing package /packages/All/p5-SWF-Builder-0.16_2.txz Installing p5-SWF-Builder-0.16_2... `-- Installing p5-Math-Bezier-Convert-0.02_1... `-- Extracting p5-Math-Bezier-Convert-0.02_1: ... done `-- Installing p5-SWF-File-0.42_2,1... | `-- Installing p5-Data-TemporaryBag-0.09_1... | `-- Extracting p5-Data-TemporaryBag-0.09_1: ... done `-- Extracting p5-SWF-File-0.42_2,1: .......... done Extracting p5-SWF-Builder-0.16_2: .......... done ===> p5-Bio-Phylo-0.58 depends on package: p5-SWF-Builder>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-LibXML>=0 - not found ===> Installing existing package /packages/All/p5-XML-LibXML-2.0126,1.txz 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 ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-LibXML>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-Twig>=0 - not found ===> Installing existing package /packages/All/p5-XML-Twig-3.49.txz 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-HTML-Tree-5.03_1... | `-- Installing p5-HTML-Parser-3.72... | | `-- Installing p5-HTML-Tagset-3.20_1... | | `-- Extracting p5-HTML-Tagset-3.20_1: ... done | `-- Extracting p5-HTML-Parser-3.72: .......... done `-- Extracting p5-HTML-Tree-5.03_1: .......... done `-- Installing p5-libwww-6.15... | `-- Installing p5-Net-HTTP-6.09... | | `-- Installing p5-URI-1.71... | | `-- Extracting p5-URI-1.71: .......... done | | `-- Installing p5-IO-Socket-SSL-2.038... | | `-- Installing p5-Net-SSLeay-1.78... | | | `-- Installing libressl-2.4.3... | | | `-- Extracting libressl-2.4.3: .......... done | | `-- 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 p5-Socket-2.021... | | `-- Extracting p5-Socket-2.021: ........ done | | `-- Extracting p5-IO-Socket-SSL-2.038: .......... done | `-- Extracting p5-Net-HTTP-6.09: .......... done | `-- Installing p5-HTTP-Daemon-6.01_1... | | `-- Installing p5-HTTP-Message-6.11... | | `-- Installing p5-Encode-Locale-1.05... | | `-- Extracting p5-Encode-Locale-1.05: ... done | | `-- Installing p5-IO-HTML-1.001_1... | | `-- Extracting p5-IO-HTML-1.001_1: ....... done | | `-- Installing p5-HTTP-Date-6.02_1... | | `-- Extracting p5-HTTP-Date-6.02_1: ....... done | | `-- Installing p5-LWP-MediaTypes-6.02_1... | | `-- Extracting p5-LWP-MediaTypes-6.02_1: .... done | | `-- Extracting p5-HTTP-Message-6.11: .......... done | `-- Extracting p5-HTTP-Daemon-6.01_1: ....... done | `-- Installing p5-HTTP-Negotiate-6.01_1... | `-- Extracting p5-HTTP-Negotiate-6.01_1: ....... done | `-- Installing p5-WWW-RobotRules-6.02_1... | `-- Extracting p5-WWW-RobotRules-6.02_1: ..... done | `-- Installing p5-HTTP-Cookies-6.01_1... | `-- Extracting p5-HTTP-Cookies-6.01_1: .......... done | `-- Installing p5-File-Listing-6.04_1... | `-- Extracting p5-File-Listing-6.04_1: ....... done | `-- Installing p5-Authen-NTLM-1.09_1... | | `-- Installing p5-Digest-HMAC-1.03_1... | | `-- Extracting p5-Digest-HMAC-1.03_1: ....... done | `-- Extracting p5-Authen-NTLM-1.09_1: ..... done `-- Extracting p5-libwww-6.15: .......... done `-- Installing p5-XML-Parser-2.44... `-- Extracting p5-XML-Parser-2.44: .......... done `-- Installing p5-XML-XPath-1.37... `-- Extracting p5-XML-XPath-1.37: .......... done Extracting p5-XML-Twig-3.49: .......... done ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-Twig>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-XML2JSON>=0 - not found ===> Installing existing package /packages/All/p5-XML-XML2JSON-0.06_1.txz Installing p5-XML-XML2JSON-0.06_1... `-- Installing p5-YAML-Syck-1.27_1... `-- Extracting p5-YAML-Syck-1.27_1: ........ done Extracting p5-XML-XML2JSON-0.06_1: ....... done ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-XML2JSON>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-bioperl>=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... `-- Extracting p5-Set-Scalar-1.26_1: .......... done `-- Installing p5-Data-Stag-0.14_2... `-- Extracting p5-Data-Stag-0.14_2: .......... done `-- Installing p5-XML-DOM-1.44_1... | `-- Installing p5-libxml-0.08_1... | `-- Extracting p5-libxml-0.08_1: .......... done | `-- Installing p5-XML-RegExp-0.04_1... | `-- Extracting p5-XML-RegExp-0.04_1: ... done `-- Extracting p5-XML-DOM-1.44_1: .......... done `-- 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... | `-- 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-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 p5-Sub-Uplevel-0.2500... | | `-- Extracting p5-Sub-Uplevel-0.2500: ... done | `-- Extracting p5-Test-Warn-0.30_2: ....... done | `-- Installing p5-Exception-Class-1.40... | | `-- Installing p5-Class-Data-Inheritable-0.08_1... | | `-- Extracting p5-Class-Data-Inheritable-0.08_1: ... done | | `-- Installing p5-Devel-StackTrace-2.01... | | `-- Extracting p5-Devel-StackTrace-2.01: ........ done | `-- Extracting p5-Exception-Class-1.40: ......... done | `-- Installing p5-Test-Differences-0.630,1... | | `-- Installing p5-Text-Diff-1.41_1... | | `-- Installing p5-Algorithm-Diff-1.1903... | | `-- Extracting p5-Algorithm-Diff-1.1903: ......... done | | `-- Extracting p5-Text-Diff-1.41_1: .......... done | `-- Extracting p5-Test-Differences-0.630,1: ....... done | `-- Installing p5-Test-Exception-0.43... | `-- Extracting p5-Test-Exception-0.43: ....... done | `-- Installing p5-Test-Deep-1.123... | | `-- Installing p5-Test-Simple-1.302056... | | `-- Extracting p5-Test-Simple-1.302056: .......... 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... `-- 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-Error-0.17024... `-- Extracting p5-Error-0.17024: ......... 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 kbproto-1.0.7: .......... done | | | `-- Installing libXdmcp-1.1.2... | | | `-- Extracting libXdmcp-1.1.2: ......... done | | | `-- Installing libxcb-1.11.1... | | | `-- Installing libpthread-stubs-0.3_6... | | | `-- Extracting libpthread-stubs-0.3_6: ..... done | | | `-- Installing libXau-1.0.8_3... | | | `-- Extracting libXau-1.0.8_3: .......... done | | | `-- Extracting libxcb-1.11.1: .......... done | | `-- Extracting libX11-1.6.3,1: .......... done | | `-- Extracting libXt-1.1.5,1: .......... done | | `-- Installing 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| `-- Installing p5-Tie-ToObject-0.03_2... | | `-- Extracting p5-Tie-ToObject-0.03_2: ... done | `-- Extracting p5-Hash-AutoHash-1.17_1: ....... done | `-- Installing p5-Hash-AutoHash-Args-1.18_1... | `-- Extracting p5-Hash-AutoHash-Args-1.18_1: ......... done `-- Extracting p5-Class-AutoClass-1.56_1: ........ done `-- Installing p5-Spreadsheet-ParseExcel-0.65_2,1... | `-- Installing p5-Digest-Perl-MD5-1.9_1... | `-- Extracting p5-Digest-Perl-MD5-1.9_1: ... done | `-- Installing p5-Crypt-RC4-2.02_1... | `-- Extracting p5-Crypt-RC4-2.02_1: ... done | `-- Installing p5-OLE-Storage_Lite-0.19_1... | `-- Extracting p5-OLE-Storage_Lite-0.19_1: ... done `-- Extracting p5-Spreadsheet-ParseExcel-0.65_2,1: .......... done `-- Installing p5-XML-Simple-2.22... | `-- Installing p5-XML-SAX-Expat-0.51_1... | `-- Extracting p5-XML-SAX-Expat-0.51_1: ....... done `-- Extracting p5-XML-Simple-2.22: ......... done `-- Installing p5-XML-Writer-0.625_1... `-- Extracting p5-XML-Writer-0.625_1: ... done `-- Installing p5-PostScript-0.06_2... `-- Extracting p5-PostScript-0.06_2: ......... done `-- Installing p5-Algorithm-Munkres-0.08_1... `-- Extracting p5-Algorithm-Munkres-0.08_1: ... done `-- Installing p5-Clone-0.38... `-- Extracting p5-Clone-0.38: ..... done `-- Installing p5-YAML-1.14... `-- Extracting p5-YAML-1.14: .......... done `-- Installing p5-Text-Tabs+Wrap-2013.0523_1... `-- Extracting p5-Text-Tabs+Wrap-2013.0523_1: ..... done Extracting p5-bioperl-1.6.924_4: .......... done 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-Bio-Phylo-0.58 depends on package: p5-bioperl>=0 - found ===> Returning to build of p5-Bio-Phylo-0.58 ===> p5-Bio-Phylo-0.58 depends on package: p5-libxml>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for p5-Bio-Phylo-0.58 *** The optional dependency "JSON" can't be loaded. I will continue, but some functionality will not be available. Refer to the Bio::Phylo README file for more information. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Phylo Writing MYMETA.yml and MYMETA.json =========================================================================== =================================================== ===> Building for p5-Bio-Phylo-0.58 --- blib/lib/Bio/.exists --- --- blib/arch/.exists --- --- blib/lib/auto/Bio/Phylo/.exists --- --- blib/arch/auto/Bio/Phylo/.exists --- --- blib/bin/.exists --- --- blib/script/.exists --- --- blib/man1/.exists --- --- blib/man3/.exists --- --- subdirs --- --- dynamic --- --- pm_to_blib --- --- linkext --- --- blibdirs --- --- config --- --- pm_to_blib --- cp lib/Bio/Phylo/NeXML/Writable.pm blib/lib/Bio/Phylo/NeXML/Writable.pm cp lib/Bio/Phylo/Matrices/Datatype/Standard.pm blib/lib/Bio/Phylo/Matrices/Datatype/Standard.pm cp lib/Bio/Phylo/Util/MOP.pm blib/lib/Bio/Phylo/Util/MOP.pm cp lib/Bio/Phylo/Treedrawer/Canvas.pm blib/lib/Bio/Phylo/Treedrawer/Canvas.pm cp lib/Bio/Phylo/Matrices/Datatype/Restriction.pm blib/lib/Bio/Phylo/Matrices/Datatype/Restriction.pm cp lib/Bio/Phylo/Parsers/Taxlist.pm blib/lib/Bio/Phylo/Parsers/Taxlist.pm cp lib/Bio/Phylo/Matrices/Datatype/Continuous.pm blib/lib/Bio/Phylo/Matrices/Datatype/Continuous.pm cp lib/Bio/Phylo/Util/Dependency.pm blib/lib/Bio/Phylo/Util/Dependency.pm cp lib/Bio/Phylo/Forest.pm blib/lib/Bio/Phylo/Forest.pm cp lib/Bio/Phylo/Treedrawer/Abstract.pm blib/lib/Bio/Phylo/Treedrawer/Abstract.pm cp lib/Bio/Phylo/PhyloWS/Service/Tolweb.pm blib/lib/Bio/Phylo/PhyloWS/Service/Tolweb.pm cp lib/Bio/Phylo/Treedrawer/Svg.pm blib/lib/Bio/Phylo/Treedrawer/Svg.pm cp lib/Bio/Phylo/Unparsers/Mrp.pm blib/lib/Bio/Phylo/Unparsers/Mrp.pm cp lib/Bio/Phylo/Matrices/DatumRole.pm blib/lib/Bio/Phylo/Matrices/DatumRole.pm cp lib/Bio/Phylo/NeXML/DOM.pm blib/lib/Bio/Phylo/NeXML/DOM.pm cp lib/Bio/Phylo/NeXML/DOM/Element/Libxml.pm blib/lib/Bio/Phylo/NeXML/DOM/Element/Libxml.pm cp lib/Bio/Phylo/Matrices/Character.pm blib/lib/Bio/Phylo/Matrices/Character.pm cp lib/Bio/Phylo/Matrices.pm blib/lib/Bio/Phylo/Matrices.pm cp lib/Bio/Phylo/Parsers/Ubiocbmeta.pm blib/lib/Bio/Phylo/Parsers/Ubiocbmeta.pm cp lib/Bio/Phylo/Util/Exceptions.pm blib/lib/Bio/Phylo/Util/Exceptions.pm cp lib/Bio/PhyloRole.pm blib/lib/Bio/PhyloRole.pm cp lib/Bio/Phylo/Util/OptionalInterface.pm blib/lib/Bio/Phylo/Util/OptionalInterface.pm cp lib/Bio/Phylo/Unparsers/Fasta.pm blib/lib/Bio/Phylo/Unparsers/Fasta.pm cp lib/Bio/Phylo/EvolutionaryModels.pm blib/lib/Bio/Phylo/EvolutionaryModels.pm cp lib/Bio/Phylo/Matrices/Datatype/Custom.pm blib/lib/Bio/Phylo/Matrices/Datatype/Custom.pm cp lib/Bio/Phylo/Unparsers/Rss1.pm blib/lib/Bio/Phylo/Unparsers/Rss1.pm cp lib/Bio/Phylo/PhyloWS.pm blib/lib/Bio/Phylo/PhyloWS.pm cp lib/Bio/Phylo/Unparsers/Nexml.pm blib/lib/Bio/Phylo/Unparsers/Nexml.pm cp lib/Bio/Phylo/Forest/TreeRole.pm blib/lib/Bio/Phylo/Forest/TreeRole.pm cp lib/Bio/Phylo/PhyloWS/Client.pm blib/lib/Bio/Phylo/PhyloWS/Client.pm cp lib/Bio/Phylo/PhyloWS/Service/Timetree.pm blib/lib/Bio/Phylo/PhyloWS/Service/Timetree.pm cp lib/Bio/Phylo/Matrices/Datatype/Mixed.pm blib/lib/Bio/Phylo/Matrices/Datatype/Mixed.pm cp lib/Bio/Phylo/Models/Substitution/Dna/F81.pm blib/lib/Bio/Phylo/Models/Substitution/Dna/F81.pm cp lib/Bio/Phylo/Forest/DrawNodeRole.pm blib/lib/Bio/Phylo/Forest/DrawNodeRole.pm cp lib/Bio/Phylo/IO.pm blib/lib/Bio/Phylo/IO.pm cp lib/Bio/Phylo/Parsers/Adjacency.pm blib/lib/Bio/Phylo/Parsers/Adjacency.pm cp lib/Bio/Phylo/Unparsers/Nwmsrdf.pm blib/lib/Bio/Phylo/Unparsers/Nwmsrdf.pm cp lib/Bio/Phylo/Matrices/Datum.pm blib/lib/Bio/Phylo/Matrices/Datum.pm cp lib/Bio/Phylo/Factory.pm blib/lib/Bio/Phylo/Factory.pm cp lib/Bio/Phylo/Matrices/Characters.pm blib/lib/Bio/Phylo/Matrices/Characters.pm cp lib/Bio/Phylo/NeXML/DOM/Element/Twig.pm blib/lib/Bio/Phylo/NeXML/DOM/Element/Twig.pm cp lib/Bio/Phylo/NeXML/Meta.pm blib/lib/Bio/Phylo/NeXML/Meta.pm cp lib/Bio/Phylo/Parsers/Ubiosearch.pm blib/lib/Bio/Phylo/Parsers/Ubiosearch.pm cp lib/Bio/Phylo/Parsers/Phyloxml.pm blib/lib/Bio/Phylo/Parsers/Phyloxml.pm cp lib/Bio/Phylo/Treedrawer/Gif.pm blib/lib/Bio/Phylo/Treedrawer/Gif.pm cp lib/Bio/Phylo/PhyloWS/Resource/Description.pm blib/lib/Bio/Phylo/PhyloWS/Resource/Description.pm cp lib/Bio/Phylo/Unparsers/Json.pm blib/lib/Bio/Phylo/Unparsers/Json.pm cp lib/Bio/Phylo/Matrices/TypeSafeData.pm blib/lib/Bio/Phylo/Matrices/TypeSafeData.pm cp lib/Bio/Phylo/Util/CONSTANT/Int.pm blib/lib/Bio/Phylo/Util/CONSTANT/Int.pm cp lib/Bio/Phylo/Parsers/Table.pm blib/lib/Bio/Phylo/Parsers/Table.pm cp lib/Bio/Phylo/Util/StackTrace.pm blib/lib/Bio/Phylo/Util/StackTrace.pm cp lib/Bio/Phylo/Matrices/Datatype/Solexa.pm blib/lib/Bio/Phylo/Matrices/Datatype/Solexa.pm cp lib/Bio/Phylo/Taxa/TaxonLinker.pm blib/lib/Bio/Phylo/Taxa/TaxonLinker.pm cp lib/Bio/Phylo/Parsers/Ubiometa.pm blib/lib/Bio/Phylo/Parsers/Ubiometa.pm cp lib/Bio/Phylo/Models/Substitution/Dna/JC69.pm blib/lib/Bio/Phylo/Models/Substitution/Dna/JC69.pm cp lib/Bio/Phylo.pm blib/lib/Bio/Phylo.pm cp lib/Bio/Phylo/Parsers/Nexus.pm blib/lib/Bio/Phylo/Parsers/Nexus.pm cp lib/Bio/Phylo/Parsers/Tnrs.pm blib/lib/Bio/Phylo/Parsers/Tnrs.pm cp lib/Bio/Phylo/Identifiable.pm blib/lib/Bio/Phylo/Identifiable.pm cp lib/Bio/Phylo/NeXML/Meta/XMLLiteral.pm blib/lib/Bio/Phylo/NeXML/Meta/XMLLiteral.pm cp lib/Bio/Phylo/NeXML/DOM/Element.pm blib/lib/Bio/Phylo/NeXML/DOM/Element.pm cp lib/Bio/Phylo/Forest/Node.pm blib/lib/Bio/Phylo/Forest/Node.pm cp lib/Bio/Phylo/Models/Substitution/Dna/HKY85.pm blib/lib/Bio/Phylo/Models/Substitution/Dna/HKY85.pm cp lib/Bio/Phylo/Matrices/MatrixRole.pm blib/lib/Bio/Phylo/Matrices/MatrixRole.pm cp lib/Bio/Phylo/Taxa.pm blib/lib/Bio/Phylo/Taxa.pm cp lib/Bio/Phylo/PhyloWS/Service/UbioClassificationBank.pm blib/lib/Bio/Phylo/PhyloWS/Service/UbioClassificationBank.pm cp lib/Bio/Phylo/Unparsers/Adjacency.pm blib/lib/Bio/Phylo/Unparsers/Adjacency.pm cp lib/Bio/Phylo/NeXML/DOM/Document/Libxml.pm blib/lib/Bio/Phylo/NeXML/DOM/Document/Libxml.pm cp lib/Bio/Phylo/Treedrawer/Pdf.pm blib/lib/Bio/Phylo/Treedrawer/Pdf.pm cp lib/Bio/Phylo/Parsers/Phylip.pm blib/lib/Bio/Phylo/Parsers/Phylip.pm cp lib/Bio/Phylo/Mediators/TaxaMediator.pm blib/lib/Bio/Phylo/Mediators/TaxaMediator.pm cp lib/Bio/Phylo/Parsers/Abstract.pm blib/lib/Bio/Phylo/Parsers/Abstract.pm cp lib/Bio/Phylo/Parsers/Tolweb.pm blib/lib/Bio/Phylo/Parsers/Tolweb.pm cp lib/Bio/Phylo/Forest/NodeRole.pm blib/lib/Bio/Phylo/Forest/NodeRole.pm cp lib/Bio/Phylo/Unparsers/Hennig86.pm blib/lib/Bio/Phylo/Unparsers/Hennig86.pm cp lib/Bio/Phylo/PhyloWS/Service/UbioNameBank.pm blib/lib/Bio/Phylo/PhyloWS/Service/UbioNameBank.pm cp lib/Bio/Phylo/Matrices/Datatype/Protein.pm blib/lib/Bio/Phylo/Matrices/Datatype/Protein.pm cp lib/Bio/Phylo/ListableRole.pm blib/lib/Bio/Phylo/ListableRole.pm cp lib/Bio/Phylo/NeXML/DOM/Document.pm blib/lib/Bio/Phylo/NeXML/DOM/Document.pm cp lib/Bio/Phylo/Matrices/Datatype/Dna.pm blib/lib/Bio/Phylo/Matrices/Datatype/Dna.pm cp lib/Bio/Phylo/NeXML/DOM/Document/Twig.pm blib/lib/Bio/Phylo/NeXML/DOM/Document/Twig.pm cp lib/Bio/Phylo/Manual.pod blib/lib/Bio/Phylo/Manual.pod cp lib/Bio/Phylo/Models/Substitution/Dna.pm blib/lib/Bio/Phylo/Models/Substitution/Dna.pm cp lib/Bio/Phylo/Unparsers/Newick.pm blib/lib/Bio/Phylo/Unparsers/Newick.pm cp lib/Bio/Phylo/Listable.pm blib/lib/Bio/Phylo/Listable.pm cp lib/Bio/Phylo/Project.pm blib/lib/Bio/Phylo/Project.pm cp lib/Bio/Phylo/Treedrawer/Jpeg.pm blib/lib/Bio/Phylo/Treedrawer/Jpeg.pm cp lib/Bio/Phylo/Matrices/Datatype/Rna.pm blib/lib/Bio/Phylo/Matrices/Datatype/Rna.pm cp lib/Bio/Phylo/Models/Substitution/Dna/K80.pm blib/lib/Bio/Phylo/Models/Substitution/Dna/K80.pm cp lib/Bio/Phylo/Generator.pm blib/lib/Bio/Phylo/Generator.pm cp lib/Bio/Phylo/Parsers/Json.pm blib/lib/Bio/Phylo/Parsers/Json.pm cp lib/Bio/Phylo/PhyloWS/Resource.pm blib/lib/Bio/Phylo/PhyloWS/Resource.pm cp lib/Bio/Phylo/Parsers/Newick.pm blib/lib/Bio/Phylo/Parsers/Newick.pm cp lib/Bio/Phylo/Matrices/Datatype.pm blib/lib/Bio/Phylo/Matrices/Datatype.pm cp lib/Bio/Phylo/Treedrawer.pm blib/lib/Bio/Phylo/Treedrawer.pm cp lib/Bio/Phylo/Treedrawer/Swf.pm blib/lib/Bio/Phylo/Treedrawer/Swf.pm cp lib/Bio/Phylo/PhyloWS/Service.pm blib/lib/Bio/Phylo/PhyloWS/Service.pm cp lib/Bio/Phylo/Parsers/Fastq.pm blib/lib/Bio/Phylo/Parsers/Fastq.pm cp lib/Bio/Phylo/Models/Substitution/Dna/GTR.pm blib/lib/Bio/Phylo/Models/Substitution/Dna/GTR.pm cp lib/Bio/Phylo/Unparsers/Html.pm blib/lib/Bio/Phylo/Unparsers/Html.pm cp lib/Bio/Phylo/Matrices/Datatype/Illumina.pm blib/lib/Bio/Phylo/Matrices/Datatype/Illumina.pm cp lib/Bio/Phylo/Unparsers/Taxlist.pm blib/lib/Bio/Phylo/Unparsers/Taxlist.pm cp lib/Bio/Phylo/Unparsers/Pagel.pm blib/lib/Bio/Phylo/Unparsers/Pagel.pm cp lib/Bio/Phylo/Forest/DrawTreeRole.pm blib/lib/Bio/Phylo/Forest/DrawTreeRole.pm cp lib/Bio/Phylo/Set.pm blib/lib/Bio/Phylo/Set.pm cp lib/Bio/Phylo/Parsers/Figtree.pm blib/lib/Bio/Phylo/Parsers/Figtree.pm cp lib/Bio/Phylo/Util/CONSTANT.pm blib/lib/Bio/Phylo/Util/CONSTANT.pm cp lib/Bio/Phylo/Unparsers/Phyloxml.pm blib/lib/Bio/Phylo/Unparsers/Phyloxml.pm cp lib/Bio/Phylo/Treedrawer/Png.pm blib/lib/Bio/Phylo/Treedrawer/Png.pm cp lib/Bio/Phylo/Unparsers/Abstract.pm blib/lib/Bio/Phylo/Unparsers/Abstract.pm cp lib/Bio/Phylo/Parsers/Nexml.pm blib/lib/Bio/Phylo/Parsers/Nexml.pm cp lib/Bio/Phylo/Forest/Tree.pm blib/lib/Bio/Phylo/Forest/Tree.pm cp lib/Bio/Phylo/NeXML/Entities.pm blib/lib/Bio/Phylo/NeXML/Entities.pm cp lib/Bio/Phylo/Taxa/Taxon.pm blib/lib/Bio/Phylo/Taxa/Taxon.pm cp lib/Bio/Phylo/Util/IDPool.pm blib/lib/Bio/Phylo/Util/IDPool.pm cp lib/Bio/Phylo/Treedrawer/Processing.pm blib/lib/Bio/Phylo/Treedrawer/Processing.pm cp lib/Bio/Phylo/Util/Logger.pm blib/lib/Bio/Phylo/Util/Logger.pm cp lib/Bio/Phylo/Matrices/Matrix.pm blib/lib/Bio/Phylo/Matrices/Matrix.pm cp lib/Bio/Phylo/Unparsers/Nexus.pm blib/lib/Bio/Phylo/Unparsers/Nexus.pm cp lib/Bio/Phylo/Unparsers/Phylip.pm blib/lib/Bio/Phylo/Unparsers/Phylip.pm cp lib/Bio/Phylo/Taxa/TaxaLinker.pm blib/lib/Bio/Phylo/Taxa/TaxaLinker.pm cp lib/Bio/Phylo/Unparsers/Cdao.pm blib/lib/Bio/Phylo/Unparsers/Cdao.pm cp lib/Bio/Phylo/Matrices/Datatype/Sanger.pm blib/lib/Bio/Phylo/Matrices/Datatype/Sanger.pm cp lib/Bio/Phylo/Parsers/Fasta.pm blib/lib/Bio/Phylo/Parsers/Fasta.pm --- pure_all --- --- manifypods --- Manifying blib/man3/Bio::Phylo.3 Manifying blib/man3/Bio::Phylo::EvolutionaryModels.3 Manifying blib/man3/Bio::Phylo::Factory.3 Manifying blib/man3/Bio::Phylo::Forest.3 Manifying blib/man3/Bio::Phylo::Forest::DrawNodeRole.3 Manifying blib/man3/Bio::Phylo::Forest::DrawTreeRole.3 Manifying blib/man3/Bio::Phylo::Forest::Node.3 Manifying blib/man3/Bio::Phylo::Forest::NodeRole.3 Manifying blib/man3/Bio::Phylo::Forest::Tree.3 Manifying blib/man3/Bio::Phylo::Forest::TreeRole.3 Manifying blib/man3/Bio::Phylo::Generator.3 Manifying blib/man3/Bio::Phylo::IO.3 Manifying blib/man3/Bio::Phylo::Identifiable.3 Manifying blib/man3/Bio::Phylo::Listable.3 Manifying blib/man3/Bio::Phylo::ListableRole.3 Manifying blib/man3/Bio::Phylo::Manual.3 Manifying blib/man3/Bio::Phylo::Matrices.3 Manifying blib/man3/Bio::Phylo::Matrices::Character.3 Manifying blib/man3/Bio::Phylo::Matrices::Characters.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Continuous.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Custom.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Dna.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Illumina.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Mixed.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Protein.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Restriction.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Rna.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Sanger.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Solexa.3 Manifying blib/man3/Bio::Phylo::Matrices::Datatype::Standard.3 Manifying blib/man3/Bio::Phylo::Matrices::Datum.3 Manifying blib/man3/Bio::Phylo::Matrices::DatumRole.3 Manifying blib/man3/Bio::Phylo::Matrices::Matrix.3 Manifying blib/man3/Bio::Phylo::Matrices::MatrixRole.3 Manifying blib/man3/Bio::Phylo::Matrices::TypeSafeData.3 Manifying blib/man3/Bio::Phylo::Mediators::TaxaMediator.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM::Document.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM::Document::Libxml.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM::Document::Twig.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM::Element.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM::Element::Libxml.3 Manifying blib/man3/Bio::Phylo::NeXML::DOM::Element::Twig.3 Manifying blib/man3/Bio::Phylo::NeXML::Entities.3 Manifying blib/man3/Bio::Phylo::NeXML::Meta.3 Manifying blib/man3/Bio::Phylo::NeXML::Meta::XMLLiteral.3 Manifying blib/man3/Bio::Phylo::NeXML::Writable.3 Manifying blib/man3/Bio::Phylo::Parsers::Abstract.3 Manifying blib/man3/Bio::Phylo::Parsers::Adjacency.3 Manifying blib/man3/Bio::Phylo::Parsers::Fasta.3 Manifying blib/man3/Bio::Phylo::Parsers::Fastq.3 Manifying blib/man3/Bio::Phylo::Parsers::Figtree.3 Manifying blib/man3/Bio::Phylo::Parsers::Json.3 Manifying blib/man3/Bio::Phylo::Parsers::Newick.3 Manifying blib/man3/Bio::Phylo::Parsers::Nexml.3 Manifying blib/man3/Bio::Phylo::Parsers::Nexus.3 Manifying blib/man3/Bio::Phylo::Parsers::Phylip.3 Manifying blib/man3/Bio::Phylo::Parsers::Phyloxml.3 Manifying blib/man3/Bio::Phylo::Parsers::Table.3 Manifying blib/man3/Bio::Phylo::Parsers::Taxlist.3 Manifying blib/man3/Bio::Phylo::Parsers::Tnrs.3 Manifying blib/man3/Bio::Phylo::Parsers::Tolweb.3 Manifying blib/man3/Bio::Phylo::Parsers::Ubiocbmeta.3 Manifying blib/man3/Bio::Phylo::Parsers::Ubiometa.3 Manifying blib/man3/Bio::Phylo::Parsers::Ubiosearch.3 Manifying blib/man3/Bio::Phylo::PhyloWS.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Client.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Resource.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Resource::Description.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Service.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Service::Timetree.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Service::Tolweb.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Service::UbioClassificationBank.3 Manifying blib/man3/Bio::Phylo::PhyloWS::Service::UbioNameBank.3 Manifying blib/man3/Bio::Phylo::Project.3 Manifying blib/man3/Bio::Phylo::Set.3 Manifying blib/man3/Bio::Phylo::Taxa.3 Manifying blib/man3/Bio::Phylo::Taxa::TaxaLinker.3 Manifying blib/man3/Bio::Phylo::Taxa::Taxon.3 Manifying blib/man3/Bio::Phylo::Taxa::TaxonLinker.3 Manifying blib/man3/Bio::Phylo::Treedrawer.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Abstract.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Canvas.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Gif.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Jpeg.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Pdf.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Png.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Processing.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Svg.3 Manifying blib/man3/Bio::Phylo::Treedrawer::Swf.3 Manifying blib/man3/Bio::Phylo::Unparsers::Abstract.3 Manifying blib/man3/Bio::Phylo::Unparsers::Adjacency.3 Manifying blib/man3/Bio::Phylo::Unparsers::Cdao.3 Manifying blib/man3/Bio::Phylo::Unparsers::Fasta.3 Manifying blib/man3/Bio::Phylo::Unparsers::Hennig86.3 Manifying blib/man3/Bio::Phylo::Unparsers::Html.3 Manifying blib/man3/Bio::Phylo::Unparsers::Json.3 Manifying blib/man3/Bio::Phylo::Unparsers::Mrp.3 Manifying blib/man3/Bio::Phylo::Unparsers::Newick.3 Manifying blib/man3/Bio::Phylo::Unparsers::Nexml.3 Manifying blib/man3/Bio::Phylo::Unparsers::Nexus.3 Manifying blib/man3/Bio::Phylo::Unparsers::Nwmsrdf.3 Manifying blib/man3/Bio::Phylo::Unparsers::Pagel.3 Manifying blib/man3/Bio::Phylo::Unparsers::Phylip.3 Manifying blib/man3/Bio::Phylo::Unparsers::Phyloxml.3 Manifying blib/man3/Bio::Phylo::Unparsers::Rss1.3 Manifying blib/man3/Bio::Phylo::Unparsers::Taxlist.3 Manifying blib/man3/Bio::Phylo::Util::CONSTANT.3 Manifying blib/man3/Bio::Phylo::Util::CONSTANT::Int.3 Manifying blib/man3/Bio::Phylo::Util::Dependency.3 Manifying blib/man3/Bio::Phylo::Util::Exceptions.3 Manifying blib/man3/Bio::Phylo::Util::IDPool.3 Manifying blib/man3/Bio::Phylo::Util::Logger.3 Manifying blib/man3/Bio::Phylo::Util::MOP.3 Manifying blib/man3/Bio::Phylo::Util::OptionalInterface.3 Manifying blib/man3/Bio::Phylo::Util::StackTrace.3 Manifying blib/man3/Bio::PhyloRole.3 --- all --- =========================================================================== =================================================== ===> p5-Bio-Phylo-0.58 depends on package: p5-GD>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-Math-CDF>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-Math-Random>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-PDF-API2>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-SVG>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-SWF-Builder>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-LibXML>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-Twig>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-XML-XML2JSON>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-bioperl>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: p5-libxml>=0 - found ===> p5-Bio-Phylo-0.58 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== ===> Staging for p5-Bio-Phylo-0.58 ===> Generating temporary packing list Manifying blib/man3/Bio::Phylo.3 Manifying blib/man3/Bio::Phylo::EvolutionaryModels.3 Manifying blib/man3/Bio::Phylo::Factory.3 Manifying blib/man3/Bio::Phylo::Forest.3 Manifying blib/man3/Bio::Phylo::Forest::DrawNodeRole.3 Manifying blib/man3/Bio::Phylo::Forest::DrawTreeRole.3 Manifying blib/man3/Bio::Phylo::Forest::Node.3 Manifying blib/man3/Bio::Phylo::Forest::NodeRole.3 Manifying blib/man3/Bio::Phylo::Forest::Tree.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/PhyloRole.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Set.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/EvolutionaryModels.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Listable.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/PhyloWS.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Matrices.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Identifiable.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Taxa.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Factory.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Forest.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Generator.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/IO.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/ListableRole.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Manual.pod Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Treedrawer.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Project.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/Writable.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/Meta.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/Entities.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/Meta/XMLLiteral.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM/Element.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM/Document.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM/Document/Twig.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM/Document/Libxml.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM/Element/Twig.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/NeXML/DOM/Element/Libxml.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Newick.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Phylip.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Phyloxml.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Abstract.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Html.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Nexml.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Taxlist.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Adjacency.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Nwmsrdf.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Rss1.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Json.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Hennig86.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Fasta.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Mrp.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Pagel.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Nexus.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Unparsers/Cdao.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Mediators/TaxaMediator.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/Dependency.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/StackTrace.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/Logger.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/OptionalInterface.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/IDPool.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/CONSTANT.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/Exceptions.pm Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/Bio/Phylo/Util/MOP.pm Installing 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/wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Mediators::TaxaMediator.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Parsers::Nexml.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Matrices::Characters.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Unparsers::Nexml.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Util::StackTrace.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Unparsers::Newick.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Parsers::Newick.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Util::CONSTANT::Int.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Unparsers::Mrp.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Matrices::Datatype::Rna.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Parsers::Ubiosearch.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::Unparsers::Json.3 Installing /wrkdirs/biology/p5-Bio-Phylo/stage/usr/local/lib/perl5/site_perl/man/man3/Bio::Phylo::NeXML::Writable.3 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for p5-Bio-Phylo-0.58 file sizes/checksums [247]: ... done packing files [247]: ... done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for p5-Bio-Phylo-0.58 build of biology/p5-Bio-Phylo ended at Tue Oct 4 19:31:09 PDT 2016 build time: 00:01:21